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Sample records for derived interaction parameters

  1. Chemical potential derivatives and preferential interaction parameters in biological systems from Kirkwood-Buff theory.

    PubMed

    Smith, Paul E

    2006-08-01

    New expressions for chemical potential derivatives and preferential interaction parameters for ternary mixtures are derived for open, semiopen, and closed ensembles in terms of Kirkwood-Buff integrals, where all three components are present at finite concentrations. This is achieved using a simple approach that avoids the use of the general matrix formulation of Kirkwood-Buff theory. The resulting expressions provide a rigorous foundation for the analysis of experimental and simulation data. Using the results, a simple model is developed and used to investigate the possible effects of finite protein concentrations on the corresponding cosolvent dependent chemical potential and denaturation thermodynamics. PMID:16679363

  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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    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.

  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. PMID:27131542

  6. Perturbative unitarity of Higgs derivative interactions

    NASA Astrophysics Data System (ADS)

    Kikuta, Yohei; Yamamoto, Yasuhiro

    2013-05-01

    We study the perturbative unitarity bound given by dimension six derivative interactions consisting of Higgs doublets. These interactions emerge from kinetic terms of composite Higgs models or integrating out heavy particles that interact with Higgs doublets. They lead to new phenomena beyond the Standard Model. One of characteristic contributions from derivative interactions appear in vector boson scattering processes. Longitudinal modes of massive vector bosons can be regarded as Nambu Goldstone bosons eaten by each vector field. Since their effects become larger and larger as the collision energy of vector bosons increases, vector boson scattering processes become important in the high energy region around the TeV scale. On the other hand, in such a high energy region, we have to take into account the unitarity of amplitudes. We have obtained the unitarity condition in terms of the parameter included in the effective Lagrangian for one Higgs doublet models. Applying it to some models, we have found that contributions of derivative interactions are not so large enough to clearly discriminate them from the Standard Model ones. We also study the unitarity bound in two Higgs doublet models. Because they are too complex to obtain it in the general effective Lagrangian, we have calculated it in explicit models. These analyses tell that the perturbative unitarity bounds are highly model dependent.

  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. 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

  9. qPIPSA: Relating enzymatic kinetic parameters and interaction fields

    PubMed Central

    Gabdoulline, Razif R; Stein, Matthias; Wade, Rebecca C

    2007-01-01

    Background The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. Results We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure. Conclusion Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes

  10. Photon Interaction Parameters for Some Borate Glasses

    NASA Astrophysics Data System (ADS)

    Mann, Nisha; Kaur, Updesh; Singh, Tejbir; Sharma, J. K.; Singh, Parjit S.

    2010-11-01

    Some photon interaction parameters of dosimetric interest such as mass attenuation coefficients, effective atomic number, electron density and KERMA relative to air have been computed in the wide energy range from 1 keV to 100 GeV for some borate glasses viz. barium-lead borate, bismuth-borate, calcium-strontium borate, lead borate and zinc-borate glass. It has been observed that lead borate glass and barium-lead borate glass have maximum values of mass attenuation coefficient, effective atomic number and KERMA relative to air. Hence, these borate glasses are suitable as gamma ray shielding material, packing of radioactive sources etc.

  11. Photon Interaction Parameters for Some Borate Glasses

    SciTech Connect

    Mann, Nisha; Kaur, Updesh; Singh, Tejbir; Sharma, J. K.; Singh, Parjit S.

    2010-11-06

    Some photon interaction parameters of dosimetric interest such as mass attenuation coefficients, effective atomic number, electron density and KERMA relative to air have been computed in the wide energy range from 1 keV to 100 GeV for some borate glasses viz. barium-lead borate, bismuth-borate, calcium-strontium borate, lead borate and zinc-borate glass. It has been observed that lead borate glass and barium-lead borate glass have maximum values of mass attenuation coefficient, effective atomic number and KERMA relative to air. Hence, these borate glasses are suitable as gamma ray shielding material, packing of radioactive sources etc.

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Kawakatsu, Hitoshi

    2016-04-01

    Kawakatsu et al. (2015) and Kawakatsu (2016) introduced a new fifth parameter, ηκ, to describe transverse isotropy (TI). Considering that ηκ characterizes the incidence angle dependence of bodywave phase velocities for TI models, its relevance for bodywave seismology is obvious. Here we derive expressions for partial derivatives (sensitivity kernels) of surface wave phase velocity and normal mode eigen-frequency 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 (1981) and Anderson & Dziewonski (1982), 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.

  15. Modeling Interactions of Erythromycin Derivatives with Ribosomes.

    PubMed

    Shishkina, A V; Makarova, T M; Tereshchenkov, A G; Makarov, G I; Korshunova, G A; Bogdanov, A A

    2015-11-01

    Using a method of static simulation, a series of erythromycin A analogs was designed with aldehyde functions introduced instead of one of the methyl substituents in the 3'-N-position of the antibiotic that was potentially capable of forming a covalent bond with an amino group of one of the nucleotide residues of the 23S rRNA in the ribosomal exit tunnel. Similar interaction is observed for antibiotics of the tylosin series, which bind tightly to the large ribosomal subunit and demonstrate high antibacterial activity. Binding of novel erythromycin derivatives with the bacterial ribosome was investigated with the method of fluorescence polarization. It was found that the erythromycin analog containing a 1-methyl-3-oxopropyl group in the 3'-N-position demonstrates the best binding. Based on the ability to inhibit protein biosynthesis, it is on the same level as erythromycin, and it is significantly better than desmethyl-erythromycin. Molecular dynamic modeling of complexes of the derivatives with ribosomes was conducted to explain the observed effects. PMID:26615442

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. A study of photon interaction parameters in lung tissue substitutes.

    PubMed

    Manjunatha, H C

    2014-04-01

    The study of photon interaction with different composite materials has become a topic of prime importance for radiation physicists. Some parameters of dosimetric interest are the mass attenuation coefficient, effective atomic number, and electron density; these help in the basic understanding of photon interactions with composite materials. The photon interaction parameters such as mass attenuation coefficient (μ/ρ), effective atomic number (Zeff), and effective electron density (N el) must be identical for the phantom material and their tissue. In the present study, we have evaluated the photon interaction parameters such as (μ/ρ), Z eff and N el of 13 lung tissue substitutes. The variations of these parameters of lung tissue substitutes with photon energy are graphically represented. The photon interaction parameters of lung tissue substitutes are compared with that of lung tissue. The variation of photon interaction parameters of the studied lung tissue substitutes is similar that of the lung. Logically, it can be shown that Alderson lung is good substitute for lung than the other substitutes. PMID:24872609

  1. Upscaling water cycle parameters using geomorphometric terrain parameters and topographic indices derived from interferometric DEM

    NASA Astrophysics Data System (ADS)

    Etzrodt, N.; Zimmermann, R.; Conrad, O.

    2002-01-01

    For assessing a regional water balance in boreal landscapes the extend to which evapo-transpiration is subject to spatial variations needs to be known. Water cycle parameters such as transpiration rates of vegetation are depending on both the vegetation type and hydro-pedologic stand conditions since poor soil drainage respective seasonal soil drought affect water consumption by vegetation. The spatial distribution of the pristine boreal vegetation types can be obtained by SAR or optical remote sensing sensors on a regional scale. Many works have been dealing with this subject in the past and it is widely known how remote sensing can contribute to vegetation mapping. To assess hydro-pedologic stand conditions on a regional scale an alternative method is required. Our approach to resolve this problem is based on the fact that soil water status is essentially a function of topographic properties. For that reason morphometric terrain parameters derived from a Digital Elevation Model (DEM) has been used to indicate regions with homogeneous hydro-pedologic stand conditions, so called "hydropedotopes". To delineate the required hydropedotopes two indicators pertaining to soilwater status and pedo-hydrology were derived from InSAR DEM: (1) The wetness-index and (2) the vertical distance to streams and bottom lines. In a further step the resulting map of hydropedotopes is intersected with a remote sensing derived map of the actual spatial distribution of the boreal vegetation types. This step results in a map which marks out landscape units of homogeneous properties in terms of vegetation type and hydro-pedologic conditions which is the basis for upscaling canopy transpiration measurements. From our approach which uses in addition to conventional remote sensing data the results of an automated digital terrain analysis we expect a substantially enhanced knowledge of the spatial variability of water flux rates conditional on canopy transpiration. The process of our approach

  2. Predicting pharmacokinetic profiles using in silico derived parameters.

    PubMed

    Hosea, Natalie A; Jones, Hannah M

    2013-04-01

    Human pharmacokinetic (PK) predictions play a critical role in assessing the quality of potential clinical candidates where the accurate estimation of clearance, volume of distribution, bioavailability, and the plasma-concentration-time profiles are the desired end points. While many methods for conducting predictions utilize in vivo data, predictions can be conducted successfully from in vitro or in silico data, applying modeling and simulation techniques. This approach can be facilitated using commercially available prediction software such as GastroPlus which has been reported to accurately predict the oral PK profile of small drug-like molecules. Herein, case studies are described where GastroPlus modeling and simulation was employed using in silico or in vitro data to predict PK profiles in early discovery. The results obtained demonstrate the feasibility of adequately predicting plasma-concentration-time profiles with in silico derived as well as in vitro measured parameters and hence predicting PK profiles with minimal data. The applicability of this approach can provide key information enabling decisions on either dose selection, chemistry strategy to improve compounds, or clinical protocol design, thus demonstrating the value of modeling and simulation in both early discovery and exploratory development for predicting absorption and disposition profiles. PMID:23427934

  3. 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.

  4. Interaction between gliadins and anthocyan derivatives.

    PubMed

    Mazzaracchio, Palmira; Tozzi, Silvia; Boga, Carla; Forlani, Luciano; Pifferi, Pier Giorgio; Barbiroli, Giancarlo

    2011-12-01

    The interaction of gliadins with some anthocyanins (e.g. myrtillin, malvin, keracyanin, callistephin) and anthocyanidins (e.g. delphinidin, pelargonidin, cyanidin) has been analysed in aqueous solution at pH condition of the stomach, in which these compounds are initially metabolized. NMR, FT-IR and UV-Vis spectroscopic methods have been employed to determine the anthocyanin binding mode. The spectroscopic data seem to indicate that anthocyans are located along the polypeptide chains of gliadins in a generical molecular interaction between the two moieties. Our data do not exclude that hydrogen bonding interaction too is operating. Anthocyan-gliadins complexes are very soluble in acidic conditions. The results provide new insights into anthocyan-protein interaction and may have relevance to human health. PMID:25212343

  5. Counterintuitive interaction of anions with benzene derivatives

    NASA Astrophysics Data System (ADS)

    Quiñonero, David; Garau, Carolina; Frontera, Antonio; Ballester, Pau; Costa, Antonio; Deyà, Pere M.

    2002-06-01

    Ab initio calculations were carried out on complexes between 1,3,5-trinitrobenzene (TNB) and anions, where the anion is positioned over the ring along the C3 axis. This study combines crystallographic and computational evidences to demonstrate an attractive interaction between the anion and the π-cloud of TNB. This interaction is rationalized based on the important role of the quadrupole moment of TNB and the anion-induced polarization. In addition, this study has been extended to 1,3,5-trifluorobenzene (TFB), which possesses a very small quadrupole moment. As a result, minimum energy complexes have been found between TFB and both anions and cations due to the stabilization obtained from the ion-induced polarization.

  6. Effects of Ignoring Item Interaction on Item Parameter Estimation and Detection of Interacting Items

    ERIC Educational Resources Information Center

    Chen, Cheng-Te; Wang, Wen-Chung

    2007-01-01

    This study explores the effects of ignoring item interaction on item parameter estimation and the efficiency of using the local dependence index Q[subscript 3] and the SAS NLMIXED procedure to detect item interaction under the three-parameter logistic model and the generalized partial credit model. Through simulations, it was found that ignoring…

  7. Inflationary magnetogenesis, derivative couplings, and relativistic Van der Waals interactions

    NASA Astrophysics Data System (ADS)

    Giovannini, Massimo

    2015-08-01

    When the gauge fields have derivative couplings to scalars, like in the case of the relativistic theory of Van der Waals (or Casimir-Polder) interactions, conformal invariance is broken but the magnetic and electric susceptibilities are not bound to coincide. We analyze the formation of large-scale magnetic fields in slow-roll inflation and find that they are generated at the level of a few hundredths of a nG and over typical length scales between few Mpc and 100 Mpc. Using a new time parametrization that reduces to conformal time but only for coincident susceptibilities, the gauge action is quantized while the evolution equations of the corresponding mode functions are more easily solvable. The power spectra depend on the normalized rates of variation of the two susceptibilities (or of the corresponding gauge couplings) and on the absolute value of their ratio at the beginning of inflation. We pin down explicit regions in the parameter space where all the physical requirements (i.e., the backreaction constraints, the magnetogenesis bounds and the naturalness of the initial conditions of the scenario) are jointly satisfied. Weakly coupled initial data are favored if the gauge couplings are of the same order at the end of inflation. Duality is systematically used to simplify the analysis of the wide parameter space of the model.

  8. 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.

  9. 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.

  10. A Flexible Terpyridine Derivative Interacts Specifically with G-Quadruplexes.

    PubMed

    De Rache, Aurore; Gueddouda, Nassima Meriem; Bourdoncle, Anne; Hommes, Paul; Reissig, Hans-Ulrich; Mergny, Jean-Louis

    2016-08-26

    G-quadruplexes formed by nucleic acids are implicated in pathologies ranging from cancers to neurodegenerative diseases. We evaluated interactions of 29 bi- and terpyridine derivatives with G-quadruplexes and duplexes. FRET-melting, circular dichroism, and (1) H NMR spectroscopy showed that one terpyridine derivative interacted very selectively with G-quadruplexes. This G-quadruplex ligand inhibited helicase activity and should influence G-quadruplex-related biological processes. PMID:27410717

  11. Parameter uncertainty and interaction in complex environmental models

    NASA Astrophysics Data System (ADS)

    Spear, Robert C.; Grieb, Thomas M.; Shang, Nong

    1994-11-01

    Recently developed models for the estimation of risks arising from the release of toxic chemicals from hazardous waste sites are inherently complex both structurally and parametrically. To better understand the impact of uncertainty and interaction in the high-dimensional parameter spaces of these models, the set of procedures termed regional sensitivity analysis has been extended and applied to the groundwater pathway of the MMSOILS model. The extension consists of a tree-structured density estimation technique which allows the characterization of complex interaction in that portion of the parameter space which gives rise to successful simulation. Results show that the parameter space can be partitioned into small, densely populated regions and relatively large, sparsely populated regions. From the high-density regions one can identify the important or controlling parameters as well as the interaction between parameters in different local areas of the space. This new tool can provide guidance in the analysis and interpretation of site-specific application of these complex models.

  12. 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

  13. 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.

  14. Quality assessment parameters for EST-derived SNPs from catfish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two factors were found to be most significant for validation of EST-derived SNPs: the contig size and the minor allele sequence frequency. The larger the contigs were, the greater the validation rate although the validation rate was reasonably high when the contig sizes were equal to or larger than...

  15. 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.

  16. 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

  17. Three-parameter tunable Tilt-Integral-Derivative (TID) controller

    NASA Technical Reports Server (NTRS)

    Lurie, Boris J. (Inventor)

    1994-01-01

    A feedback control system compensator of the PID type is provided, wherein the proportional component of the compensator is replaced with a tilted component having a transfer function s to the power of -1/n. The resulting transfer function of the entire compensator more closely approximates an optimal transfer function, thereby achieving improved feedback controller. Further, as compared to conventional PID compensators, the TID compensator allows for simpler tuning, better disturbance rejection ratio, and smaller effects of plant parameter variations on closed loop response.

  18. 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

  19. 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.

  20. 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

  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. 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

  3. 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

  4. 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.

  5. 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.

  6. Cubic derivative interactions and asymptotic dynamics of the galileon vacuum

    NASA Astrophysics Data System (ADS)

    De Arcia, Roberto; Gonzalez, Tame; Leon, Genly; Nucamendi, Ulises; Quiros, Israel

    2016-06-01

    In this paper we apply the tools of the dynamical systems theory in order to uncover the whole asymptotic structure of the vacuum interactions of a galileon model with a cubic derivative interaction term. It is shown that, contrary to what occurs in the presence of background matter, the galileon interactions of vacuum appreciably modify the late-time cosmic dynamics. In particular, a local late-time attractor representing phantom behavior arises which is inevitably associated with a big rip singularity. It seems that the gravitational interactions of the background matter with the galileon screen the effects of the gravitational self-interactions of the galileon, thus erasing any potential modification of the late-time dynamics by the galileon vacuum processes. Unlike other galileon models inspired in the DGP scenario, self-accelerating solutions do not arise in this model.

  7. 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.

  8. 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.

  9. 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

  10. Analytical first derivatives of the RE-squared interaction potential

    NASA Astrophysics Data System (ADS)

    Babadi, M.; Ejtehadi, M. R.; Everaers, R.

    2006-12-01

    We derive exact expressions for the forces and torques between biaxial molecules interacting via the RE-squared potential, a recent variant of the Gay-Berne potential. Moreover, efficient routines have been provided for rigid body MD simulations, resulting in 1.6 times speedup compared to the two-point finite difference approach. It has also been shown that the time cost of a MD simulation will be almost equal to a similar MC simulation, making use of the provided routines.

  11. 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. PMID:26076445

  12. 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

  13. 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.

  14. Composition dependence of the interaction parameter in isotopic polymer blends

    SciTech Connect

    Londono, J.D.; Narten, A.H.; Wignall, G.D. ); Honnell, K.G.; Hsieh, E.T.; Johnson, T.W. . Research and Development); Bates, F.S. . Dept. of Chemical Engineering)

    1994-05-09

    Isotopic polymer mixtures lack the structural asymmetries and specific interactions encountered in blends of chemically distinct species. In this respect, they form ideal model systems for exploring the limitations of the widely-used Flory-Huggins (FH) lattice model and for testing and improving new theories of polymer thermodynamics. The FH interaction parameter between deuterium-labeled and unlabeled segments of the same species ([sub [chi]HD]) should in principle be independent of concentration ([phi]), through previous small-angle neutron scattering (SANS) experiments have shown that it exhibits a minimum at [phi] [approximately] 0.5 for poly(vinylethylene) (PVE) and poly(ethylethylene) (PEE). The authors report new data on polyethylene (PE) as a function of molecular weight, temperature (T), and [phi], which show qualitatively similar behavior. However, measurements on [sub [chi]HD]([phi]) for polystyrene (PS) show a maximum at [phi] [approximately]0.5, in contrast to PVE, PEE, and PE. Reproducing the concentration dependence of [phi] in different model isotopic systems should serve as a sensitive test of the way in which theories of polymer thermodynamics can account for the details of the local packing and also the effects of noncombinatorial entropy, which appear to be the main cause of the variation of [sub [chi]HD]([phi]) for PE. These data also serve to quantify the effects of isotopic substitution in SANS experiments on polyolefin blends and thus lay the ground work for definitive studies of the compatibility of branched and linear polyethylenes.

  15. Binding interactions of water-soluble camptothecin derivatives with bovine serum albumin

    NASA Astrophysics Data System (ADS)

    Li, Qingyong; Zhu, Qiaochu; Deng, Xiaoqiu; He, Wuna; Zhao, Tengfei; Zhang, Baoyou

    2012-02-01

    In this study, the binding interactions of the water-soluble camptothecin derivatives hydroxycamptothecin (10-HCPT), topotecan (TPT), and camptothecin quaternary salt (CPT8), to bovine serum albumin (BSA) were determined using fluorescence spectra and UV-vis spectra. The results revealed that the fluorescence of BSA was strongly quenched by the binding of camptothecin derivatives to BSA. The quenching mechanism of the camptothecin derivatives was found to be static according to the Stern-Volmer equation. The binding constant and binding sites were confirmed by fluorescence quenching spectra. The thermodynamic parameters Gibbs free energy change (Δ G < 0), enthalpy change (Δ H > 0), and entropy change (Δ S > 0) implied that the interaction process was spontaneous and endothermic, and the interaction forces between camptothecin compounds and BSA were found to be hydrophobic. According to Föster non-radioactive energy transfer, the binding distances between 10-HCPT, TPT, and CPT8, and BSA were determined to be 1.73 nm, 1.63 nm, and 1.61 nm, respectively. The synchronous fluorescence spectra confirmed that the camptothecin compounds cannot cause conformational changes in BSA. A rapid and sensitive method for determining the binding interaction between water-soluble camptothecin derivatives and BSA was established based on these principles of fluorescence quenching.

  16. 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.

  17. Mass-based hygroscopicity parameter interaction model and measurement of atmospheric aerosol water uptake

    NASA Astrophysics Data System (ADS)

    Mikhailov, E.; Vlasenko, S.; Rose, D.; Pöschl, U.

    2013-01-01

    In this study we derive and apply a mass-based hygroscopicity parameter interaction model for efficient description of concentration-dependent water uptake by atmospheric aerosol particles with complex chemical composition. The model approach builds on the single hygroscopicity parameter model of Petters and Kreidenweis (2007). We introduce an observable mass-based hygroscopicity parameter κm which can be deconvoluted into a dilute hygroscopicity parameter (κm0) and additional self- and cross-interaction parameters describing non-ideal solution behavior and concentration dependencies of single- and multi-component systems. For reference aerosol samples of sodium chloride and ammonium sulfate, the κm-interaction model (KIM) captures the experimentally observed concentration and humidity dependence of the hygroscopicity parameter and is in good agreement with an accurate reference model based on the Pitzer ion-interaction approach (Aerosol Inorganic Model, AIM). Experimental results for pure organic particles (malonic acid, levoglucosan) and for mixed organic-inorganic particles (malonic acid - ammonium sulfate) are also well reproduced by KIM, taking into account apparent or equilibrium solubilities for stepwise or gradual deliquescence and efflorescence transitions. The mixed organic-inorganic particles as well as atmospheric aerosol samples exhibit three distinctly different regimes of hygroscopicity: (I) a quasi-eutonic deliquescence & efflorescence regime at low-humidity where substances are just partly dissolved and exist also in a non-dissolved phase, (II) a gradual deliquescence & efflorescence regime at intermediate humidity where different solutes undergo gradual dissolution or solidification in the aqueous phase; and (III) a dilute regime at high humidity where the solutes are fully dissolved approaching their dilute hygroscopicity. For atmospheric aerosol samples collected from boreal rural air and from pristine tropical rainforest air (secondary

  18. Derivatives of buckling loads and vibration frequencies with respect to stiffness and initial strain parameters

    NASA Technical Reports Server (NTRS)

    Haftka, Raphael T.; Cohen, Gerald A.; Mroz, Zenon

    1990-01-01

    A uniform variational approach to sensitivity analysis of vibration frequencies and bifurcation loads of nonlinear structures is developed. Two methods of calculating the sensitivities of bifurcation buckling loads and vibration frequencies of nonlinear structures, with respect to stiffness and initial strain parameters, are presented. A direct method requires calculation of derivatives of the prebuckling state with respect to these parameters. An adjoint method bypasses the need for these derivatives by using instead the strain field associated with the second-order postbuckling state. An operator notation is used and the derivation is based on the principle of virtual work. The derivative computations are easily implemented in structural analysis programs. This is demonstrated by examples using a general purpose, finite element program and a shell-of-revolution program.

  19. Derivative-free optimization for parameter estimation in computational nuclear physics

    NASA Astrophysics Data System (ADS)

    Wild, Stefan M.; Sarich, Jason; Schunck, Nicolas

    2015-03-01

    We consider optimization problems that arise when estimating a set of unknown parameters from experimental data, particularly in the context of nuclear density functional theory. We examine the cost of not having derivatives of these functionals with respect to the parameters. We show that the POUNDERS code for local derivative-free optimization obtains consistent solutions on a variety of computationally expensive energy density functional calibration problems. We also provide a primer on the operation of the POUNDERS software in the Toolkit for advanced optimization.

  20. 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

  1. 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

  2. Parameter derivation for an acoustic cloak based on scattering theory and realization with tunable metamaterials

    NASA Astrophysics Data System (ADS)

    Shen, Huijie; Wen, Jihong; Païdoussis, Michael P.; Yu, Dianlong; Cai, Li; Wen, Xisen

    2013-09-01

    This work derives the set of acoustic parameters of a metamaterial for an ideal cylindrical cloak through scattering theory. A multilayered cloak with homogeneous isotropic materials is introduced to approximate the ideal cloak. An active metamaterial, consisting of active arrays of acoustic cavities separated by piezo-diaphragms, is addressed to achieve the required parameters for each layer of the multilayered cloak. In particular, with the aid of a multi-control strategy that takes into account the coupling between adjacent cells, the effective parameters for the cloak can be accurately realized.

  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. 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.

  5. 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.

  6. Derivation of the Direct-Interaction Approximation Using Novikov's Theorem

    NASA Astrophysics Data System (ADS)

    Krommes, J. A.

    2015-11-01

    The direct-interaction approximation (DIA) is a crucially important statistical closure for both neutral fluids and plasmas. Kraichnan's original derivation proceeded in k space and assumed a large number N of interacting Fourier modes. That is problematic; the DIA can be formulated even for N = 3 . In the present work an alternate x-space procedure based on Novikov's theorem is described. That theorem is a statement about the correlations of certain Gaussian functionals. Turbulence cannot be Gaussian due to nonlinearity, but Novikov's theorem can be used to formulate self-consistent equations for a Gaussian component of the turbulence. The DIA emerges under the assumption that certain higher-order correlations are small. In essence, this procedure is merely a restatement of Kraichnan's arguments, but it adds additional perspective because the assumption of large N is not required. Details can be found in a lengthy set of tutorial Lecture Notes. Work supported by U.S.D.o.E. Contract DE-AC02-09CH11466.

  7. 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

  8. Interactions of Some Divalent Metal Ions with Thymine and Uracil Thiosemicarbazide Derivatives.

    PubMed

    Hammud, Hassan H; El-Dakdouki, Mohammad H; Sonji, Nada; Sonji, Ghassan; Bouhadir, Kamal H

    2016-05-01

    The study of interactions between metal ions and nucleobases, nucleosides, nucleotides, or nucleic acids has become an active research area in chemical, biological, and therapeutic fields. In this respect, the coordination behavior of nucleobase derivatives to transition metals was studied in order to get a better understanding about DNA-metal interactions in in vitro and in vivo systems. Two nucleobase derivatives, 3-benzoyl-1-[3-(thymine-1-yl)propamido]thiourea and 3-benzoyl-1-[3-(uracil-1-yl)propamido]thiourea, were synthesized and their dissociation constants were determined at different temperatures and 0.3 ionic strength. Potentiometric studies were carried out on the interaction of the derivatives towards some divalent metals in 50% v/v ethanol-water containing 0.3 mol.dm(-3) KCl, at five different temperatures. The formation constants of the metal complexes for both ligands follow the order: Cu(2+) > Ni(2+) > Co(2+) > Zn(2+) > Pb(2+) > Cd(2+) > Mn(2+). The thermodynamic parameters were estimated; the complexation process has been found to be spontaneous, exothermic, and entropically favorable. PMID:27049340

  9. Auroral energy deposition rate, characteristic electron energy, and ionospheric parameters derived from Dynamics Explorer 1 images

    NASA Technical Reports Server (NTRS)

    Rees, M. H.; Lummerzheim, D.; Roble, R. G.; Winningham, J. D.; Craven, J. D.

    1988-01-01

    Auroral images obtained by the Spin Scan Auroral Imager (SAI) aboard the DE-1 satellite were used to derive auroral energy deposition rate, characteristic electron energy, and ionospheric parameters. The principles involved in the imaging technique and the physical mechanisms that underlie the relationship between the spectral images and the geophysical parameters are discussed together with the methodology for implementing such analyses. It is shown that images obtained with the SAI provide global parameters at 12-min temporal resolution; the spatial resolution is limited by the field of view of a pixel. The analysis of the 12-min images presented yielded a representation of ionospheric parameters that was better than can be obtained using empirical models based on local measurements averaged over long periods of time.

  10. 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. PMID:24051802

  11. Identification of fractional-derivative-model parameters of viscoelastic materials from measured FRFs

    NASA Astrophysics Data System (ADS)

    Kim, Sun-Yong; Lee, Doo-Ho

    2009-07-01

    The dynamic properties of viscoelastic damping materials are highly frequency- and temperature-dependent. Numerical methods of structural and acoustic systems require the mathematical model for these dependencies. The fractional-derivative model on damping material has become a powerful solution that describes the frequency-dependent dynamic characteristics of damping materials. The model parameters on a damping material are very important information both for describing the responses of damped structures and in the design of damped structures. The authors proposed an efficient identification method of the material parameters using an optimization technique, showing its applicability through numerical studies in a previous work. In this study, the proposed procedure is applied to a damping material to identify the fractional-derivative-model parameters of viscoelastic materials. In the proposed method, frequency response functions (FRFs) are measured via a cantilever beam impact test. The FRFs on the points identical to those measured are calculated using an FE model with the equivalent stiffness approach. The differences between the measured and the calculated FRFs are minimized using a gradient-based optimization algorithm in order to estimate the true values of the parameters. The FRFs of a damped beam structure are measured in an environmental chamber at different temperatures and used as reference responses. A light impact hammer and a laser vibrometer are used to measure the reference responses. Both linear and nonlinear relationships between the logarithmically scaled shift factors and temperatures are examined during the identification of the material parameters. The applied results show that the proposed method accurately identifies the fractional-derivative-model parameters of a viscoelastic material.

  12. On the coverage dependence of Arrhenius parameters in thermal desorption of interacting adsorbates

    NASA Astrophysics Data System (ADS)

    Zuniga-Hansen, Nayeli; Silbert, Leonardo E.; Calbi, M. Mercedes

    2014-03-01

    In temperature programmed desorption (TPD) the ``compensation effect'' is a linear relationship between the activation energy, Ea, and the preexponential factor, νn, of the Arrhenius equation. From the Arrhenius plot ln -θ/˙ θ vs. 1/T, we can extract the activation energy and the preexponential factor to test the validity of linearity. A linear relationship has been demonstrated to be valid when the kinetic parameters are independent of the surface coverage. In the presence of adsorbate-adsorbate interactions this analysis fails because the second order effects come into play. The compensation effect arises from the assumption that the second order terms in the derivative of the plot sum to zero. Some authors refer to this as a ``forced'' compensation effect and show that it can yield misleading results. Therefore this effect has not been completely understood. We use kinetic Monte Carlo simulations on ordered and disordered surface configurations to investigate the coverage dependence of the kinetic parameters to verify whether the compensation effect provides reliable information for our system, we do this over a range of binding and interaction energies.

  13. On the design derivatives of eigenvalues and eigenvectors for distributed parameter systems

    NASA Technical Reports Server (NTRS)

    Reiss, R.

    1985-01-01

    In this paper, analytic expressions are obtained for the design derivatives of eigenvalues and eigenfunctions of self-adjoint linear distributed parameter systems. Explicit treatment of boundary conditions is avoided by casting the eigenvalue equation into integral form. Results are expressed in terms of the linear operators defining the eigenvalue problem, and are therefore quite general. Sufficiency conditions appropriate to structural optimization of eigenvalues are obtained.

  14. 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. PMID:25874941

  15. Interaction of aldehydes derived from lipid peroxidation and membrane proteins

    PubMed Central

    Pizzimenti, Stefania; Ciamporcero, Eric; Daga, Martina; Pettazzoni, Piergiorgio; Arcaro, Alessia; Cetrangolo, Gianpaolo; Minelli, Rosalba; Dianzani, Chiara; Lepore, Alessio; Gentile, Fabrizio; Barrera, Giuseppina

    2013-01-01

    A great variety of compounds are formed during lipid peroxidation of polyunsaturated fatty acids of membrane phospholipids. Among them, bioactive aldehydes, such as 4-hydroxyalkenals, malondialdehyde (MDA) and acrolein, have received particular attention since they have been considered as toxic messengers that can propagate and amplify oxidative injury. In the 4-hydroxyalkenal class, 4-hydroxy-2-nonenal (HNE) is the most intensively studied aldehyde, in relation not only to its toxic function, but also to its physiological role. Indeed, HNE can be found at low concentrations in human tissues and plasma and participates in the control of biological processes, such as signal transduction, cell proliferation, and differentiation. Moreover, at low doses, HNE exerts an anti-cancer effect, by inhibiting cell proliferation, angiogenesis, cell adhesion and by inducing differentiation and/or apoptosis in various tumor cell lines. It is very likely that a substantial fraction of the effects observed in cellular responses, induced by HNE and related aldehydes, be mediated by their interaction with proteins, resulting in the formation of covalent adducts or in the modulation of their expression and/or activity. In this review we focus on membrane proteins affected by lipid peroxidation-derived aldehydes, under physiological and pathological conditions. PMID:24027536

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

    DOE PAGESBeta

    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

  17. 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.

  18. 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.

  19. Studies on interaction between an imidazole derivative and bovine serum by spectral methods

    NASA Astrophysics Data System (ADS)

    Jayabharathi, Jayaraman; Thanikachalam, Venugopal; Venkatesh Perumal, Marimuthu

    The interaction between a trifluoromethyl substituted imidazole derivative 2-(4-(trifluoromethyl)phenyl)-1-phenyl-1H-imidazo[4,5-f] [1,10] phenanthroline (tfmppip) and bovine serum albumin (BSA) was investigated by solution spectral studies. The observed experimental result shows that the imidazole derivative has strong ability to quench the fluorescence of BSA by forming complex which is stabilized by electrostatic interactions. The effective quenching constants (ksv) were 2.79 × 104, 2.51 × 104, and 2.32 × 104 at 301, 310 and 318 K respectively. The Stern-Volmer quenching constant (Ksv), binding site number (n), apparent binding constant (KA) and corresponding thermodynamic parameters (ΔG, ΔH and ΔS) were calculated. The distance between the donor (BSA) and acceptor (tfmppip) was obtained according to fluorescence resonance energy transfer (FRET). Conformational changes of BSA were observed from synchronous fluorescence technique. The effect of metal ions such as Cu2+, Zn2+, Ca2+, Mg2+, Ni2+, Co2+ and Fe2+ on the binding constants between the imidazole derivative and BSA were also studied.

  20. 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

  1. 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.

  2. 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

  3. Constraining the nonstandard interaction parameters in long baseline neutrino experiments

    NASA Astrophysics Data System (ADS)

    Huitu, Katri; Kärkkäinen, Timo J.; Maalampi, Jukka; Vihonen, Sampsa

    2016-03-01

    In this article we investigate the prospects for probing the strength of the possible nonstandard neutrino interactions (NSI) in long baseline neutrino oscillation experiments. We find that these experiments are sensitive to NSI couplings down to the level of 0.01-0.1 depending on the oscillation channel and the baseline length, as well as on the detector's fiducial mass. We also investigate the interference of the leptonic C P angle δC P with the constraining of the NSI couplings. It is found that the interference is strong in the case of the νe↔νμ and νe↔ντ transitions but not significant in other transitions. In our numerical analysis we apply the GLoBES software and use the LBNO setup as our benchmark.

  4. Solar wind and its interaction with the magnetosphere - Measured parameters

    NASA Astrophysics Data System (ADS)

    Schwenn, R.

    The sun and the solar wind are considered in terms of the 'ballerina' model first proposed by Alfven (1977), taking into account high speed streams, the slow solar wind, stream-stream interactions, the relation of streams and magnetic structure, and transients caused by solar activity. The main features of the solar wind behavior are illustrated with the aid of data, covering one complete solar rotation in 1974/1975, which were obtained with instruments aboard the Helios-1 solar probe. It is pointed out that the solar wind acts like a huge buffer pushing onto the earth's magnetosphere with a highly variable pressure. Of the energy in the highly variable solar wind reservoir only a tiny fraction is absorbed by the magnetosphere in an obviously very nonstationary way.

  5. Ground Motion Simulations for Bursa Region (Turkey) Using Input Parameters derived from the Regional Seismic Network

    NASA Astrophysics Data System (ADS)

    Unal, B.; Askan, A.

    2014-12-01

    Earthquakes are among the most destructive natural disasters in Turkey and it is important to assess seismicity in different regions with the use of seismic networks. Bursa is located in Marmara Region, Northwestern Turkey and to the south of the very active North Anatolian Fault Zone. With around three million inhabitants and key industrial facilities of the country, Bursa is the fourth largest city in Turkey. Since most of the focus is on North Anatolian Fault zone, despite its significant seismicity, Bursa area has not been investigated extensively until recently. For reliable seismic hazard estimations and seismic design of structures, assessment of potential ground motions in this region is essential using both recorded and simulated data. In this study, we employ stochastic finite-fault simulation with dynamic corner frequency approach to model previous events as well to assess potential earthquakes in Bursa. To ensure simulations with reliable synthetic ground motion outputs, the input parameters must be carefully derived from regional data. In this study, using strong motion data collected at 33 stations in the region, site-specific parameters such as near-surface high frequency attenuation parameter and amplifications are obtained. Similarly, source and path parameters are adopted from previous studies that as well employ regional data. Initially, major previous events in the region are verified by comparing the records with the corresponding synthetics. Then simulations of scenario events in the region are performed. We present the results in terms of spatial distribution of peak ground motion parameters and time histories at selected locations.

  6. Analysis of shallow landslides by morphometry parameters derived from terrestrial laser scanning point clouds

    NASA Astrophysics Data System (ADS)

    Mayr, A.; Rutzinger, M.; Bremer, M.; Wiegand, C.; Kringer, K.; Geitner, C.

    2012-04-01

    Erosion by shallow landslides is a widespread and growing phenomenon in mountainous areas. The major consequences are loss of soil and regolith as well as damages on infrastructure and provision of unconsolidated material for secondary processes such as mudflows. In this study we present a concept for extracting morphometry parameters from terrestrial laser scanning (TLS) point clouds in order to investigate the relation between slope surface structure and regolith depth. TLS is used to collect high-resolution point cloud data of an affected slope in the Schmirn Valley (Tyrol, Austria). Regolith depth is considered to be one of the important factors for the development of shallow landslides. However, direct field measurements are labour- and time-consuming. In this study we developed an approach, to investigate the relation between regolith depth and surface morphometry parameters. The reference regolith depth information is derived from lightweight dynamic cone penetrometer tests (DCPT) within the test site. The suggested approach integrates spatial analysis of Geographic Information Systems and point cloud processing algorithms. It will help to enhance the prediction of shallow landslide occurrence by (i) deriving high resolution 3D morphometric parameters and (ii) determining regolith depth with a reasonable effort due to automation. In future we want to be able to contribute with this concept to the detailed modelling of shallow landslide susceptibility on alpine slopes.

  7. 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

  8. 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.

  9. 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

  10. Understanding Variability in the AVIRIS-Derived Parameters from Vegetation Cover

    NASA Technical Reports Server (NTRS)

    Goetz, Alexander F. H.

    2000-01-01

    This project was carried out in two phases, the first was an investigation of the possible sources of variability in the canopy leaf chemistry parameters derived from AVERJS data on a year-to-year basis, and the second was a follow-on effort to improve the atmospheric correction program ATREM as well as to provide support to the community on the use of ATREM. This final report embodies a general review of the results obtained over the life of the contract as well as detailed interim reports and copies of the six papers published in AVIRIS Workshop Proceedings over the last 3 years.

  11. 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.

  12. Sensitivity derivatives for advanced CFD algorithm and viscous modelling parameters via automatic differentiation

    NASA Technical Reports Server (NTRS)

    Green, Lawrence L.; Newman, Perry A.; Haigler, Kara J.

    1993-01-01

    The computational technique of automatic differentiation (AD) is applied to a three-dimensional thin-layer Navier-Stokes multigrid flow solver to assess the feasibility and computational impact of obtaining exact sensitivity derivatives typical of those needed for sensitivity analyses. Calculations are performed for an ONERA M6 wing in transonic flow with both the Baldwin-Lomax and Johnson-King turbulence models. The wing lift, drag, and pitching moment coefficients are differentiated with respect to two different groups of input parameters. The first group consists of the second- and fourth-order damping coefficients of the computational algorithm, whereas the second group consists of two parameters in the viscous turbulent flow physics modelling. Results obtained via AD are compared, for both accuracy and computational efficiency with the results obtained with divided differences (DD). The AD results are accurate, extremely simple to obtain, and show significant computational advantage over those obtained by DD for some cases.

  13. 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.

  14. Virchow-Robin Spaces: Correlations with Polysomnography-Derived Sleep Parameters

    PubMed Central

    Berezuk, Courtney; Ramirez, Joel; Gao, Fuqiang; Scott, Christopher J.M.; Huroy, Menal; Swartz, Richard H.; Murray, Brian J.; Black, Sandra E.; Boulos, Mark I.

    2015-01-01

    Study Objectives: To test the hypothesis that enlarged Virchow-Robin space volumes (VRS) are associated with objective measures of poor quality sleep. Design: Retrospective cross-sectional study. Setting: Sunnybrook Health Sciences Centre. Patients: Twenty-six patients being evaluated for cerebrovascular disease were assessed using polysomnography and high-resolution structural magnetic resonance imaging. Measurements and Results: Regionalized VRS were quantified from three-dimensional high-resolution magnetic resonance imaging and correlated with measures of polysomnography-derived sleep parameters while controlling for age, stroke volume, body mass index, systolic blood pressure, and ventricular cerebrospinal fluid volume. Sleep efficiency was negatively correlated with total VRS (rho = −0.47, P = 0.03) and basal ganglia VRS (rho = −0.54, P = 0.01), whereas wake after sleep onset was positively correlated with basal ganglia VRS (rho = 0.52, P = 0.02). Furthermore, VRS in the basal ganglia were negatively correlated with duration of N3 (rho = −0.53, P = 0.01). Conclusions: These preliminary results suggest that sleep may play a role in perivascular clearance in ischemic brain disease, and invite future research into the potential relevance of Virchow-Robin spaces as an imaging biomarker for nocturnal metabolite clearance. Citation: Berezuk C, Ramirez J, Gao F, Scott CJ, Huroy M, Swartz RH, Murray BJ, Black SE, Boulos MI. Virchow-Robin spaces: correlations with polysomnography-derived sleep parameters. SLEEP 2015;38(6):853–858. PMID:26163465

  15. CRISM-Derived Spectral Scattering Parameters for Surfaces in the Vicinity of Opportunity Mars Rover Traverses

    NASA Astrophysics Data System (ADS)

    Shaw, A.; Arvidson, R. E.; Wolff, M. J.; Seelos, F. P.; Wiseman, S. M.; Cull, S.

    2011-12-01

    CRISM (Compact Reconnaissance Imaging Spectrometer for Mars) data were used to retrieve scattering parameters of surfaces traversed by the Opportunity Mars rover, as well as adjacent areas. Our estimates agree with those retrieved by Johnson et al. [2006] using Opportunity's Panoramic Camera data, and we are able to extend estimates of the Hapke single particle scattering albedo and asymmetry parameter (from the one-term Henyey Greenstein single particle phase function) to a greater spectral resolution and spectral range. This analysis allows us to distinguish between surface units that otherwise look relatively uniform spectrally. This work also provides photometric functions essential for converting spectra to a single viewing geometry which will yield more accurate spectral comparisons. Our method involves simultaneously modeling surface and atmospheric contributions, iterating through surface scattering parameters until a Levenberg-Marquardt least squares best fit is achieved. Retrieved single scattering albedos range from 0.42 to 0.57 (0.5663 - 2.2715 micrometers), and retrieved asymmetry parameters range from -0.27 to -0.17 (moderately backscattering). All surfaces become more backscattering with increasing wavelength. Further, the northern and western portions of Victoria crater's ejecta apron are more backscattering than surrounding regions, indicating a change in physical properties. In images taken when the rover traversed this unit, a surface with small ripples and a dense cover of hematitic spherules is apparent, providing agreement with lab experiments by Johnson et al. [2006] showing increased backscattering with the addition of hematitic spherules. The CRISM-derived scattering parameters also show that bedrock-dominated surfaces are less backscattering than soil-covered surfaces.

  16. 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.

  17. ELECTRONIC FACTOR IN QSAR: MO-PARAMETERS, COMPETING INTERACTIONS, REACTIVITY AND TOXICITY

    EPA Science Inventory

    Reactive chemicals pose unique problems in the development of SAR and QSAR in environmental chemistry and toxicology. odels of the stereoelectronic interactions of reactive toxicants with biological systems require formulation of parameters that quantify the electronic structure ...

  18. 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.

  19. Troposphere Parameters Derived from Multi-GNSS Data Processing at GFZ

    NASA Astrophysics Data System (ADS)

    Deng, Zhiguo; Uhlemann, Maik; Fritsche, Mathias; Dick, Galina; Wickert, Jens

    2015-04-01

    Usually, the processing of Global Navigation Satellite System (GNSS) observations requires a thorough consideration of atmospheric parameters for precise applications. Accordingly, GPS meteorology has become a tool which uses measurements from ground-based GPS receivers for atmospheric water vapor sounding. Zenith total delay (ZTD) products derived from GNSS complement different other meteorological observing systems. GPS-based ZTD estimates have also been assimilated into numerical weather prediction (NWP) models. In addition to GPS and GLONASS, the new and emerging satellite navigation systems BeiDou and Galileo provide the potential for extended and more precise GNSS applications. Accordingly, the International GNSS Service (IGS) has initiated the Multi-GNSS Experiment (MGEX) to acquire and analyze data from all four constellations. In view of the increased number of actively transmitting satellites, the ZTD parameter estimation will particularly benefit from an improved spatial distribution of observations tracked by the ground-based receivers. In this contribution, we report on the status of our multi-system (GPS, GLONASS, BeiDou, Galileo) data processing at GFZ. Based on data from the MGEX network we produce multi-GNSS solutions including parameter estimates for satellite orbits, clock, station coordinates and site-specific ZTDs. Our presentation focusses on the validation of ZTDs from the multi-GNSS processing and a comparison with single-system ZTD solutions and GFZ's operational near real-time troposphere products.

  20. Urban thermal environment and its biophysical parameters derived from satellite remote sensing imagery

    NASA Astrophysics Data System (ADS)

    Zoran, Maria A.; Savastru, Roxana S.; Savastru, Dan M.; Tautan, Marina N.; Baschir, Laurentiu V.

    2013-10-01

    In frame of global warming, the field of urbanization and urban thermal environment are important issues among scientists all over the world. This paper investigated the influences of urbanization on urban thermal environment as well as the relationships of thermal characteristics to other biophysical variables in Bucharest metropolitan area of Romania based on satellite remote sensing imagery Landsat TM/ETM+, time series MODIS Terra/Aqua data and IKONOS acquired during 1990 - 2012 period. Vegetation abundances and percent impervious surfaces were derived by means of linear spectral mixture model, and a method for effectively enhancing impervious surface has been developed to accurately examine the urban growth. The land surface temperature (Ts), a key parameter for urban thermal characteristics analysis, was also retrieved from thermal infrared band of Landsat TM/ETM+, from MODIS Terra/Aqua datasets. Based on these parameters, the urban growth, urban heat island effect (UHI) and the relationships of Ts to other biophysical parameters have been analyzed. Results indicated that the metropolitan area ratio of impervious surface in Bucharest increased significantly during two decades investigated period, the intensity of urban heat island and heat wave events being most significant. The correlation analyses revealed that, at the pixel-scale, Ts possessed a strong positive correlation with percent impervious surfaces and negative correlation with vegetation abundances at the regional scale, respectively. This analysis provided an integrated research scheme and the findings can be very useful for urban ecosystem modeling.

  1. 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

  2. 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

  3. Derivatives of the local ballooning growth rate with respect to surface label, field line label, and ballooning parameter

    SciTech Connect

    Hudson, S.R.

    2006-04-15

    Expressions for the derivative of the local ballooning growth rate with respect to surface label, field line label, and ballooning-parameter are presented. Such expressions lead to increased computational efficiency for ballooning stability applications.

  4. Sounding-derived parameters associated with tornado occurrence in Poland and Universal Tornadic Index

    NASA Astrophysics Data System (ADS)

    Taszarek, M.; Kolendowicz, L.

    2013-12-01

    This study is mainly devoted to operational meteorology, to improve tornado forecast in Poland and create a Universal Tornadic Index formula. A study is focusing on climatology of sounding-derived parameters associated with tornadoes in Poland and their potential value for tornado forecasting. The data was collected from soundings made in 10 stations in and around Poland which were closely in time and space connected with tornado occurrence. The main aim of the study was to analyze the thermodynamic and kinematic parameters derived from soundings and formulate an index. The information about tornado incidents was taken from media reports and the European Severe Weather Database for the years 1977-2012. Total of 97 tornado cases were divided according to their strength for significant (F2/F3), weak (F0/F1) and unrated cases, and also according to their environmental surface temperature, for warm (> 18 °C) and cold (< 18 °C) tornadoes. As it turned out, depending on the temperature, tornadoes tended to present different environmental conditions for tornadogenesis. In warm cases, the most important factor was instability while for cold cases it was dynamic wind field. It was also proven that significant tornadoes in Poland occur in conditions accompanied by high moisture content, moderate instability and high wind shear conditions. The results of this study were used to create a Universal Tornadic Index designed to forecast activity in warm and cold, and weak and strong tornadic environments. The quality of this index was tested for the period with increased tornado activity in Poland from 2008 to 2010.

  5. Sounding-derived parameters associated with large hail and tornadoes in the Netherlands

    NASA Astrophysics Data System (ADS)

    Groenemeijer, P. H.; van Delden, A.

    2007-02-01

    A study is presented focusing on the potential value of parameters derived from radiosonde data or data from numerical atmospheric models for the forecasting of severe weather associated with convective storms. Parameters have been derived from soundings in the proximity of large hail, tornadoes (including tornadoes over water: waterspouts) and thunderstorms in the Netherlands. 66,365 radiosonde soundings from six stations in and around the Netherlands between 1 Dec. 1975 to 31 Aug. 2003 were classified as being associated or not associated with these weather phenomena using observational data from voluntary observers, the Dutch National Meteorological Institute (KNMI) and lightning data from the U.K. Met. Office. It was found that instability as measured by the Lifted Index or CAPE and 0-6 km wind shear independently have considerable skill in distinguishing environments of large hail and of non-hail-producing thunderstorms. It was also found that CAPE released below 3 km above ground level is on average high near waterspouts and weak tornadoes that mostly occur with low shear in the lowest 1 km above the Earth's surface. On the other hand, low-level shear is strong in environments of stronger (F1 and F2) tornadoes and increases with increasing F-scale. This is consistent with the notion that stretching of pre-existing vertical vorticity is the most important mechanism for the formation of weak tornadoes while the tilting of vorticity is more important with stronger tornadoes. The presented results may assist forecasters to assess the likelihood of severe hail or tornadoes.

  6. Parametric computation predicts a multiplicative interaction between synaptic strength parameters that control gamma oscillations

    PubMed Central

    Chambers, Jordan D.; Bethwaite, Blair; Diamond, Neil T.; Peachey, Tom; Abramson, David; Petrou, Steve; Thomas, Evan A.

    2012-01-01

    Gamma oscillations are thought to be critical for a number of behavioral functions, they occur in many regions of the brain and through a variety of mechanisms. Fast repetitive bursting (FRB) neurons in layer 2 of the cortex are able to drive gamma oscillations over long periods of time. Even though the oscillation is driven by FRB neurons, strong feedback within the rest of the cortex must modulate properties of the oscillation such as frequency and power. We used a highly detailed model of the cortex to determine how a cohort of 33 parameters controlling synaptic drive might modulate gamma oscillation properties. We were interested in determining not just the effects of parameters individually, but we also wanted to reveal interactions between parameters beyond additive effects. To prevent a combinatorial explosion in parameter combinations that might need to be simulated, we used a fractional factorial design (FFD) that estimated the effects of individual parameters and two parameter interactions. This experiment required only 4096 model runs. We found that the largest effects on both gamma power and frequency came from a complex interaction between efficacy of synaptic connections from layer 2 inhibitory neurons to layer 2 excitatory neurons and the parameter for the reciprocal connection. As well as the effect of the individual parameters determining synaptic efficacy, there was an interaction between these parameters beyond the additive effects of the parameters alone. The magnitude of this effect was similar to that of the individual parameters, predicting that it is physiologically important in setting gamma oscillation properties. PMID:22837747

  7. 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.

  8. 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.

  9. Poromechanics Parameters of Fluid-Saturated Chemically Active Fibrous Media Derived from a Micromechanical Approach.

    PubMed

    Misra, Anil; Parthasarathy, Ranganathan; Singh, Viraj; Spencer, Paulette

    2013-01-01

    The authors have derived macroscale poromechanics parameters for chemically active saturated fibrous media by combining microstructure-based homogenization with Hill's volume averaging. The stress-strain relationship of the dry fibrous media is first obtained by considering the fiber behavior. The constitutive relationships applicable to saturated media are then derived in the poromechanics framework using Hill's Lemmas. The advantage of this approach is that the resultant continuum model assumes a form suited to study porous materials, while retaining the effect of discrete fiber deformation. As a result, the model is able to predict the influence of microscale phenomena such as fiber buckling on the overall behavior, and in particular, on the poromechanics constants. The significance of the approach is demonstrated using the effect of drainage and fiber nonlinearity on monotonic compressive stress-strain behavior. The model predictions conform to the experimental observations for articular cartilage. The method can potentially be extended to other porous materials such as bone, clays, foams, and concrete. PMID:25419475

  10. 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.

  11. 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.

  12. Poromechanics Parameters of Fluid-Saturated Chemically Active Fibrous Media Derived from a Micromechanical Approach

    PubMed Central

    Parthasarathy, Ranganathan; Singh, Viraj; Spencer, Paulette

    2014-01-01

    The authors have derived macroscale poromechanics parameters for chemically active saturated fibrous media by combining microstructure-based homogenization with Hill's volume averaging. The stress-strain relationship of the dry fibrous media is first obtained by considering the fiber behavior. The constitutive relationships applicable to saturated media are then derived in the poromechanics framework using Hill's Lemmas. The advantage of this approach is that the resultant continuum model assumes a form suited to study porous materials, while retaining the effect of discrete fiber deformation. As a result, the model is able to predict the influence of microscale phenomena such as fiber buckling on the overall behavior, and in particular, on the poromechanics constants. The significance of the approach is demonstrated using the effect of drainage and fiber nonlinearity on monotonic compressive stress-strain behavior. The model predictions conform to the experimental observations for articular cartilage. The method can potentially be extended to other porous materials such as bone, clays, foams, and concrete. PMID:25419475

  13. 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.

  14. 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.

  15. 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

  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. 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

  18. Higher-order semirational solutions and nonlinear wave interactions for a derivative nonlinear Schrödinger equation

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Zhu, Yu-Jie; Wang, Zi-Zhe; Qi, Feng-Hua; Guo, Rui

    2016-04-01

    We present the semirational solution in terms of the determinant form for the derivative nonlinear Schrödinger equation. It describes the nonlinear combinations of breathers and rogue waves (RWs). We show here that the solution appears as a mixture of polynomials with exponential functions. The k-order semirational solution includes k - 1 types of nonlinear superpositions, i.e., the l-order RW and (k-l)-order breather for l = 1 , 2 , … , k - 1 . By adjusting the shift and spectral parameters, we display various patterns of the semirational solutions for describing the interactions among the RWs and breathers. We find that k-order RW can be derived from a l-order RW interacting with 1/2(k - l) (k + l + 1) neighboring elements of a (k - l)-order breather for l = 1 , 2 , … , k - 1 .

  19. 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.

  20. Connection between Dynamically Derived Initial Mass Function Normalization and Stellar Population Parameters

    NASA Astrophysics Data System (ADS)

    McDermid, Richard M.; Cappellari, Michele; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Serra, Paolo; Weijmans, Anne-Marie; Young, Lisa M.

    2014-09-01

    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 ATLAS3D project. We study trends between our dynamically derived IMF normalization αdyn ≡ (M/L)stars/(M/L)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 αdyn at a given population parameter. As a result, we find weak αdyn-[α/Fe] and αdyn -Age correlations and no significant αdyn -[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.

  1. 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.

  2. 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.

  3. 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

  4. An Analysis of Interaction of Anxiety, Aspiration Level and Ability Derived From Ecological Systems Theory.

    ERIC Educational Resources Information Center

    Loose, Kenneth D.; Unruh, Waldemar R.

    A technique for the analysis of ecosystems developed by Odum focuses on the nature of interactions which take place within the system being considered. This technique can be used to assess the contribution of any variable to an interaction. Using data derived from previous research conducted by Feather, the authors employ this technique to examine…

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. Interaction of human serum albumin with novel imidazole derivatives studied by spectroscopy and molecular docking.

    PubMed

    Yue, Yuanyuan; Sun, Yangyang; Dong, Qiao; Liu, Ren; Yan, Xuyang; Zhang, Yajie; Liu, Jianming

    2016-05-01

    This study was a detailed characterization of the interaction of a series of imidazole derivatives with a model transport protein, human serum albumin (HSA). Fluorescence and time-resolved fluorescence results showed the existence of a static quenching mode for the HSA-imidazole derivative interaction. The binding constant at 296 K was in the order of 10(4) M(-1) , showing high affinity between the imidazole derivatives and HSA. A site marker competition study combined with molecular docking revealed that the imidazole derivatives bound to subdomain IIA of HSA (Sudlow's site I). Furthermore, the results of synchronous, 3D, Fourier transform infrared, circular dichroism and UV-vis spectroscopy demonstrated that the secondary structure of HSA was altered in the presence of the imidazole derivatives. The specific binding distance, r, between the donor and acceptor was obtained according to fluorescence resonance energy transfer. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26364804

  12. 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

  13. A state parameter-based model for static recrystallization interacting with precipitation

    NASA Astrophysics Data System (ADS)

    Buken, Heinrich; Sherstnev, Pavel; Kozeschnik, Ernst

    2016-03-01

    In the present work, we develop a state parameter-based model for the treatment of simultaneous precipitation and recrystallization based on a single-parameter representation of the total dislocation density and a multi-particle multi-component framework for precipitation kinetics. In contrast to conventional approaches, the interaction of particles with recrystallization is described with a non-zero grain boundary mobility even for the case where the Zener pressure exceeds the driving pressure for recrystallization. The model successfully reproduces the experimentally observed particle-induced recrystallization stasis and subsequent continuation in micro-alloyed steel with a single consistent set of input parameters. In addition, as a state parameter-based approach, our model naturally supports introspection into the physical mechanisms governing the competing recrystallization and recovery processes.

  14. Pulse-to-pulse interaction analysis and parameter optimization for future-generation ophthalmic laser systems

    NASA Astrophysics Data System (ADS)

    Tinne, N.; Kaune, B.; Bleeker, S.; Lubatschowski, H.; Krüger, A.; Ripken, T.

    2014-02-01

    The immediate pulse-to-pulse interaction becomes more and more important for future-generation high-repetition rate ophthalmic laser systems. Therefore, we investigated the interaction of two laser pulses with different spatial and temporal separation by time-resolved photography. There are various different characteristic interaction mechanisms which are divided into 11 interaction scenarios. Furthermore, the parameter range has been constricted regarding the medical application; here, the efficiency was optimized to a maximum jet velocity along the scanning axis with minimum applied pulse energy as well as unwanted side effects at the same time. In conclusion, these results are of great interest for the prospective optimization of the ophthalmic surgical process with future-generation fs-lasers.

  15. 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

  16. 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.

  17. Quantum integrable models of interacting bosons and classical r-matrices with spectral parameters

    NASA Astrophysics Data System (ADS)

    Skrypnyk, T.

    2015-11-01

    Using the technique of classical r-matrices with spectral parameters we construct a general form of quantum Lax operators of interacting boson systems corresponding to an arbitrary simple (or reductive) Lie algebra. We prove quantum integrability of these models in the physically important case of g = gl(n) and "diagonal" in the root basis classical r-matrices. We consider in detail two classes of non-skew-symmetric classical r-matrices with spectral parameters and obtain the corresponding quantum Lax operators and quantum integrable many-boson hamiltonians that generalize Bose-Hubbard dimer hamiltonians.

  18. 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.

  19. 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.

  20. 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

  1. Automated optimization of water-water interaction parameters for a coarse-grained model.

    PubMed

    Fogarty, Joseph C; Chiu, See-Wing; Kirby, Peter; Jakobsson, Eric; Pandit, Sagar A

    2014-02-13

    We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment. PMID:24460506

  2. Automated Optimization of Water–Water Interaction Parameters for a Coarse-Grained Model

    PubMed Central

    2015-01-01

    We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder–Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment. PMID:24460506

  3. Comparison of photon interaction parameters of some tissues and their substitutes.

    PubMed

    Manjunatha, H C

    2014-02-01

    The photon interaction parameters such as mass attenuation coefficient (μ/ρ), effective atomic number (Z eff) and effective electron density (N el) must be identical for the phantom material and their tissue. In the present study, the μ/ρ, Z eff, and N el for muscle, breast, lung tissue have been computed, and their substitutes such as Griffith muscle, Griffith breast, Griffith lung, Alderson muscle A, Alderson muscle, and Alderson lung. Also compared were μ/ρ, Z eff, and N el for muscle, breast, lung tissue, and their substitutes. It can be shown that Alderson muscle B is better substitute for muscle than Griffith muscle and Alderson muscle A. Similarly, the photon interaction parameters of tissue substitutes of lung and breast with their original tissue were also compared. PMID:24378560

  4. Interaction of the Heparin-Binding Consensus Sequence of β-Amyloid Peptides with Heparin and Heparin-Derived Oligosaccharides.

    PubMed

    Nguyen, Khanh; Rabenstein, Dallas L

    2016-03-10

    Alzheimer's disease (AD) is characterized by the presence of amyloid plaques in the AD brain. Comprised primarily of the 40- and 42-residue β-amyloid (Aβ) peptides, there is evidence that the heparan sulfate (HS) of heparan sulfate proteoglycans (HSPGs) plays a role in amyloid plaque formation and stability; however, details of the interaction of Aβ peptides with HS are not known. We have characterized the interaction of heparin and heparin-derived oligosaccharides with a model peptide for the heparin- and HS-binding domain of Aβ peptides (Ac-VHHQKLV-NH2; Aβ(12-18)), with mutants of Aβ(12-18), and with additional histidine-containing peptides. The nature of the binding interaction was characterized by NMR, binding constants and other thermodynamic parameters were determined by isothermal titration calorimetry (ITC), and relative binding affinities were determined by heparin affinity chromatography. The binding of Aβ(12-18) by heparin and heparin-derived oligosaccharides is pH-dependent, with the imidazolium groups of the histidine side chains interacting site-specifically within a cleft created by a trisaccharide sequence of heparin, the binding is mediated by electrostatic interactions, and there is a significant entropic contribution to the binding free energy as a result of displacement of Na(+) ions from heparin upon binding of cationic Aβ(12-18). The binding constant decreases as the size of the heparin-derived oligosaccharide decreases and as the concentration of Na(+) ion in the bulk solution increases. Structure-binding relationships characterized in this study are analyzed and discussed in terms of the counterion condensation theory of the binding of cationic peptides by anionic polyelectrolytes. PMID:26872053

  5. 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

  6. 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

  7. 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.

  8. 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

  9. Investigation of interaction parameters in mixed micelle using pulsed field gradient NMR spectroscopy.

    PubMed

    Gharibi, H; Javadian, S; Sohrabi, B; Behjatmanesh, R

    2005-05-01

    Pulsed field gradient NMR spectroscopy was used to determine the partitioning of surfactant between monomeric and micellar forms in a mixed CTAB (hexadecyltetramethylammonium bromide) and Triton X-100 [p-(1,1,3-tetramethylbutyl)polyoxyethylene] system. In addition, potentiometric and surface tension measurements were used to determine the free concentration of ionic surfactant and the critical micelle concentration (CMC) of mixtures of n-alkyltrimethylammonium bromide (C(n)TAB, n=12, 14, 16, 18) and Triton X-100. Regular solution theory cannot describe the behavior of the activity coefficient and the excess Gibbs free energy of mixtures of ionic and nonionic surfactants. To overcome these shortcomings, we developed a new model that combines Van Laar expressions and the theory of nonrandom mixing in mixed micelles. The Van Laar expressions contain an additional parameter, rho, which reflects differences in the size of the components of the mixture. Nonrandom mixing theory was introduced to describe nonrandom mixing in mixed micelles. This effect was modeled by a packing parameter, P*. The proposed model provided a good description of the behavior of binary surfactant mixtures. The results indicated that head group size and packing constraints are important contributors to nonideal surfactant behavior. In addition, the results showed that as the chain length of the C(n)TAB molecule in C(n)TAB/Triton X-100 mixtures was increased, the head group size parameter remained constant, but the interaction and packing parameters increased. Increase of the temperature caused an increase in the interaction parameter beta and a decrease in the packing parameter (P*). PMID:15797433

  10. 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.

  11. Theory of electronic structure and nuclear quadrupole interactions in the BF3-NH3 complex and methyl derivatives

    NASA Astrophysics Data System (ADS)

    Pink, R. H.; Dubey, Archana; Mahato, Dip N.; Badu, S. R.; Scheicher, R. H.; Mahanti, Mahendra K.; Huang, M. B.; Saha, H. P.; Chow, Lee; Das, T. P.

    Magnetic Hyperfine and Nuclear Quadrupole Interactions (HPI and NQI) are now important tools for characterization of systems of interest in materials research and industry. Boron-Trifluoride is an inorganic compound that is very important in this respect as a catalyst in chemical physics research and industry, forming complexes in the process with compounds like ammonia, water and methyl alcohol. The present paper deals with the BP3-NH3 complex and methyl derivatives BP3NHx(CH3)3-x for which we have studied the electronic structures, binding energies, and 19F* (I=5/2) nuclear quadrupole interactions using the first-principles Hartree-Fock-Roothaan procedure combined with electron correlation effects. Our results for the 19F* nuclear quadrupole coupling constant (e 2qQ/h) in units of MHz compare well with experiment. Trends in the binding energies and NQI parameters between the complexes are discussed.

  12. Theory of electronic structure and nuclear quadrupole interactions in the BF3 NH3 complex and methyl derivatives

    NASA Astrophysics Data System (ADS)

    Pink, R. H.; Dubey, Archana; Mahato, Dip N.; Badu, S. R.; Scheicher, R. H.; Mahanti, Mahendra K.; Huang, M. B.; Saha, H. P.; Chow, Lee; Das, T. P.

    2007-04-01

    Magnetic Hyperfine and Nuclear Quadrupole Interactions (HFI and NQI) are now important tools for characterization of systems of interest in materials research and industry. Boron-Trifluoride is an inorganic compound that is very important in this respect as a catalyst in chemical physics research and industry, forming complexes in the process with compounds like ammonia, water and methyl alcohol. The present paper deals with the BF3 NH3 complex and methyl derivatives BF3NHx(CH3)3-x for which we have studied the electronic structures, binding energies, and 19F* ( I = 5/2) nuclear quadrupole interactions using the first-principles Hartree Fock Roothaan procedure combined with electron correlation effects. Our results for the 19F* nuclear quadrupole coupling constant ( e 2 qQ/ h) in units of MHz compare well with experiment. Trends in the binding energies and NQI parameters between the complexes are discussed.

  13. 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.

  14. 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

  15. 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...

  16. 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

  17. 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

  18. 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.

  19. Derivation and Implementation of the Gradient of the R(-7) Dispersion Interaction in the Effective Fragment Potential Method.

    PubMed

    Guidez, Emilie B; Xu, Peng; Gordon, Mark S

    2016-02-01

    The dispersion interaction energy may be expressed as a sum over R(-n) terms, with n ≥ 6. Most implementations of the dispersion interaction in model potentials are terminated at n = 6. Those implementations that do include higher order contributions commonly only include even power terms, despite the fact that odd power terms can be important. Because the effective fragment potential (EFP) method contains no empirically fitted parameters, the EFP method provides a useful vehicle for examining the importance of the leading R(-7) odd power term in the dispersion expansion. To fully evaluate the importance of the R(-7) contribution to the dispersion energy, it is important to have analytic energy first derivatives for all terms. In the present work, the gradients of the term E7 ∼ R(-7) are derived analytically, implemented in the GAMESS software package, and evaluated relative to other terms in the dispersion expansion and relative to the total EFP interaction energy. Periodic boundary conditions in the minimum image convention are also implemented. A more accurate dispersion energy contribution can now be obtained during molecular dynamics simulations. PMID:26745447

  20. Spectroscopic studies on the interaction of cinnamic acid and its hydroxyl derivatives with human serum albumin

    NASA Astrophysics Data System (ADS)

    Min, Jiang; Meng-Xia, Xie; Dong, Zheng; Yuan, Liu; Xiao-Yu, Li; Xing, Chen

    2004-04-01

    Cinnamic acid and its derivatives possess various biological effects in remedy of many diseases. Interaction of cinnamic acid and its hydroxyl derivatives, p-coumaric acid and caffeic acid, with human serum albumin (HSA), and concomitant changes in its conformation were studied using fluorescence and Fourier transform infrared spectroscopic methods. Fluorescence data revealed the presence of one binding site on HSA for cinnamic acid and its hydroxyl derivatives, and their binding constants ( KA) are caffeic acid> p-coumaric acid> cinnamic acid when Cdrug/ CHSA ranging from 1 to 10. The changes of the secondary structure of HSA after interacting with the three drugs are estimated, respectively by combining the curve-fitting results of amid I and amid III bands. The α-helix structure has a decrease of ≈9, 5 and 3% after HSA interacted with caffeic acid, p-coumaric acid and cinnamic acid, respectively. It was found that the hydroxyls substituted on aromatic ring of the drugs play an important role in the changes of protein's secondary structure. Combining the result of fluorescence quenching and the changes of secondary structure of HSA after interaction with the three drugs, the drug-HSA interaction mode was discussed.

  1. 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.

  2. 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. PMID:27451180

  3. Fundamental electron-precursor-solid interactions derived from time dependent electron beam induced deposition simulations and experiments

    SciTech Connect

    Fowlkes, Jason Davidson; Rack, Philip D

    2010-01-01

    Unknown parameters critical to understanding the electron-precursor substrate interactions during electron beam induced deposition (EBID) have long limited our ability to fully control this nanoscale, directed assembly method. We report here values for the fundamental interaction parameters of D, the precursor surface diffusion coefficient, delta, the sticking probability and tau, the mean surface residence time which are critical parameters for understanding the assembly of EBID deposits. Values of D=6.4um2s-1, delta=0.0250 and tau=3.2ms were determined for a commonly used precursor molecule tungsten hexacarbonyl W(CO)6. Space and time predictions of the adsorbed precursor coverage C(r,t) were solved by an explicit finite differencing numerical scheme. Evolving nanopillar surface morphology was derived from solutions of C(r,t) considering electron induced dissociation as the critical depletion term. This made it possible to infer the space and time dependent precursor coverage both on, and around nanopillar structures to better understand local precursor dynamics during mass transport limited (MTL) and reaction rate limited (RRL) EBID.

  4. 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...

  5. 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

  6. Relationships between 6.7 micrometer imagery and radiosonde-derived parameters

    NASA Technical Reports Server (NTRS)

    Stewart, Michael R.; Fuelberg, Henry E.

    1986-01-01

    The relationships between water vapor images and various thermodynamic and kinematic patterns derived from ground-based data obtained on March 6-7, 1982 are investigated. The synoptic-scale characteristics of the observed image streaks are studied. Water vapor budgets were calculated from sonde data. Variations in black body temperatures are analyzed using water vapor budgets. The data reveal that the observed warm image streaks are caused by subsidence and horizontal flux divergence of vapor.

  7. 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.

  8. Identification and calibration of the interaction matrix parameters for AO and MCAO systems

    NASA Astrophysics Data System (ADS)

    Neichel, Benoit; Parisot, Amelie; Petit, Cyril; Fusco, Thierry; Rigaut, François

    2012-07-01

    New tomographic Adaptive Optics (AO) concepts require a good knowledge of the system geometry and characteristics. These parameters are used to feed the tomographic reconstructors. In this paper we present a method to precisely identify the parameters required to construct an accurate synthetic set of models such as inuence functions, mis-registrations, directions of analysis or altitude of the DMs. The method is based on a multiparameter t of the interaction matrix. This identication method nds also its application in high contrast AO systems, such as SPHERE : in that case it is used as a diagnostic tool in order to precisely realign the system. The method has been tested and successfully implemented on HOMER, SPHERE and GeMS. Experimental results for these three systems are presented.

  9. Sequential Model-Based Parameter Optimization: an Experimental Investigation of Automated and Interactive Approaches

    NASA Astrophysics Data System (ADS)

    Hutter, Frank; Bartz-Beielstein, Thomas; Hoos, Holger H.; Leyton-Brown, Kevin; Murphy, Kevin P.

    This work experimentally investigates model-based approaches for optimizing the performance of parameterized randomized algorithms. Such approaches build a response surface model and use this model for finding good parameter settings of the given algorithm. We evaluated two methods from the literature that are based on Gaussian process models: sequential parameter optimization (SPO) (Bartz-Beielstein et al. 2005) and sequential Kriging optimization (SKO) (Huang et al. 2006). SPO performed better "out-of-the-box," whereas SKO was competitive when response values were log transformed. We then investigated key design decisions within the SPO paradigm, characterizing the performance consequences of each. Based on these findings, we propose a new version of SPO, dubbed SPO+, which extends SPO with a novel intensification procedure and a log-transformed objective function. In a domain for which performance results for other (modelfree) parameter optimization approaches are available, we demonstrate that SPO+ achieves state-of-the-art performance. Finally, we compare this automated parameter tuning approach to an interactive, manual process that makes use of classical

  10. 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.

  11. Liquid metal magnetohydrodynamic flows in circular ducts at intermediate Hartmann numbers and interaction parameters

    NASA Astrophysics Data System (ADS)

    Molokov, S.; Reed, C. B.

    2003-12-01

    Magnetohydrodynamic flows in circular ducts in nonuniform magnetic fields are studied with reference to liquid metal blankets and divertors of fusion reactors. Flows in small and medium size reactors are characterized by moderate and low values of the Hartmann number (˜ 50-2000) and the interaction parameter (˜ 0.1-1000). The validity of the high-Hartmann number flow model for the intermediate range is discussed and the results of theoretical and experimental investigations are presented. Tables 2, Figs 5, Refs 8.

  12. LEOrbit: A program to calculate parameters relevant to modeling Low Earth Orbit spacecraft-plasma interaction

    NASA Astrophysics Data System (ADS)

    Marchand, R.; Purschke, D.; Samson, J.

    2013-03-01

    Understanding the physics of interaction between satellites and the space environment is essential in planning and exploiting space missions. Several computer models have been developed over the years to study this interaction. In all cases, simulations are carried out in the reference frame of the spacecraft and effects such as charging, the formation of electrostatic sheaths and wakes are calculated for given conditions of the space environment. In this paper we present a program used to compute magnetic fields and a number of space plasma and space environment parameters relevant to Low Earth Orbits (LEO) spacecraft-plasma interaction modeling. Magnetic fields are obtained from the International Geophysical Reference Field (IGRF) and plasma parameters are obtained from the International Reference Ionosphere (IRI) model. All parameters are computed in the spacecraft frame of reference as a function of its six Keplerian elements. They are presented in a format that can be used directly in most spacecraft-plasma interaction models. Catalogue identifier: AENY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENY_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 270308 No. of bytes in distributed program, including test data, etc.: 2323222 Distribution format: tar.gz Programming language: FORTRAN 90. Computer: Non specific. Operating system: Non specific. RAM: 7.1 MB Classification: 19, 4.14. External routines: IRI, IGRF (included in the package). Nature of problem: Compute magnetic field components, direction of the sun, sun visibility factor and approximate plasma parameters in the reference frame of a Low Earth Orbit satellite. Solution method: Orbit integration, calls to IGRF and IRI libraries and transformation of coordinates from geocentric to spacecraft

  13. 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.

  14. Adsorption interaction parameter of polyethers in ternary mobile phases: the critical adsorption line.

    PubMed

    Nguyen, V Cuong; Trathnigg, Bernd

    2010-04-01

    It is shown that in LC of polymers, the interaction parameter in ternary mobile phases can be described by a plane, which is determined by the dependencies in binary mobile phases. Instead of a critical adsorption point, critical conditions are observed along a straight line of composition between the two critical points in binary mobile phases. Consequently, a separation of block copolymers under critical conditions for one block by an adsorption mechanism for the other block can be achieved in ternary mobile phases of different compositions, which allows an adjustment of the retention of the adsorbing block. PMID:20222074

  15. 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.

  16. 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

  17. 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

  18. Running of oscillation parameters in matter with flavor-diagonal non-standard interactions of the neutrino

    NASA Astrophysics Data System (ADS)

    Agarwalla, Sanjib Kumar; Kao, Yee; Saha, Debashis; Takeuchi, Tatsu

    2015-11-01

    In this article we unravel the role of matter effect in neutrino oscillation in the presence of lepton-flavor-conserving, non-universal non-standard interactions (NSI's) of the neutrino. Employing the Jacobi method, we derive approximate analytical expressions for the effective mass-squared differences and mixing angles in matter. It is shown that, within the effective mixing matrix, the Standard Model (SM) W -exchange interaction only affects θ 12 and θ 13, while the flavor-diagonal NSI's only affect θ 23. The CP-violating phase δ remains unaffected. Using our simple and compact analytical approximation, we study the impact of the flavor-diagonal NSI's on the neutrino oscillation probabilities for various appearance and disappearance channels. At higher energies and longer baselines, it is found that the impact of the NSI's can be significant in the ν μ → ν μ channel, which can probed in future atmospheric neutrino experiments, if the NSI's are of the order of their current upper bounds. Our analysis also enables us to explore the possible degeneracy between the octant of θ 23 and the sign of the NSI parameter for a given choice of mass hierarchy in a simple manner.

  19. 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

  20. 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.

  1. Deriving Heterospecific Self-Assembling Protein–Protein Interactions Using a Computational Interactome Screen

    PubMed Central

    Crooks, Richard O.; Baxter, Daniel; Panek, Anna S.; Lubben, Anneke T.; Mason, Jody M.

    2016-01-01

    Interactions between naturally occurring proteins are highly specific, with protein-network imbalances associated with numerous diseases. For designed protein–protein interactions (PPIs), required specificity can be notoriously difficult to engineer. To accelerate this process, we have derived peptides that form heterospecific PPIs when combined. This is achieved using software that generates large virtual libraries of peptide sequences and searches within the resulting interactome for preferentially interacting peptides. To demonstrate feasibility, we have (i) generated 1536 peptide sequences based on the parallel dimeric coiled-coil motif and varied residues known to be important for stability and specificity, (ii) screened the 1,180,416 member interactome for predicted Tm values and (iii) used predicted Tm cutoff points to isolate eight peptides that form four heterospecific PPIs when combined. This required that all 32 hypothetical off-target interactions within the eight-peptide interactome be disfavoured and that the four desired interactions pair correctly. Lastly, we have verified the approach by characterising all 36 pairs within the interactome. In analysing the output, we hypothesised that several sequences are capable of adopting antiparallel orientations. We subsequently improved the software by removing sequences where doing so led to fully complementary electrostatic pairings. Our approach can be used to derive increasingly large and therefore complex sets of heterospecific PPIs with a wide range of potential downstream applications from disease modulation to the design of biomaterials and peptides in synthetic biology. PMID:26655848

  2. 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

  3. 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

  4. Deriving Heterospecific Self-Assembling Protein-Protein Interactions Using a Computational Interactome Screen.

    PubMed

    Crooks, Richard O; Baxter, Daniel; Panek, Anna S; Lubben, Anneke T; Mason, Jody M

    2016-01-29

    Interactions between naturally occurring proteins are highly specific, with protein-network imbalances associated with numerous diseases. For designed protein-protein interactions (PPIs), required specificity can be notoriously difficult to engineer. To accelerate this process, we have derived peptides that form heterospecific PPIs when combined. This is achieved using software that generates large virtual libraries of peptide sequences and searches within the resulting interactome for preferentially interacting peptides. To demonstrate feasibility, we have (i) generated 1536 peptide sequences based on the parallel dimeric coiled-coil motif and varied residues known to be important for stability and specificity, (ii) screened the 1,180,416 member interactome for predicted Tm values and (iii) used predicted Tm cutoff points to isolate eight peptides that form four heterospecific PPIs when combined. This required that all 32 hypothetical off-target interactions within the eight-peptide interactome be disfavoured and that the four desired interactions pair correctly. Lastly, we have verified the approach by characterising all 36 pairs within the interactome. In analysing the output, we hypothesised that several sequences are capable of adopting antiparallel orientations. We subsequently improved the software by removing sequences where doing so led to fully complementary electrostatic pairings. Our approach can be used to derive increasingly large and therefore complex sets of heterospecific PPIs with a wide range of potential downstream applications from disease modulation to the design of biomaterials and peptides in synthetic biology. PMID:26655848

  5. 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

  6. 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

  7. 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.

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

    PubMed

    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. PMID:25681892

  9. 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

  10. Nonstandard interaction effects on neutrino parameters at medium-baseline reactor antineutrino experiments

    NASA Astrophysics Data System (ADS)

    Ohlsson, Tommy; Zhang, He; Zhou, Shun

    2014-01-01

    Precision measurements of leptonic mixing parameters and the determination of the neutrino mass hierarchy are the primary goals of the forthcoming medium-baseline reactor antineutrino experiments, such as JUNO and RENO-50. In this work, we investigate the impact of nonstandard neutrino interactions (NSIs) on the measurements of {sin2 θ12,Δm212} and {sin2 θ13,Δm312}, and on the sensitivity to the neutrino mass hierarchy, at the medium-baseline reactor experiments by assuming a typical experimental setup. It turns out that the true mixing parameter sin2 θ12 can be excluded at a more than 3σ level if the NSI parameter ɛ or ɛ is as large as 2% in the most optimistic case. However, the discovery reach of NSI effects has been found to be small, and depends crucially on the CP-violating phases. Finally, we show that NSI effects could enhance or reduce the discrimination power of the JUNO and RENO-50 experiments between the normal and inverted neutrino mass hierarchies.

  11. Comprehensive Reference Ranges for Hematology and Clinical Chemistry Laboratory Parameters Derived from Normal Nigerian Adults

    PubMed Central

    Miri-Dashe, Timzing; Osawe, Sophia; Tokdung, Monday; Daniel, Nenbammun; Choji, Rahila Pam; Mamman, Ille; Deme, Kurt; Damulak, Dapus; Abimiku, Alash’le

    2014-01-01

    Background Interpretation of laboratory test results with appropriate diagnostic accuracy requires reference or cutoff values. This study is a comprehensive determination of reference values for hematology and clinical chemistry in apparently healthy voluntary non-remunerated blood donors and pregnant women. Methods and findings Consented clients were clinically screened and counseled before testing for HIV, Hepatitis B, Hepatitis C and Syphilis. Standard national blood donors’ questionnaire was administered to consented blood donors. Blood from qualified volunteers was used for measurement of complete hematology and chemistry parameters. Blood samples were analyzed from a total of 383 participants, 124 (32.4%) males, 125 (32.6%) non-pregnant females and 134 pregnant females (35.2%) with a mean age of 31 years. Our results showed that the red blood cells count (RBC), Hemoglobin (HB) and Hematocrit (HCT) had significant gender difference (p = 0.000) but not for total white blood count (p>0.05) which was only significantly higher in pregnant verses non-pregnant women (p = 0.000). Hemoglobin and Hematocrit values were lower in pregnancy (P = 0.000). Platelets were significantly higher in females than men (p = 0.001) but lower in pregnant women (p = 0.001) with marked difference in gestational period. For clinical chemistry parameters, there was no significant difference for sodium, potassium and chloride (p>0.05) but gender difference exists for Bicarbonate (HCO3), Urea nitrogen, Creatinine as well as the lipids (p<0.05). Total bilirubin was significantly higher in males than females (p = 0.000). Significant differences exist for all chemistry parameters between pregnant and non-pregnant women in this study (p<0.05), except Amylase and total cholesterol (p>0.05). Conclusions Hematological and Clinical Chemistry reference ranges established in this study showed significant gender differences. Pregnant women also differed from non

  12. 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

  13. Development of the smooth orthogonal decomposition method to derive the modal parameters of vehicle suspension system

    NASA Astrophysics Data System (ADS)

    Rezaee, Mousa; Shaterian-Alghalandis, Vahid; Banan-Nojavani, Ali

    2013-04-01

    In this paper, the smooth orthogonal decomposition (SOD) method is developed to the light damped systems in which the inputs are time shifted functions of one or more random processes. An example of such practical cases is the vehicle suspension system in which the random inputs due to the road roughness applied to the rear wheels are the shifted functions of the same random inputs on the front wheels with a time lag depending on the vehicle wheelbase as well as its velocity. The developed SOD method is applied to determine the natural frequencies and mode shapes of a certain vehicle suspension system and the results are compared with the true values obtained by the structural eigenvalue problem. The consistency of the results indicates that the SOD method can be applied with a high degree of accuracy to calculate the modal parameters of vibrating systems in which the system inputs are shifted functions of one or more random processes.

  14. 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.

  15. 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

    2005-01-01

    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 1K, and layer precipitable water with an rms error of 20%, in cases with up to 80% effective cloud cover. The basic theory used to analyze 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. HSB failed in February 2005, 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 in April 2005 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.

  16. 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.

  17. Assessing sounding-derived parameters as storm predictors in different latitudes

    NASA Astrophysics Data System (ADS)

    Sánchez, José Luis; Marcos, José Luis; Dessens, Jean; López, Laura; Bustos, Carlos; García-Ortega, Eduardo

    Many thermodynamic parameters and indices are currently being used as thunderstorm predictors because of their high correlations with the beginning and development of convection. Many of these indices have been developed for one specific area and their forecasting accuracy has generally been assessed in that zone and not in others. It is a highly intriguing question whether there are parameters or indices that may function adequately as thunderstorm predictors, as far as the Probability of Detection is concerned, irrespective of the latitude of the study zone. In order to approach this issue the present study focuses on data from 1692 sounding days in León (Spain), Zaragoza (Spain), Bordeaux (France) and Mendoza (Argentina). Specific discriminant models have already been developed for these areas. When comparing the results found by the different models constructed for each of the four study zones it may be noticed that there are no indices that function extremely well in all of the zones. Rather, a common ingredient pattern is observed for the beginning of convection): atmospheric instability and moist layers in the low atmosphere. It may also be concluded that sounding data alone are not enough to detect accurately the triggering mechanism, which is the third ingredient necessary for convection. The aim of this paper is to build a logistic equation integrating the four study zones. The stepwise method was employed with this purpose because it allows for the gradual inclusion of variables in the final equation according to their discriminating power. The results obtained suggest that Showalter Index and 850 hPa Dew Point Temperature are the variables that best characterize preconvective conditions irrespective of the geographic area considered. The values for POD (Probability of Detection) and FAR (False Alarm Ratio) are acceptable, but they are clearly lower than the ones obtained by each of the models in the study zone for which they were developed.

  18. 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.

  19. An Updated Natural History Model of Cervical Cancer: Derivation of Model Parameters

    PubMed Central

    Campos, Nicole G.; Burger, Emily A.; Sy, Stephen; Sharma, Monisha; Schiffman, Mark; Rodriguez, Ana Cecilia; Hildesheim, Allan; Herrero, Rolando; Kim, Jane J.

    2014-01-01

    Mathematical models of cervical cancer have been widely used to evaluate the comparative effectiveness and cost-effectiveness of preventive strategies. Major advances in the understanding of cervical carcinogenesis motivate the creation of a new disease paradigm in such models. To keep pace with the most recent evidence, we updated a previously developed microsimulation model of human papillomavirus (HPV) infection and cervical cancer to reflect 1) a shift towards health states based on HPV rather than poorly reproducible histological diagnoses and 2) HPV clearance and progression to precancer as a function of infection duration and genotype, as derived from the control arm of the Costa Rica Vaccine Trial (2004–2010). The model was calibrated leveraging empirical data from the New Mexico Surveillance, Epidemiology, and End Results Registry (1980–1999) and a state-of-the-art cervical cancer screening registry in New Mexico (2007–2009). The calibrated model had good correspondence with data on genotype- and age-specific HPV prevalence, genotype frequency in precancer and cancer, and age-specific cancer incidence. We present this model in response to a call for new natural history models of cervical cancer intended for decision analysis and economic evaluation at a time when global cervical cancer prevention policy continues to evolve and evidence of the long-term health effects of cervical interventions remains critical. PMID:25081182

  20. An updated natural history model of cervical cancer: derivation of model parameters.

    PubMed

    Campos, Nicole G; Burger, Emily A; Sy, Stephen; Sharma, Monisha; Schiffman, Mark; Rodriguez, Ana Cecilia; Hildesheim, Allan; Herrero, Rolando; Kim, Jane J

    2014-09-01

    Mathematical models of cervical cancer have been widely used to evaluate the comparative effectiveness and cost-effectiveness of preventive strategies. Major advances in the understanding of cervical carcinogenesis motivate the creation of a new disease paradigm in such models. To keep pace with the most recent evidence, we updated a previously developed microsimulation model of human papillomavirus (HPV) infection and cervical cancer to reflect 1) a shift towards health states based on HPV rather than poorly reproducible histological diagnoses and 2) HPV clearance and progression to precancer as a function of infection duration and genotype, as derived from the control arm of the Costa Rica Vaccine Trial (2004-2010). The model was calibrated leveraging empirical data from the New Mexico Surveillance, Epidemiology, and End Results Registry (1980-1999) and a state-of-the-art cervical cancer screening registry in New Mexico (2007-2009). The calibrated model had good correspondence with data on genotype- and age-specific HPV prevalence, genotype frequency in precancer and cancer, and age-specific cancer incidence. We present this model in response to a call for new natural history models of cervical cancer intended for decision analysis and economic evaluation at a time when global cervical cancer prevention policy continues to evolve and evidence of the long-term health effects of cervical interventions remains critical. PMID:25081182

  1. 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.

  2. Predictive value of various Doppler-derived parameters of atrial conduction time for successful atrial fibrillation ablation

    PubMed Central

    Valtuille, Lucas; Choy, Jonathan B; Becher, Harald

    2015-01-01

    Various Doppler-derived parameters of left atrial electrical remodeling have been demonstrated to predict recurrence of atrial fibrillation (AF) after AF ablation. The aim of this study was to compare three Doppler-derived measures of atrial conduction time in patients undergoing AF ablation, and to investigate their predictive value for successful procedure. In 32 prospectively enrolled patients undergoing the first AF ablation, atrial conduction time was estimated by measuring the time delay between the onset of P-wave on the surface ECG to the peak of the a′-wave on the pulsed-wave Doppler and color-coded tissue Doppler imaging of the left atrial lateral wall, and to the peak of the A-wave on the pulsed-wave Doppler of the mitral inflow. There was a significant difference in the baseline atrial conduction time measured by different echocardiographic techniques. Most (88%) patients had normal or only mildly dilated left atrium. At 6 months, 12 patients (38%) had recurrent AF/atrial tachycardia. The duration of history of AF was the only predictor of AF/atrial tachycardia recurrence following the first AF ablation (P=0.024; OR 1.023, CI 1.003–1.044). A combination of normal left atrial volume and history of paroxysmal AF of ≤48 months was associated with the best outcome. Predictive value of the Doppler derived parameters of atrial conduction time may be reduced in the early stages of left atrial remodeling. Future studies may determine which echocardiographic parameter correlates best with the extent of left atrial remodeling and is most predictive of successful AF ablation. PMID:26795694

  3. Urban Heat Island Modeling in Conjunction with Satellite-Derived Surface/Soil Parameters.

    NASA Astrophysics Data System (ADS)

    Hafner, Jan; Kidder, Stanley Q.

    1999-04-01

    Although it has been studied for over 160 years, the urban heat island (UHI) effect is still not completely understood, yet it is increasingly important. The main purpose of this work is to improve UHI modeling by using AVHRR (Advanced Very High Resolution Radiometer) satellite data to retrieve the surface parameters (albedo, as well as soil thermal and moisture properties). In this study, a hydrostatic three-dimensional mesoscale model was used to perform the numerical modeling. The Carlson technique was applied to retrieve the thermal inertia and moisture availability using the thermal AVHRR channels 4 and 5. The net urban effect was determined as the difference between urban and nonurban simulations, in which urban parameters were replaced by rural parameters.Two winter days were each used for two numerical simulations: a control and an urban-to-rural replacement run. Moisture availability values on the less windy day showed generally a south to north gradient downwind of the city and urban values less than rural values (the urban dry island day). Moisture availability was higher on the windy day, with uniform values in the rural and urban areas (uniform soil moisture day). The only exceptions were variations in the rural hills north of the city and the low rural values under the polluted urban plume downwind of the city.While thermal inertia values showed no urban-rural differences on the uniform soil moisture day, they exhibited larger values over Atlanta than in surrounding rural area on the (less moist) dry island day. Two puzzling facts exist in the data: 1) lack of a north-south thermal inertia gradient on the dry soil day to correspond to its above-mentioned moisture availability gradient and 2) rural thermal inertia values do not change between both days in spite of their large difference in soil moisture. The observed lack of corresponding urban change is expected, as its thermal inertia values depend more on urban building materials than on moisture of

  4. 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).

  5. Large-scale erosion processes and parameters derived from a modeling of the Messinian salinity crisis

    NASA Astrophysics Data System (ADS)

    Loget, N.; Davy, P.; van den Driessche, J.

    2003-04-01

    The closing of the Gibraltar strait during Messinian have produced a drop of the sea level of about 1500 m in less than half a million year. This certainly constitutes one of the largest perturbation of erosion systems in the Earth, whose analysis in terms of form and dynamics should bring invaluable constraints on erosion processes and parameters. In addition to a precise chronology of the bulk crisis, the main data consists of the reconstruction of paleocanyons, that were eroded during sea drop and refilled during sea rise. The Rhone's canyon is certainly the most documented, with numerous seismic lines and boreholes. We have now a reasonable estimation of the canyon profile from its outlet to the Bresse graben, more 500 km upslope. Sparse data are also available in the Languedoc region, in the Pyrenees, for some drainage basins of the Var-Ligure coast, in the gulf of Valence. A particularity of this erosion phase was to propagate very far inland along the main rivers, but in a very localized way in the sense that hillslopes or upslope drainage basins were barely affected. All these data were compiled in a database that we used to constrain erosion processes. We assume that the erosion law belongs to the classical power-law framework, where the erosion flux depends on local slope s, and water flow q, such as: e=k qmsn-ec, where k and ec are two constants which depend on material strength properties, and m and n are two exponents which are found to play an important role in the time-length scaling. The transfer model must be completed by a transfer or deposition terms that we assume to be controlled by a deposition length Ld. If Ld is very small, the model comes to the transport-limited case where the height variation is proportional to the gradient of the erosion flux e. In contrast if Ld is very large, rivers can carry all the eroded sediment out; the process is usually called detachment-limited. We simulate the erosion dynamics, induced by the Messinian sea

  6. 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

  7. 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

  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. 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.

  10. 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.

  11. 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.

  12. Ab initio DFT study of bisphosphonate derivatives as a drug for inhibition of cancer: NMR and NQR parameters.

    PubMed

    Aghabozorg, Hussein; Sohrabi, Beheshteh; Mashkouri, Sara; Aghabozorg, Hamid Reza

    2012-03-01

    DFT computations were carried out to characterize the (17)Oand (2)H electric field gradient, EFG, in various bisphosphonate derivatives. The computations were performed at the B3LYP level with 6-311++G (d,P) standard basis set. Calculated EFG tensors were used to determine the (17)O and (2)H nuclear quadrupole coupling constant, χ and asymmetry parameter, η. For better understanding of the bonding and electronic structure of bisphosphonates, isotropic and anisotropic NMR chemical shieldings were calculated for the (13)C, (17)O and (31)P nuclei using GIAO method for the optimized structure of intermediate bisphosphonates at B3LYP level of theory using 6-311++G (d, p) basis set. The results showed that various substituents have a strong effect on the nuclear quadrupole resonance (NQR) parameters (χ, η) of (17)O in contrast with (2)H NQR parameters. The NMR and NQR parameters were studied in order to find the correlation between electronic structure and the activity of the desired bisphosphonates. In addition, the effect of substitutions on the bisphosphonates polarity was investigated. Molecular polarity was determined via the DFT calculated dipole moment vectors and the results showed that substitution of bromine atom on the ring would increase the activity of bisphosphonates. PMID:21633790

  13. 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. PMID:26990788

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. Concentration dependence of the Flory-Huggins interaction parameter in aqueous solutions of capped PEO chains

    NASA Astrophysics Data System (ADS)

    Chaudhari, M. I.; Pratt, L. R.; Paulaitis, M. E.

    2014-12-01

    The dependence on volume fraction φ of the Flory-Huggins interaction parameter χ wp (φ) describing the free energy of mixing of polymers in water is obtained by exploiting the connection of χ wp (φ) to the chemical potential of the water, for which quasi-chemical theory is satisfactory. We test this theoretical approach with simulation data for aqueous solutions of capped PEO (polyethylene oxide) oligomers. For CH3(CH2-O-CH2)mCH3 (m = 11), χ wp (φ) depends strongly on φ, consistent with experiment. These results identify coexisting water-rich and water-poor solutions at T = 300 K and p = 1 atm. Direct observation of the coexistence of these two solutions on simulation time scales supports that prediction for the system studied. This approach directly provides the osmotic pressures. The osmotic second virial coefficient for these chains is positive, reflecting repulsive interactions between the chains in the water, a good solvent for these chains.

  1. Concentration dependence of the Flory-Huggins interaction parameter in aqueous solutions of capped PEO chains.

    PubMed

    Chaudhari, M I; Pratt, L R; Paulaitis, M E

    2014-12-28

    The dependence on volume fraction φ of the Flory-Huggins interaction parameter χwp(φ) describing the free energy of mixing of polymers in water is obtained by exploiting the connection of χwp(φ) to the chemical potential of the water, for which quasi-chemical theory is satisfactory. We test this theoretical approach with simulation data for aqueous solutions of capped PEO (polyethylene oxide) oligomers. For CH3(CH2-O-CH2)mCH3 (m = 11), χwp(φ) depends strongly on φ, consistent with experiment. These results identify coexisting water-rich and water-poor solutions at T = 300 K and p = 1 atm. Direct observation of the coexistence of these two solutions on simulation time scales supports that prediction for the system studied. This approach directly provides the osmotic pressures. The osmotic second virial coefficient for these chains is positive, reflecting repulsive interactions between the chains in the water, a good solvent for these chains. PMID:25554181

  2. 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

  3. ESTIMATES OF GENETIC PARAMETERS AND AN EVALUATION OF GENOTYPE X ENVIRONMENT INTERACTION FOR WEANING WEIGHT IN NELLORE CATTLE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Records of 105,645 Nellore calves born from 1977 to 1994 in eight different regions of Brazil were used to estimate genetic parameters for weaning weight (kg). The objective of this study was to estimate genetic and environmental parameters and evaluate genotype x environment interaction for weaning...

  4. The effects of isoflurane anaesthesia on some Doppler-derived cardiac parameters in the common buzzard (Buteo buteo).

    PubMed

    Straub, Jens; Forbes, Neil A; Thielebein, Jens; Pees, Michael; Krautwald-Junghanns, Maria E

    2003-11-01

    In order to gain an initial overview of the influence of anaesthesia on the results of Doppler-derived blood flow measurements in raptors, the heart rate as well as three different sample volumes of pulsed-wave spectral Doppler-derived flow velocity (diastolic flow across the left and right atrioventricular valve, systolic flow across the aortic valve) were determined in 10 common buzzards (Buteo buteo). Measurements were taken once in conscious and once in anaesthetized birds. Anaesthesia was shown to produce significant changes in cardiac parameters recorded in the same birds whilst conscious. When comparing conscious birds with each other (with one exception for right sided ventricular inflow velocity) no correlation between the heart frequency and measured blood flow velocities was evident. This was also the case under anaesthesia. However, significant differences in these parameters were evident when comparing the results obtained before and under anaesthesia. The results suggest that the influence of anaesthesia in raptors is more than a simple reduction of heart rate and that there is also reduction in blood flow velocity. PMID:14550740

  5. Comparison of radiation and cloud parameters derived from satellite and aircraft measurements during FIRE 2 cirrus IFO

    NASA Technical Reports Server (NTRS)

    Heck, Patrick W.; Mayor, Shalini; Young, David F.; Minnis, Patrick; Takano, Yoshihide; Liou, Kuo-Nan; Spinhirne, James D.

    1993-01-01

    Meteorological satellite instrument pixel sizes are often much greater than the individual cloud elements in a given scene. Partially cloud-filled pixels can be misinterpreted in many analysis schemes because the techniques usually assume that all of the cloudy pixels are cloud filled. Coincident Landsat and Geostationary Operational Environmental Satellite (GOES) data and degraded-resolution Landsat data were used to study the effects of both sensor resolution and analysis techniques on satellite-derived cloud parameters. While extremely valuable for advancing the understanding of these effects, these previous studies were relatively limited in the number of cloud conditions that were observed and by the limited viewing and illumination conditions. During the First ISCCP Regional Experiment (FIRE) Phase 2 (13 Nov. - 7 Dec. 1991), the NASA ER-2 made several flights over a wide range of cloud fields and backgrounds with several high resolution sensors useful for a variety of purposes including serving as ground truth for satellite-based cloud retrievals. This paper takes a first look at utilizing the ER-2 for validating cloud parameters derived from GOES and NOAA-11 Advanced Very High Resolution Radiometer (AVHRR) data.

  6. 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

  7. 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.

  8. Characterization of Lesion Formation and Bubble Activities during High Intensity Focused Ultrasound Ablation using Temperature-Derived Parameters

    PubMed Central

    Hsiao, Yi-Sing; Kumon, Ronald E.; Deng, Cheri X.

    2013-01-01

    Successful high-intensity focused ultrasound (HIFU) thermal tissue ablation relies on accurate information of the tissue temperature and tissue status. Often temperature measurements are used to predict and monitor the ablation process. In this study, we conducted HIFU ablation experiments with ex vivo porcine myocardium tissue specimens to identify changes in temperature associated with tissue coagulation and bubble/cavity formation. Using infrared (IR) thermography and synchronized bright-field imaging with HIFU applied near the tissue surface, parameters derived from the spatiotemporal evolution of temperature were correlated with HIFU-induced lesion formation and overheating, of which the latter typically results in cavity generation and/or tissue dehydration. Emissivity of porcine myocardium was first measured to be 0.857 ± 0.006 (n = 3). HIFU outcomes were classified into non-ablative, normal lesion, and overheated lesion. A marked increase in the rate of temperature change during HIFU application was observed with lesion formation. A criterion using the maximum normalized second time derivative of temperature change provided 99.1% accuracy for lesion identification with a 0.05 s−1 threshold. Asymmetric temperature distribution on the tissue surface was observed to correlate with overheating and/or bubble generation. A criterion using the maximum displacement of the spatial location of the peak temperature provided 90.9% accuracy to identify overheated lesion with a 0.16 mm threshold. Spatiotemporal evolution of temperature obtained using IR imaging allowed determination of the cumulative equivalent minutes at 43 °C (CEM43) for lesion formation to be 170 min. Similar temperature characteristics indicative of lesion formation and overheating were identified for subsurface HIFU ablation. These results suggest that parameters derived from temperature changes during HIFU application are associated with irreversible changes in tissue and may provide useful

  9. Characterization of Lesion Formation and Bubble Activities during High Intensity Focused Ultrasound Ablation using Temperature-Derived Parameters.

    PubMed

    Hsiao, Yi-Sing; Kumon, Ronald E; Deng, Cheri X

    2013-09-01

    Successful high-intensity focused ultrasound (HIFU) thermal tissue ablation relies on accurate information of the tissue temperature and tissue status. Often temperature measurements are used to predict and monitor the ablation process. In this study, we conducted HIFU ablation experiments with ex vivo porcine myocardium tissue specimens to identify changes in temperature associated with tissue coagulation and bubble/cavity formation. Using infrared (IR) thermography and synchronized bright-field imaging with HIFU applied near the tissue surface, parameters derived from the spatiotemporal evolution of temperature were correlated with HIFU-induced lesion formation and overheating, of which the latter typically results in cavity generation and/or tissue dehydration. Emissivity of porcine myocardium was first measured to be 0.857 ± 0.006 (n = 3). HIFU outcomes were classified into non-ablative, normal lesion, and overheated lesion. A marked increase in the rate of temperature change during HIFU application was observed with lesion formation. A criterion using the maximum normalized second time derivative of temperature change provided 99.1% accuracy for lesion identification with a 0.05 s(-1) threshold. Asymmetric temperature distribution on the tissue surface was observed to correlate with overheating and/or bubble generation. A criterion using the maximum displacement of the spatial location of the peak temperature provided 90.9% accuracy to identify overheated lesion with a 0.16 mm threshold. Spatiotemporal evolution of temperature obtained using IR imaging allowed determination of the cumulative equivalent minutes at 43 °C (CEM 43) for lesion formation to be 170 min. Similar temperature characteristics indicative of lesion formation and overheating were identified for subsurface HIFU ablation. These results suggest that parameters derived from temperature changes during HIFU application are associated with irreversible changes in tissue and may provide useful

  10. Characterization of lesion formation and bubble activities during high-intensity focused ultrasound ablation using temperature-derived parameters

    NASA Astrophysics Data System (ADS)

    Hsiao, Yi-Sing; Kumon, Ronald E.; Deng, Cheri X.

    2013-09-01

    Successful high-intensity focused ultrasound (HIFU) thermal tissue ablation relies on accurate information of the tissue temperature and tissue status. Often temperature measurements are used to predict and monitor the ablation process. In this study, we conducted HIFU ablation experiments with ex vivo porcine myocardium tissue specimens to identify changes in temperature associated with tissue coagulation and bubble/cavity formation. Using infrared (IR) thermography and synchronized bright-field imaging with HIFU applied near the tissue surface, parameters derived from the spatiotemporal evolution of temperature were correlated with HIFU-induced lesion formation and overheating, of which the latter typically results in cavity generation and/or tissue dehydration. Emissivity of porcine myocardium was first measured to be 0.857 ± 0.006 (n = 3). HIFU outcomes were classified into non-ablative, normal lesion, and overheated lesion. A marked increase in the rate of temperature change during HIFU application was observed with lesion formation. A criterion using the maximum normalized second time derivative of temperature change provided 99.1% accuracy for lesion identification with a 0.05 s-1 threshold. Asymmetric temperature distribution on the tissue surface was observed to correlate with overheating and/or bubble generation. A criterion using the maximum displacement of the spatial location of the peak temperature provided 90.9% accuracy to identify overheated lesion with a 0.16 mm threshold. Spatiotemporal evolution of temperature obtained using IR imaging allowed determination of the critical cumulative equivalent minutes at 43 °C (CEM43) for lesion formation to be 170 min. Similar temperature characteristics indicative of lesion formation and overheating were identified for subsurface HIFU ablation. These results suggest that parameters derived from temperature changes during HIFU application are associated with irreversible changes in tissue and may provide

  11. 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

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

    PubMed

    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

  13. New Amphiphilic Neamine Derivatives Active against Resistant Pseudomonas aeruginosa and Their Interactions with Lipopolysaccharides

    PubMed Central

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

    2014-01-01

    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. PMID:24867965

  14. Evaluation of morphometric parameters of drainage networks derived from topographic maps and DEM in point of floods

    NASA Astrophysics Data System (ADS)

    Ozdemir, Hasan; Bird, Deanne

    2009-02-01

    An evaluation of morphometric parameters of two drainage networks derived from different sources was done to determine the influence of sub-basins to flooding on the main channel in the Havran River basin (Balıkesir-Turkey). Drainage networks for the sub-basins were derived from both topographic maps scaled 1:25.000 and a 10-m resolution digital elevation model (DEM) using geographic information systems (GIS). Blue lines, representing fluvial channels on the topographic maps were accepted as a drainage network, which does not depict all exterior links in the basin. The second drainage network was extracted from the DEM using minimum accumulation area threshold to include all exterior links. Morphometric parameters were applied to the two types of drainage networks at sub-basin levels. These parameters were used to assess the influence of the sub-basins on the main channel with respect to flooding. The results show that the drainage network of sub-basin 4—where a dam was constructed on its outlet to mitigate potential floods—has a lower influence morphometrically to produce probable floods on the main channel than that of sub-basins 1, 3, and 5. The construction of the dam will help reduce flooding on the main channel from sub-basin 4 but it will not prevent potential flooding from sub-basin 1, 3 and 5, which join the main channel downstream of sub-basin 4. Therefore, flood mitigation efforts should be considered in order to protect the settlement and agricultural lands on the floodplain downstream of the dam. In order to increase our understanding of flood hazards, and to determine appropriate mitigation solutions, drainage morphometry research should be included as an essential component to hydrologic studies.

  15. SCS macrophages suppress melanoma by restricting tumor-derived vesicle-B cell interactions.

    PubMed

    Pucci, Ferdinando; Garris, Christopher; Lai, Charles P; Newton, Andita; Pfirschke, Christina; Engblom, Camilla; Alvarez, David; Sprachman, Melissa; Evavold, Charles; Magnuson, Angela; von Andrian, Ulrich H; Glatz, Katharina; Breakefield, Xandra O; Mempel, Thorsten R; Weissleder, Ralph; Pittet, Mikael J

    2016-04-01

    Tumor-derived extracellular vesicles (tEVs) are important signals in tumor-host cell communication, yet it remains unclear how endogenously produced tEVs affect the host in different areas of the body. We combined imaging and genetic analysis to track melanoma-derived vesicles at organismal, cellular, and molecular scales to show that endogenous tEVs efficiently disseminate via lymphatics and preferentially bind subcapsular sinus (SCS) CD169(+) macrophages in tumor-draining lymph nodes (tdLNs) in mice and humans. The CD169(+) macrophage layer physically blocks tEV dissemination but is undermined during tumor progression and by therapeutic agents. A disrupted SCS macrophage barrier enables tEVs to enter the lymph node cortex, interact with B cells, and foster tumor-promoting humoral immunity. Thus, CD169(+) macrophages may act as tumor suppressors by containing tEV spread and ensuing cancer-enhancing immunity. PMID:26989197

  16. Protein interaction hotspot identification using sequence-based frequency-derived features.

    PubMed

    Nguyen, Quang-Thang; Fablet, Ronan; Pastor, Dominique

    2013-11-01

    Finding good descriptors, capable of discriminating hotspot residues from others, is still a challenge in many attempts to understand protein interaction. In this paper, descriptors issued from the analysis of amino acid sequences using digital signal processing (DSP) techniques are shown to be as good as those derived from protein tertiary structure and/or information on the complex. The simulation results show that our descriptors can be used separately to predict hotspots, via a random forest classifier, with an accuracy of 79% and a precision of 75%. They can also be used jointly with features derived from tertiary structures to boost the performance up to an accuracy of 82% and a precision of 80%. PMID:21742567

  17. Interactions of Lysozyme and Azobenzene Derivatives in the Solution and on a Surface

    NASA Astrophysics Data System (ADS)

    Wei, Tao; Shing, Katherine

    2015-03-01

    The reversible isomerization of the azobenzene and its derivatives can control protein structure in an aqueous environment with the alternation of visible and UV lights for very promising applications in drug delivery. However, an atomistic description of Azo-molecules and protein amino acid residues is still lacking. In this study we performed atomistic molecular dynamics simulation to study the interactions between a lysozyme molecule and the Azobenzene derivative (in the bulk solution and grafted on the Silica surfaces). Protein structural arrangements (i.e., the shape and secondary structures) and its mobility, as a function of tran/cis ratio in the bulk solution and on the self-assembling monolayer surface's density and morphology, are systematically investigated.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. Structure-activity relationship of selected polyphenol derivatives as inhibitors of Bax/Bcl-xL interaction.

    PubMed

    Vo, Duc Duy; Gautier, Fabien; Juin, Philippe; Grée, René

    2012-05-01

    This paper describes the synthesis of nine selected diaryl/heteroaryl-containing phenol and polyphenol derivatives which have been evaluated against Bax/Bcl-xL interaction in comparison with ABT-737. Using a BRET assay, six of these derivatives exhibit activity comparable to ABT-737 to disrupt Bax/Bcl-xL interaction. These preliminary results demonstrate that such polyphenol-derived molecules are attractive compounds regarding anticancer activity and that the phenol at position 3 is important regarding disruption of Bax/Bcl-xL interaction. PMID:22425031

  3. Bayes cost of parameter estimation for a quantum system interacting with an environment

    NASA Astrophysics Data System (ADS)

    Ban, Masashi

    2016-05-01

    The Bayes cost of parameter estimation is studied for a quantum system which is influenced by an external environment, where the cost function is assumed to be a quadratic function of a difference between true and estimated values. When the reduced time evolution of a quantum system is determined by the time-dependent Lindblad equation, it is found how the Bayes cost changes with time. The Bayes cost increases monotonously with time for the Markovian environment, while it shows an oscillatory behavior for the non-Markovian environment due to the memory effect. Furthermore, in order to investigate how initial correlation between quantum system and environment, an analytic expression of the Bayes cost is derived for a qubit-oscillator system. It is found for both Markovian and non-Markovian environments that the Bayes cost can take a value smaller than the initial one in the presence of the initial correlation. The decrease in the Bayes cost is due to the backflow of information that is included in the initially correlated part.

  4. 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. PMID:27280946

  5. 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.

  6. 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

  7. Improving Rotor-Stator Interaction Noise Code Through Analysis of Input Parameters

    NASA Technical Reports Server (NTRS)

    Unton, Timothy J.

    2004-01-01

    There are two major sources of aircraft noise. The first is from the airframe and the second is from the engines. The focus of the acoustics branch at NASA Glenn is on the engine noise sources. There are two major sources of engine noise; fan noise and jet noise. Fan noise, produced by rotating machinery of the engine, consists of both tonal noise, which occurs at discrete frequencies, and broadband noise, which occurs across a wide range of frequencies. The focus of my assignment is on the broadband noise generated by the interaction of fan flow turbulence and the stator blades. such as the sweep and stagger angles and blade count, as well as the flow parameters such as intensity of turbulence in the flow. The tool I employed in this work is a computer program that predicts broadband noise from fans. The program assumes that the complex shape of the curved blade can be represented as a single flat plate, allowing it to use fairly simple equations that can be solved in a reasonable amount of time. While the results from such representation provided reasonable estimates of the broadband noise levels, they did not usually represent the entire spectrum accurately. My investigation found that the discrepancy between data and theory can be improved if the leading edge and the trailing edge of the blade are treated separately. Using this approach, I reduced the maximum error in noise level from a high of 30% to less than 5% for the cases investigated. Detailed results of this investigation will be discussed at my presentation. The objective of this study is to investigate the influence of geometric parameters

  8. [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

  9. 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.

  10. Interaction of tetraphenyl-porphyrin derivatives with DPPC-liposomes: an EPR study.

    PubMed

    Voszka, István; Szabó, Zsófia; Csík, Gabriella; Maillard, Philip; Gróf, Pál

    2005-05-13

    The effect of the symmetry and polarity of the porphyrin molecules on their membrane localization and interaction with membrane lipids were investigated by electron paramagnetic resonance (EPR). For this purpose, two glycoconjugated tetraphenyl porphyrin derivatives were selected, respectively, symmetrically and asymmetrically substituted. Small unilamellar liposomes composed of dipalmitoylphosphatidylcholine (DPPC) and spin labeled stearic acids were prepared. The spin probe was located at the 5th or 7th or 12th or 16th position of the hydrocarbon chain in order to monitor various regions of the lipid bilayer. EPR spectra of porphyrin-free and porphyrin-bound liposomes were recorded at various temperatures below and above the phase transition temperature of DPPC. The effect on membrane fluidity proved to be stronger with the asymmetrical porphyrin derivative than with the symmetrical one. The rigidity increased when the spin label was near lipid head groups. The difference observed between control and porphyrin-treated samples when measured below the main lipid transition temperature disappeared at higher temperature. When the spin label was near the end of the hydrophobic tails, the symmetrical porphyrin derivative caused increase in fluidity, while the asymmetrical one slightly decreased it. To explain this phenomenon we propose that the asymmetrical derivative exerts a stronger ordering effect caused by its fluorophenyl group located at the level of the lipid heads, which is attenuated to the hydrophobic tails. The perturbing effect of the symmetric derivative could not lead to similar extent of ordering at the head groups and looses the hydrocarbon chains deeper in the membrane. PMID:15878112

  11. Improving the quantity, quality and transparency of data used to derive radionuclide transfer parameters for animal products. 1. Goat milk.

    PubMed

    Howard, B J; Wells, C; Barnett, C L

    2016-04-01

    Under the MODARIA (Modelling and Data for Radiological Impact Assessments Programme of the International Atomic Energy Agency), there has been an initiative to improve the derivation, provenance and transparency of transfer parameter values for radionuclides. The approach taken for animal products is outlined here and the first revised table for goat milk is provided. Data from some references used in TRS 472 were removed and reasons given for removal. Particular efforts were made to improve the number of CR (concentration ratio) values which have some advantages over transfer coefficients. There is little difference in most of the new CR and Fm (transfer coefficient) values for goat milk compared with those in TRS 472. In TRS 472, 21 CR values were reported for goat milk. In the 2015 dataset for goat milk CR values for a further 14 elements are now included. The CR and Fm values for only one element (Co) were removed. PMID:26845198

  12. Lumpy - an interactive Lumped Parameter Modeling code based on MS Access and MS Excel.

    NASA Astrophysics Data System (ADS)

    Suckow, A.

    2012-04-01

    areas. For a user defined choice of up to five parameters (mean residence times and dispersion parameters of the two sub-LPM plus the mixing ratios of the two models) the best fit can be determined. Fits can be assessed using different methods for the Goodness Of Fit. Input and output data are send to MS Excel for interactive display of modeling result and comparison with measurements. Excel only serves as data display; computations are performed in AB throughout. Lumpy allows display of time series and any combination of tracer vs. tracer plot. In the latter, the possible output data space assessable by the input variables can be displayed, to check if any of the model combinations under consideration is able to explain the measured data. Comparison and fit to measurements is possible after each of the two sub-models and after mixing these two. The talk will demonstrate the usefulness of this approach with examples from the Croatian Karst (Babinka 2007), the Fischa tracer test (Stolp et al., 2010) and the 30 years monthly tritium time series of the Danube (Aggarwal et al., 2010).

  13. Solid Phase Synthesis and Application of Labeled Peptide Derivatives: Probes of Receptor-Opioid Peptide Interactions

    PubMed Central

    Aldrich, Jane V.; Kumar, Vivek; Dattachowdhury, Bhaswati; Peck, Angela M.; Wang, Xin; Murray, Thomas F.

    2009-01-01

    Solid phase synthetic methodology has been developed in our laboratory to incorporate an affinity label (a reactive functionality such as isothiocyanate or bromoacetamide) into peptides (Leelasvatanakij, L. and Aldrich, J. V. (2000) J. Peptide Res. 56, 80), and we have used this synthetic strategy to prepare affinity label derivatives of a variety of opioid peptides. To date side reactions have been detected only in two cases, both involving intramolecular cyclization. We have identified several peptide-based affinity labels for δ opioid receptors that exhibit wash-resistant inhibition of binding to these receptors and are valuable pharmacological tools to study opioid receptors. Even in cases where the peptide derivatives do not bind covalently to their target receptor, studying their binding has revealed subtle differences in receptor interactions with particular opioid peptide residues, especially Phe residues in the N-terminal “message” sequences. Solid phase synthetic methodology for the incorporation of other labels (e.g. biotin) into the C-terminus of peptides has also been developed in our laboratory (Kumar, V. and Aldrich, J. V. (2003) Org. Lett. 5, 613). These two synthetic approaches have been combined to prepare peptides containing multiple labels that can be used as tools to study peptide ligand-receptor interactions. These solid phase synthetic methodologies are versatile strategies that are applicable to the preparation of labeled peptides for a variety of targets in addition to opioid receptors. PMID:19956785

  14. 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

  15. 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. PMID:24011618

  16. Tritium plasma experiment: Parameters and potentials for fusion plasma-wall interaction studies

    SciTech Connect

    Shimada, Masashi; Sharpe, J. Phillip; Kolasinski, Robert D.; Causey, Rion A.

    2011-08-15

    The tritium plasma experiment (TPE) is a unique facility devoted to experiments on the behavior of deuterium/tritium in toxic (e.g., beryllium) and radioactive materials for fusion plasma-wall interaction studies. A Langmuir probe was added to the system to characterize the plasma conditions in TPE. With this new diagnostic, we found the achievable electron temperature ranged from 5.0 to 10.0 eV, the electron density varied from 5.0 x 10{sup 16} to 2.5 x 10{sup 18} m{sup -3}, and the ion flux density varied between 5.0 x 10{sup 20} to 2.5 x 10{sup 22} m{sup -2} s{sup -1} along the centerline of the plasma. A comparison of these plasma parameters with the conditions expected for the plasma facing components (PFCs) in ITER shows that TPE is capable of achieving most ({approx}800 m{sup 2} of 850 m{sup 2} total PFCs area) of the expected ion flux density and electron density conditions.

  17. Tritium Plasma Experiment (TPE) - parameters and potentials for fusion plasma-wall interaction studies

    SciTech Connect

    Masashi Shimada; Robert D. Kolasinski; J. Phillip Sharpe; Rion A. Causey

    2011-08-01

    The Tritium plasma experiment (TPE) is a unique facility devoted to experiments on the behavior of deuterium/tritium in toxic (e.g. beryllium) and radioactive materials for fusion plasma-wall interaction (PWI) studies. A Langmuir probe was added to the system to characterize the plasma conditions in TPE. With this new diagnostic, we found the achievable electron temperature ranged from 5.0 to 10.0 eV, the electron density varied from 5.0 x 10{sup 16} to 2.5 x 10{sup 18} m{sup -3}, and the ion flux density varied between 5.0 x 10{sup 20} to 2.5 x 10{sup 22} m{sup -2}s{sup -1} along the centerline of the plasma. A comparison of these plasma parameters with the conditions expected for the plasma facing components (PFCs) in ITER shows that TPE is capable of achieving most (approximately 800 m{sup 2} of 850 m{sup 2} total PFCs area) of the expected ion flux density and electron density conditions.

  18. 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.

  19. 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. PMID:25923517

  20. 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

  1. Analysis of derived optical parameters of atmospheric particles during a biomass burning event. Comparison with fossil fuel burning

    NASA Astrophysics Data System (ADS)

    Costa, A.; Mogo, S.; Cachorro, V.; de Frutos, A.; Medeiros, M.; Martins, R.; López, J. F.; Marcos, A.; Marcos, N.; Bizarro, S.; Mano, F.

    2015-12-01

    During the day November 26, 2014, a scheduled cleanup of the woods took place around the GOA-UVa aerosol measurement station located at the campus of the University of Beira Interior (40° 16’30”N, 7°30’35”W, 704m a.s.l.), Covilhã, Portugal. This cleanup included excessive vegetation removal during the morning, using fossil fuel-burning machinery, and burning of the vegetation during the afternoon. In situ measurements of aerosol optical properties were made and this study aims the characterization of the evolution of aerosol properties during the day. The optical parameters were monitored using a 3-wavelength nephelometer and a 3-wavelength particle soot absorption photometer. Selective sampling/exclusion of the coarse particles was done each 5 minutes. The scattering and absorption Ångström exponents as well as the single scattering albedo were derived and fully analyzed. The scattering and absorption coefficients increased dramatically during the event, reaching values as high as 720.3 Mm-1 and 181.9 Mm-1, respectively, for the green wavelength and PM10 size fraction. The spectral behavior of these parameters also changed wildly along the day and an inversion of the slope from positive to negative in the case of the single scattering albedo was observed.

  2. 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

  3. 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

    2016-04-22

    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. PMID:26915506

  4. 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

  5. Relationship between pairing symmetries and interaction parameters in iron-based superconductors from functional renormalization group calculations

    NASA Astrophysics Data System (ADS)

    Yuan, Jing; Hu, Jiangping

    2016-03-01

    Pairing symmetries of iron-based superconductors are investigated systematically in a five-orbital model within the different regions of interaction parameters by functional renormalization group (FRG). Even for a fixed Fermi surface with both hole and electron pockets, it is found that depending on interaction parameters, a variety of pairing symmetries, including two types of d-wave and two types of s-wave pairing symmetries, can emerge. Only the dx^2-y^2 - and the s±-waves are robustly supported by the nearest-neighbor (NN) intra-orbital J 1 and the next-nearest-neighbor (NNN) intra-orbital J 2 antiferromagnetic (AFM) exchange couplings, respectively. This study suggests that the accurate initial input of the interaction parameters is essential to make FRG a useful method to determine the leading channel of superconducting instability.

  6. 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

  7. 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

  8. 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

  9. The human poliovirus receptor. Receptor-virus interaction and parameters of disease specificity.

    PubMed

    Gromeier, M; Lu, H H; Bernhardt, G; Harber, J J; Bibb, J A; Wimmer, E

    1995-05-25

    The host range of poliovirus is determined by the expression of the hPVR, a member of the immunoglobulin superfamily. We characterized hPVR proteins biochemically and found them to be complex-type glycoproteins. The outermost V-like domain of three extracellular domains harbors the PVR function. A panel of single or multiple amino acid exchanges were introduced throughout this domain in order to localize regions involved in virus-receptor interactions. Putative contact amino acids were found to reside in the C'C"D and DE regions. Binding and uptake of poliovirus paralleled virus replication in all mutants tested suggesting that virus binding was affected without abrogating the ability to mediate subsequent events in the infection. Although the primate PVR is essential in conferring susceptibility to poliovirus infection, certain strains can induce neurological disease in rodents. Mouse neurovirulent PV isolates of divergent serotypical origin each provoked a distinctive, characteristic neurological syndrome upon intracerebral infection of wild-type mice. We analyzed clinical and histopathological features of diffuse encephalomyelitis caused by these PV strains and compared the condition with poliomyelitis in mice transgenic for the hPVR. Diffuse PV encephalomyelitis in wild-type mice could be distinguished clinically and histopathologically from hPVR-mediated poliomyelitis in trangenic mice. We localized the determinants of mouse neurovirulence of PV1(LS-a), a derivative of PV1 (Mahoney), in a portion of the viral genome encompassing parts of the capsid protein VP1 as well as the nonstructural protein 2A. Mouse neuropathogenicity could possibly be conferred by reduced particle stability of PV1(LS-a) inasmuch as we found particles to be thermolabile. PMID:7611627

  10. 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.

    1990-01-01

    Cirrus cloud radiative and physical characteristics are determined using a combination of ground-based, aircraft, and satellite measurements taken as part of the FIRE Cirrus Intensive Field Observations (IFO) during October and November 1986. Lidar backscatter data are used with rawinsonde data to define cloud base, center, and top heights and the corresponding temperatures. Coincident GOES 4-km visible (0.65 micro-m) and 8-km infrared window (11.5 micro-m) 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 model. 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 8.0 km for the 71 scenes. Mean vertical beam emittances derived from cloud-center temperatures were 0.62 for all scenes compared to 0.33 for the case study (27-28 October) reflecting the thinner clouds observed for the latter scenes. Relationships between cloud emittance, extinction coefficients, and temperature for the case study are very similar to those derived from earlier surface- based studies. The thicker clouds seen during the other IFO days yield different results. Emittances derived using cloud-top temperature were ratioed to those determined from cloud-center temperature. A nearly linear relationship between these ratios and cloud-center temperature holds promise for determining actual cloud-top temperatures and cloud thicknesses from visible and infrared radiance pairs. The mean ratio of the visible scattering optical depth to the infrared absorption optical depth was 2.13 for these data. This scattering efficiency ratio shows a significant dependence on cloud temperature. Values of mean scattering efficiency as high as 2.6 suggest the presence of small ice

  11. 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.

    1996-01-01

    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 Region Experiment (FIRE) cirrus intensive field observations (IFO) during October and November 1986. Lidar backscatter data are used with rawinsonde data to define cloud base, center and top heights and the corresponding temperatures. Coincident GOES-4 4-km visible (0.65 micrometer) and 8-km infrared window (11.5 micrometer) 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 model. 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 8.0 km for the 71 scenes. Mean vertical beam emittances derived from cloud-center temperatures were 062 for all scenes compared to 0.33 for the case study (27-28 October) reflecting the thinner clouds observed for the latter scenes. Relationships between cloud emittance , extinction coefficients, and temperature for the case study are very similar to those derived from earlier surface-based studies. The thicker clouds seen during the other IFO days yield different results. Emittances derived using cloud-top temperature wer ratioed to those determined from cloud-center temperature. A nearly linear relationship between these ratios and cloud-center temperature holds promise for determining actual cloud-top temperature and cloud thickness from visible and infrared radiance pairs. The mean ratio of the visible scattering optical depth to the infrared absorption optical depth was 2.13 for these data. This scattering efficiency ratio shows a significant dependence on cloud temperature. Values of mean scattering efficiency as high as 2

  12. Spatial Variations in CO2 Mixing Ratios Over a Heterogenous Landscape - Linking Airborne Measurements With Remote Sensing Derived Biophysical Parameters

    NASA Astrophysics Data System (ADS)

    Choi, Y.; Vadrevu, K. P.; Vay, S. A.; Woo, J.

    2006-12-01

    North American terrestrial ecosystems are major sources and sinks of carbon. Precise measurement of atmospheric CO2 concentrations plays an important role in the development and testing of carbon cycle models quantifying the influence of terrestrial CO2 exchange on the North American carbon budget. During the summer 2004 Intercontinental Chemical Transport Experiment North America (INTEX-NA) campaign, regional scale in-situ measurements of atmospheric CO2 were made from the NASA DC-8 affording the opportunity to explore how land surface heterogeneity relates to the airborne observations utilizing remote-sensing data products and GIS-based methods. These 1 Hz data reveal the seasonal biospheric uptake of CO2 over portions of the U.S. continent, especially east of 90°W below 2 km, compared to higher mixing ratios over water as well as within the upper troposphere where well-mixed, aged air masses were sampled. In this study, we use several remote sensing derived biophysical parameters from the LANDSAT, NOAA AVHRR, and MODIS sensors to specify spatiotemporal patterns of land use cover and vegetation characteristics for linking the airborne measurements of CO2 data with terrestrial sources of carbon. Also, CO2 flux footprint outputs from a 3-D Lagrangian atmospheric model have been integrated with satellite remote sensing data to infer CO2 variations across heterogeneous landscapes. In examining the landscape mosaic utilizing these available tools, preliminary results suggest that the lowest CO2 mixing ratios observed during INTEX-NA were over agricultural fields in Illinois dominated by corn then secondarily soybean crops. Low CO2 concentrations are attributable to sampling during the peak growing season over such C4 plants as corn having a higher photosynthetic rate via the C4-dicarboxylic acid pathway of carbon fixation compared to C3 plants such as soybeans. In addition to LANDSAT derived land cover data, results from comparisons of the airborne CO2 observations

  13. Relationship Between the Structure Parameters of a Solid Body and the Kinetics of Donor-Acceptor Interaction in Heterogeneous Systems

    NASA Astrophysics Data System (ADS)

    Khentov, V. Ya.; Khussein, Kh. Kh.

    2016-05-01

    Interaction of an organic ligand molecule with the surface of a d-metal or of disperse particles of chemical compounds containing covalent bonds in a nonaqueous solvent (direct synthesis of complex compounds) is determined by the structure parameters of the solid body. The relationships of the rate and energy of activation of the donor-acceptor interaction of the metal with the Grüneisen coefficient and the Debye temperature of the metal have been established.

  14. Relationship Between the Structure Parameters of a Solid Body and the Kinetics of Donor-Acceptor Interaction in Heterogeneous Systems

    NASA Astrophysics Data System (ADS)

    Khentov, V. Ya.; Khussein, Kh. Kh.

    2016-06-01

    Interaction of an organic ligand molecule with the surface of a d-metal or of disperse particles of chemical compounds containing covalent bonds in a nonaqueous solvent (direct synthesis of complex compounds) is determined by the structure parameters of the solid body. The relationships of the rate and energy of activation of the donor-acceptor interaction of the metal with the Grüneisen coefficient and the Debye temperature of the metal have been established.

  15. Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment

    PubMed Central

    2013-01-01

    Background Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of action. From a risk assessment perspective, alterations in biological pathways are a rich resource for setting toxicant thresholds, which may be more sensitive and mechanism-informed than traditional toxicity endpoints. Here we developed a novel differential networks (DNs) approach to connect pathway perturbation with toxicity threshold setting. Methods Our DNs approach consists of 6 steps: time-series gene expression data collection, identification of altered genes, gene interaction network reconstruction, differential edge inference, mapping of genes with differential edges to pathways, and establishment of causal relationships between chemical concentration and perturbed pathways. A one-sample Gaussian process model and a linear regression model were used to identify genes that exhibited significant profile changes across an entire time course and between treatments, respectively. Interaction networks of differentially expressed (DE) genes were reconstructed for different treatments using a state space model and then compared to infer differential edges/interactions. DE genes possessing differential edges were mapped to biological pathways in databases such as KEGG pathways. Results Using the DNs approach, we analyzed a time-series Escherichia coli live cell gene expression dataset consisting of 4 treatments (control, 10, 100, 1000 mg/L naphthenic acids, NAs) and 18 time points. Through comparison of reconstructed networks and construction of differential networks, 80 genes were identified as DE genes with a significant number of differential edges, and 22 KEGG pathways were altered in a concentration-dependent manner. Some of these pathways were perturbed to a degree as high as 70% even at the lowest exposure concentration, implying a high

  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. Molecular interaction of acetylcholinesterase with carnosic acid derivatives: a neuroinformatics study.

    PubMed

    Merad, M; Soufi, W; Ghalem, S; Boukli, F; Baig, M H; Ahmad, K; Kamal, Mohammad A

    2014-04-01

    Alzheimer's disease is a progressive degenerative disease of the brain marked by gradual and irreversible declines in cognitive functions. Acetylcholinesterase (AChE) plays a biological role in the termination of nerve impulse transmissions at cholinergic synapses by rapid hydrolysis of its substrate, "acetylcholine". The deficit level of acetylcholine leads to deprived nerve impulse transmission. Thus the cholinesterase inhibitors would reverse the deficit in acetylcholine level and consequently may reverse the memory impairments, which is characteristic of the Alzheimer's disease. The molecular interactions between AChE and Carnosic acid, a well known antioxidant substance found in the leaves of the rosemary plant has always been an area of interest. Here in this study we have performed in silico approach to identify carnosic acid derivatives having the potential of being a possible drug candidate against AChE. The best candidates were selected on the basis of the results of different scoring functions. PMID:24059305

  18. 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.

  19. 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

  20. 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

  1. Assistive positioning as a control parameter of social-communicative interactions between students with profound multiple disabilities and classroom staff.

    PubMed

    McEwen, I R

    1992-09-01

    This study examined the effects of assistive positioning on social-communicative interactions between 10 students, 6 to 12 years of age, with profound multiple disabilities, and their classroom staff. Interactions were videotaped in the students' classrooms when each student was positioned using a wheelchair, a sidelyer, and a mat on the floor. Data were analyzed by repeated-measures analysis of variance. During unstructured interactions, adults initiated communication at higher rates when students were positioned in their wheelchairs. During structured interactions, when students were given standardized opportunities for interaction, students functioning at lower levels of communication development were more communicative when they were supine on a mat than when in their wheelchairs or a sidelyer. In dynamic systems terms, position served as a control parameter of both adult and student communicative behaviors, which should be considered when recommending use of assistive positioning equipment for students with severe disabilities. PMID:1508971

  2. Polymer-Drug Interactions in Tyrosine-Derived Triblock Copolymer Nanospheres: a Computational Modeling Approach

    PubMed Central

    Costache, Aurora D.; Sheihet, Larisa; Zaveri, Krishna; Knight, Doyle D.; Kohn, Joachim

    2009-01-01

    A combination of Molecular Dynamics (MD) simulations and docking calculations was employed to model and predict polymer-drug interactions in self-assembled nanoparticles consisting of ABA-type triblock copolymers, where A-blocks are poly(ethylene glycol) units and B-blocks are low molecular weight tyrosine-derived polyarylates. This new computational approach was tested on three representative model compounds: nutraceutical curcumin, anti-cancer drug paclitaxel and pre-hormone vitamin D3. Based on this methodology, the calculated binding energies of polymer-drug complexes can be correlated with maximum drug loading determined experimentally. Furthermore, the modeling results provide an enhanced understanding of polymer-drug interactions, revealing subtle structural features that can significantly affect the effectiveness of drug loading (as demonstrated for a fourth tested compound, anticancer drug camptothecin). The present study suggests that computational calculations of polymer-drug pairs hold the potential of becoming a powerful prescreening tool in the process of discovery, development and optimization of new drug delivery systems, reducing both the time and the cost of the process. PMID:19650665

  3. 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

  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. A Combined Experimental and Computational Study of Vam3, a Derivative of Resveratrol, and Syk Interaction

    PubMed Central

    Jiang, Ming; Liu, Renping; Chen, Ying; Zheng, Qisheng; Fan, Saijun; Liu, Peixun

    2014-01-01

    Spleen tyrosine kinase (Syk) plays an indispensable role through preliminary extracellular antigen-induced crosslinking of Fc receptor (FcR) in the pathogenesis of autoimmune disorders, such as rheumatoid arthritis. In this study, we identify Vam3, a dimeric derivative of resveratrol isolated from grapes, as an ATP-competitive inhibitor of Syk with an IC50 of 62.95 nM in an in vitro kinase assay. Moreover, docking and molecular dynamics simulation approaches were performed to get more detailed information about the binding mode of Vam3 and Syk. The results show that 11b-OH on ring-C and 4b-OH on ring-D could form two hydrogen bonds with Glu449 and Phe382 of Syk, respectively. In addition, arene-cation interaction between ring-D of Vam3 and Lys402 of Syk was also observed. These results indicate that ring-C and D play an essential role in Vam3–Syk interaction. Our studies may be helpful in the structural optimization of Vam3, and also aid the design of novel Syk inhibitors in the future. PMID:25257535

  6. 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.

  7. 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. PMID:20199656

  8. 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

  9. Monte Carlo and experimental derivation of TG43 dosimetric parameters for CSM-type Cs-137 sources

    SciTech Connect

    Perez-Calatayud, J.; Granero, D.; Casal, E.; Ballester, F.; Puchades, V.

    2005-01-01

    In this study, complete dosimetric datasets for the CSM2 and CSM3 Cs-137 sources were obtained using the Monte Carlo GEANT4 code. The application of this calculation method was experimentally validated with thermoluminescent dosimetry (TLD). Functions and parameters following the TG43 formalism are presented: the dose rate constant, the radial dose functional, and the anisotropy function. In addition, to aid the quality control process on treatment planning systems, a two-dimensional (2D) rectangular dose rate table (the traditional along-away table), coherent with the TG43 dose calculation formalism, is given. The data given in this study complement existing information for both sources on the following aspects: (i) the source asymmetries were considered explicitly in the Monte Carlo calculations, (ii) TG43 data were derived directly from Monte Carlo calculations, (iii) the radial range of the different tables was increased as well as the angular resolution in the anisotropy function, including angles close to the longitudinal source axis. The CSM2 source TG-43 data of Liu et al. [Med. Phys. 31, 477-483 (2004)] are not consistent with the Williamson 2D along-away data [Int. J. Radiat. Oncol., Biol., Phys. 15, 227-237 (1988)] at distances closer than approximately 2 cm from the source. The data presented here for this source are consistent with this 2D along-away table, and are suitable for use in clinical practice.

  10. Monte Carlo and experimental derivation of TG43 dosimetric parameters for CSM-type Cs-137 sources.

    PubMed

    Pérez-Calatayud, J; Granero, D; Casal, E; Ballester, F; Puchades, V

    2005-01-01

    In this study, complete dosimetric datasets for the CSM2 and CSM3 Cs-137 sources were obtained using the Monte Carlo GEANT4 code. The application of this calculation method was experimentally validated with thermoluminescent dosimetry (TLD). Functions and parameters following the TG43 formalism are presented: the dose rate constant, the radial dose functional, and the anisotropy function. In addition, to aid the quality control process on treatment planning systems, a two-dimensional (2D) rectangular dose rate table (the traditional along-away table), coherent with the TG43 dose calculation formalism, is given. The data given in this study complement existing information for both sources on the following aspects: (i) the source asymmetries were considered explicitly in the Monte Carlo calculations, (ii) TG43 data were derived directly from Monte Carlo calculations, (iii) the radial range of the different tables was increased as well as the angular resolution in the anisotropy function, including angles close to the longitudinal source axis. The CSM2 source TG-43 data of Liu et al. [Med. Phys. 31, 477-483 (2004)] are not consistent with the Williamson 2D along-away data [Int. J. Radiat. Oncol., Biol., Phys. 15, 227-237 (1988)] at distances closer than approximately 2 cm from the source. The data presented here for this source are consistent with this 2D along-away table, and are suitable for use in clinical practice. PMID:15719951

  11. Correlation of Intra-Tumor 18F-FDG Uptake Heterogeneity Indices with Perfusion CT Derived Parameters in Colorectal Cancer

    PubMed Central

    Tixier, Florent; Groves, Ashley M.; Goh, Vicky; Hatt, Mathieu; Ingrand, Pierre; Le Rest, Catherine Cheze; Visvikis, Dimitris

    2014-01-01

    Application of textural features analysis to 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) images has been used to characterize intra-tumor uptake heterogeneity and has been shown to reflect disease outcome. A current hypothesis is that 18F-FDG uptake heterogeneity may reflect the physiological tracer uptake related to tumor perfusion. The purpose of our study was to investigate the correlations between intra-tumor uptake heterogeneity and vascular parameters derived from dynamic contrast enhanced (DCE) computed tomography (CT) obtained from an integrated 18F-FDG PET/perfusion CT examination. Methods Thirty patients with proven colorectal cancer prospectively underwent integrated 18F-FDG PET/DCE-CT to assess the metabolic-flow phenotype. Both CT blood flow parametric maps and PET images were analyzed. Correlations between PET heterogeneity and perfusion CT were assessed by Spearman's rank correlation analysis. Results Blood flow visualization provided by DCE-CT images was significantly correlated with 18F-FDG PET metabolically active tumor volume as well as with uptake heterogeneity for patients with stage III/IV tumors (|ρ|:0.66 to 0.78; p-value<0.02). Conclusion The positive correlation found with tumor blood flow indicates that intra-tumor heterogeneity of 18F-FDG PET accumulation reflects to some extent tracer distribution and consequently indicates that 18F-FDG PET intra-tumor heterogeneity may be associated with physiological processes such as tumor vascularization. PMID:24926986

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. Cytotoxicity of mitochondria-targeted resveratrol derivatives: interactions with respiratory chain complexes and ATP synthase.

    PubMed

    Sassi, Nicola; Mattarei, Andrea; Azzolini, Michele; Szabo', Ildiko'; Paradisi, Cristina; Zoratti, Mario; Biasutto, Lucia

    2014-10-01

    We recently reported that mitochondria-targeted derivatives of resveratrol are cytotoxic in vitro, selectively inducing mostly necrotic death of fast-growing and tumoral cells when supplied in the low μM range (N. Sassi et al., Curr. Pharm. Des. 2014). Cytotoxicity is due to H2O2 produced upon accumulation of the compounds into mitochondria. We investigate here the mechanisms underlying ROS generation and mitochondrial depolarization caused by these agents. We find that they interact with the respiratory chain, especially complexes I and III, causing superoxide production. "Capping" free hydroxyls with acetyl or methyl groups increases their effectiveness as respiratory chain inhibitors, promoters of ROS generation and cytotoxic agents. Exposure to the compounds also induces an increase in the occurrence of short transient [Ca(2+)] "spikes" in the cells. This increase is unrelated to ROS production, and it is not the cause of cell death. These molecules furthermore inhibit the F0F1 ATPase. When added to oligomycin-treated cells, the acetylated/methylated ones cause a recovery of the cellular oxygen consumption rates depressed by oligomycin. Since a protonophoric futile cycle which might account for the uncoupling effect is impossible, we speculate that the compounds may cause the transformation of the ATP synthase and/or respiratory chain complex(es) into a conduit for uncoupled proton translocation. Only in the presence of excess oligomycin the most effective derivatives appear to induce the mitochondrial permeability transition (MPT) within the cells. This may be considered to provide circumstantial support for the idea that the ATP synthase is the molecular substrate for the MPT pore. PMID:24997425

  19. Effective Soil Hydraulic Parameters Across Scales for Land-Atmosphere Interaction

    NASA Astrophysics Data System (ADS)

    Mohanty, B. P.; Ines, A. V.; Zhu, J.; Jana, R.; Das, N. N.; Sharma, S. K.

    2006-12-01

    Soil hydraulic properties (hydraulic conductivity, water retention) are by far the most important land surface parameters to govern the partitioning of soil moisture between infiltration and evaporation fluxes at a range of spatial scales. However, an obstacle to their practical application in the field, catchment, watershed, or regional scale is the difficulty of quantifying the "effective" soil hydraulic functions theta(h) and K(h), where theta is the soil water content, h is the pressure head and K is unsaturated hydraulic conductivity. Proper evaluation of the water balance near the land-atmosphere boundary depends strongly on appropriate characterization of soil hydraulic parameters under field conditions and at the appropriate process scale. In recent years we have adopted a multi-facet approach to this problem including: (1) a bottom-up approach, where larger-scale effective parameters are calculated by aggregating point-scale insitu hydraulic property measurements, (2) a top-down approach, where effective soil hydraulic parameters are estimated by inverse modeling using remotely sensed soil moisture measurements, and (3) an artificial neural network approach, where effective soil hydraulic parameters were estimated by exploiting the correlations with soil texture, topographic attributes, and vegetation characteristics at multiple spatial resolutions. Numerical and experimental results using these various effective soil hydraulic parameter estimation approaches including some comparisons between the approaches will be presented for the SGP and SMEX remote sensing experimental regions well as for the Rio Grande river basin.

  20. A review of methods for the signal quality assessment to improve reliability of heart rate and blood pressures derived parameters.

    PubMed

    Gambarotta, Nicolò; Aletti, Federico; Baselli, Giuseppe; Ferrario, Manuela

    2016-07-01

    The assessment of signal quality has been a research topic since the late 1970s, as it is mainly related to the problem of false alarms in bedside monitors in the intensive care unit (ICU), the incidence of which can be as high as 90 %, leading to alarm fatigue and a drop in the overall level of nurses and clinicians attention. The development of efficient algorithms for the quality control of long diagnostic electrocardiographic (ECG) recordings, both single- and multi-lead, and of the arterial blood pressure (ABP) signal is therefore essential for the enhancement of care quality. The ECG signal is often corrupted by noise, which can be within the frequency band of interest and can manifest similar morphologies as the ECG itself. Similarly to ECG, also the ABP signal is often corrupted by non-Gaussian, nonlinear and non-stationary noise and artifacts, especially in ICU recordings. Moreover, the reliability of several important parameters derived from ABP such as systolic blood pressure or pulse pressure is strongly affected by the quality of the ABP waveform. In this work, several up-to-date algorithms for the quality scoring of a single- or multi-lead ECG recording, based on time-domain approaches, frequency-domain approaches or a combination of the two will be reviewed, as well as methods for the quality assessment of ABP. Additionally, algorithms exploiting the relationship between ECG and pulsatile signals, such as ABP and photoplethysmographic recordings, for the reduction in the false alarm rate will be presented. Finally, some considerations will be drawn taking into account the large heterogeneity of clinical settings, applications and goals that the reviewed algorithms have to deal with. PMID:26906277

  1. 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

  2. Hydrophobic folding units derived from dissimilar monomer structures and their interactions.

    PubMed Central

    Tsai, C. J.; Nussinov, R.

    1997-01-01

    We have designed an automated procedure to cut a protein into compact hydrophobic folding units. The hydrophobic units are large enough to contain tertiary non-local interactions, reflecting potential nucleation sites during protein folding. The quality of a hydrophobic folding unit is evaluated by four criteria. The first two correspond to visual characterization of a structural domain, namely, compactness and extent of isolation. We use the definition of Zehfus and Rose (Zehfus MH, Rose GD, 1986, Biochemistry 25:35-340) to calculate the compactness of a cut protein unit. The isolation of a unit is based on the solvent accessible surface area (ASA) originally buried in the interior and exposed to the solvent after cutting. The third quantity is the hydrophobicity, equivalent to the fraction of the buried non-polar ASA with respect to the total non-polar ASA. The last criterion in the evaluation of a folding unit is the number of segments it includes. To conform with the rationale of obtaining hydrophobic units, which may relate to early folding events, the hydrophobic interactions are implicitly and explicitly applied in their generation and assessment. We follow Holm and Sander (Holm L, Sander C, 1994, Proteins 19:256-268) to reduce the multiple cutting-point problem to a one-dimensional search for all reasonable trial cuts. However, as here we focus on the hydrophobic cores, the contact matrix used to obtain the first non-trivial eigenvector contains only hydrophobic contracts, rather than all, hydrophobic and hydrophilic, interactions. This dataset of hydrophobic folding units, derived from structurally dissimilar single chain monomers, is particularly useful for investigations of the mechanism of protein folding. For cases where there are kinetic data, the one or more hydrophobic folding units generated for a protein correlate with the two or with the three-state folding process observed. We carry out extensive amino acid sequence order independent structural

  3. 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

  4. Spontaneous H2 loss through the interaction of squaric acid derivatives and BeH2.

    PubMed

    Montero-Campillo, M Merced; Yáñez, Manuel; Lamsabhi, Al Mokhtar; Mó, Otilia

    2014-04-25

    The most stable complexes between squaric acid and its sulfur- and selenium-containing analogues (C4X4H2 ; X = O, S, Se) with BeY2 (Y = H, F) were studied by means of the Gaussian 04 (G4) composite ab initio theory. Squaric acid derivatives are predicted to be very strong acids in the gas phase; their acidity increases with the size of the chalcogen, with C4Se4H2 being the strongest acid of the series and stronger than sulfuric acid. The relative stability of the C4X4H2⋅BeY2 (X = O, S, Se; Y = H, F) complexes changes with the nature of the chalcogen atom; but more importantly, the formation of the C4X4H2⋅BeF2 complexes results in a substantial acidity enhancement of the squaric moiety owing to the dramatic electron-density redistribution undergone by the system when the beryllium bond is formed. The most significant consequence of this acidity enhancement is that when BeF2 is replaced by BeH2, a spontaneous exergonic loss of H2 is observed regardless of the nature of the chalcogen atom. This is another clear piece of evidence of the important role that closed-shell interactions play in the modulation of physicochemical properties of the Lewis acid and/or the Lewis base. PMID:24665080

  5. 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

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

    PubMed Central

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

    2009-01-01

    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. PMID:17555705

  7. 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. PMID:26471667

  8. Molecular pathways: tumor-derived microvesicles and their interactions with immune cells in vivo.

    PubMed

    Pucci, Ferdinando; Pittet, Mikael J

    2013-05-15

    Cancer is not merely a cell-intrinsic genetic disease but also the result of complex cell-extrinsic interactions with host components, including immune cells. For example, effector T lymphocytes and natural killer cells are thought to participate in an immunosurveillance process, which eliminates neoplastic cells, whereas regulatory T lymphocytes and some myeloid cells, including macrophages, can create a milieu that prevents antitumor activity, supports tumor growth, and reduces survival of the host. Increasing evidence supports the notion that carcinoma cells communicate with immune cells directly, both within and away from the tumor stroma, and that this process fosters suppression of immunosurveillance and promotes tumor outgrowth. An important mode of communication between carcinoma cells and immune cells may involve tumor-derived microvesicles (tMV), also known as exosomes, ectosomes, or microparticles. These microvesicles carry lipids, proteins, mRNAs and microRNAs and travel short or long distances to deliver undegraded and undiluted material to other cells. Here, we consider the capacity of tMVs to control tumor-associated immune responses and highlight the known and unknown actions of tMVs in vivo. We also discuss why microvesicles may play a role in cancer diagnostics and prognostics and how they could be harnessed for anticancer therapy. PMID:23426276

  9. Conformational analysis and intramolecular/intermolecular interactions of N,N‧-dibenzylideneethylenediamine derivatives

    NASA Astrophysics Data System (ADS)

    Dabbagh, Hossein A.; Zamani, Mehdi; Farrokhpour, Hossein; Hossein Habibi, Mohammad; Barati, Kazem

    2010-11-01

    The molecular structures, conformational stability and molecular energy profile of three derivatives of RC 6H 4CHNCH 2CH 2NCHC 6H 4R including N, N'-dibenzylideneethylenediamine ( 1, R = H), N, N'-bis(4-trifluoromethoxybenzylidene)ethylenediamine ( 2, R = OCF 3), and N, N'-bis(4-dimethylaminobenzylidene)ethylenediamine ( 3, R = N(CH 3) 2) were obtained at B3LYP/6-31++G ** and HF/6-31++G ** levels of theory and compared with X-ray single crystal structures. The conformation of 1 and 2 is anti, while that of 3 is gauche in solid state (X-ray geometry). Based on calculations, there are seven energy minima in potential energy curves. A gauche conformer of 1, 2 and 3 has the lowest energy minimum (in the calculations modeling gas phase conditions) among all the other conformers. This is in contrast to X-ray findings (solid phase) for 1 and 2 but complements the X-ray finding for 3. These results were analyzed by natural bond orbital (NBO) and molecular orbital (MO) to determine the role of intra- and/or intermolecular interactions in the crystal structures.

  10. The interaction between nitrogen oxides and hemoglobin and endothelium-derived relaxing factor

    SciTech Connect

    Kosaka, H.; Uozumi, M.; Tyuma, I. )

    1989-01-01

    Among nitrogen oxides, NO and NO{sub 2} are free radicals and show a variety of biological effects. NO{sub 2} is a strongly oxidizing toxicant, although NO, not oxidizing as NO{sub 2}, is toxic in that it interacts with hemoglobin to form nitrosyl- and methemoglobin. Nitrosylhemoglobin shows a characteristic electron spin resonance (ESR) signal due to an odd electron localized on the nitrogen atom of NO and reacts with oxygen to yield nitrate and methemoglobin, which is rapidly reduced by methemoglobin reductase in red cells. NO was found to inhibit the reductase activity. Part of NO inhaled in the body is oxidized by oxygen to NO{sub 2}, which easily dissolves in water and converts to nitrite and nitrate. The nitrite oxidizes oxyhemoglobin autocatalytically after a lag. The mechanism of the oxidation, particularly the involvement of superoxide, was controversial. The stoichiometry of the reaction has now been established using nitrate ion electrode and a methemoglobin free radical was detected by ESR during the oxidation. Complete inhibition of the autocatalysis by aniline or aminopyrine suggests that the radical catalyzes conversion of nitrite to NO{sub 2}, which oxidizes oxyhemoglobin. Recently NO was shown to be one of endothelium-derived relaxing factors and the relaxation induced by the factor was inhibited by hemoglobin and potentiated by superoxide dismutase. 51 references.

  11. 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.

  12. 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

  13. 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

  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. Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation using NMR Data

    PubMed Central

    Venable, Richard M.; Luo, Yun; Gawrisch, Klaus; Roux, Benoît; Pastor, Richard W.

    2013-01-01

    Overbinding of ions to lipid head groups is a potentially serious artifact in simulations of charged lipid bilayers. In this study, the Lennard-Jones radii in the CHARMM force field for interactions of Na+ and lipid oxygen atoms of carboxyl, phosphate and ester groups were revised to match osmotic pressure data on sodium acetate, and electrophoresis data on palmitoyloleoyl phosphatidylcholine (POPC) vesicles. The new parameters were then validated by successfully reproducing previously published experimental NMR deuterium order parameters for dimyristoyl phosphatidylglycerol (DMPG) and newly obtained values for palmitoyloleoyl phosphatidylserine (POPS). Although the increases in Lennard-Jones diameters are only 0.02 to 0.12 Å, they are sufficient to reduce Na+ binding, and thereby increase surface areas per lipid by 5–10% compared with the unmodified parameters. PMID:23924441

  16. 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

  17. Non-Abelian monopole in the parameter space of point-like interactions

    NASA Astrophysics Data System (ADS)

    Ohya, Satoshi

    2014-12-01

    We study non-Abelian geometric phase in N = 2 supersymmetric quantum mechanics for a free particle on a circle with two point-like interactions at antipodal points. We show that non-Abelian Berry's connection is that of SU(2) magnetic monopole discovered by Moody, Shapere and Wilczek in the context of adiabatic decoupling limit of diatomic molecule.

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

    NASA Technical Reports Server (NTRS)

    Carlson, T. N. (Principal Investigator)

    1982-01-01

    Progress made in HCMM research, including testing the interactive minicomputer system and preparation of a paper on the analysis of regional scale soil moisture patterns, is summarized. An exhibit on remote sensing including a videotape display of HCMM images, most of them of the State College area, was prepared.

  19. 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.

  20. Soil hydraulic parameters and surface soil moisture of a tilled bare soil plot inversely derived from l-band brightness temperatures

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We coupled a radiative transfer approach with a soil hydrological model (HYDRUS 1D) and a global optimization routine SCE-UA to derive soil hydraulic parameters and soil surface roughness from measured brightness temperatures at 1.4 GHz (L-band) and measured rainfall and calculated potential soil ev...

  1. Effect of Intermolecular Hydrogen Bonding on the Nuclear Quadrupole Interaction in Imidazole and its Derivatives as Studied by ab initio Molecular Orbital Calculations

    NASA Astrophysics Data System (ADS)

    Nakamura, Nobuo; Masui, Hirotsugo; Ueda, Takahiro

    2000-02-01

    Ab initio Hartree-Fock molecular orbital calculations were applied to the crystalline imidazole and its derivatives in order to examine systematically the effect of possible N-H---N type hydrogen bond-ing on the nuclear quadrupole interaction parameters in these materials. The nitrogen quadrupole coupling constant (QCC) and the asymmetry parameter (η) of the electric field gradient (EFG) were found to depend strongly on the size of the molecular clusters, from single molecule, to dimer, trimer and to the infinite molecular chain, i.e., crystalline state, implying that the intermolecular N-H -N hydrogen bond affects significantly the electronic structure of imidazole molecule. A certain correla-tion between the QCC of 14N and the N-H bond distance R was also found and interpreted on the basis of the molecular orbital theory. However, we found that the value of the calculated EFG at the hy-drogen position of the N-H group, or the corresponding QCC value of 2 H, increases drastically as R-3 when R is shorter than about 0.1 nm, due probably to the inapplicability of the Gaussian basis sets to the very short chemical bond as revealed in the actual imidazole derivatives. We suggested that the ob-served N-H distances in imidazole derivatives should be re-examined.

  2. Interactions of newly designed dicationic carbazole derivatives with double-stranded DNA: syntheses, binding studies and AFM imaging.

    PubMed

    Jia, Tao; Xiang, Jin; Wang, Jing; Guo, Peng; Yu, Junping

    2013-09-01

    The design of small molecular ligands able to bind with DNA is pivotal for the development of diagnostic agents and therapeutic drugs targeting DNA. Carbazole-derivatives are potential agents against tumors and opportunistic infections of AIDS. Here, two carbazole-derived dicationic compounds, DPDI and DPPDI, were designed, synthesized and characterized using NMR, IR and MS. The DNA binding properties of DPDI and DPPDI were sensitive to ionic strength. At low ionic strength, planar and aromatic DPDI had a strongly intercalative interaction with DNA, which was confirmed by circular dichroism (CD) and gel electrophoresis. In DPPDI, a phenyl group substituting H atom at the –NH group of DPDI destroyed molecular planarity, which resulted in no intercalative interactions between DPPDI and DNA, proved by CD. The positive enhancement of CD at 260–270 nm and Hoechst 33258 competitive binding tests indicated the strong groove interactions of both DPPDI and DPDI to DNA. The similarity and difference in the structures between DPDI and DPPDI explained different interaction preferences with DNA. In groove interactions, dications of pyridinium on either DPDI or DPPDI could interact with DNA base pairs, and –NH on DPDI or –N–Ph on DPPDI pointed out of the groove, as the classical model of DNA groove binding agents. Furthermore, AFM imaging revealed that both carbazole-derivatives drove the DNA conformation more compact. All the experimental data proved that the two dicationic carbazole-derivatives interacted with DNA strongly and might act as a novel type of DNA-binding candidate. PMID:23863992

  3. 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.

  4. Psoralen derivatives as inhibitors of NF-κB interaction: the critical role of the furan ring.

    PubMed

    Marzaro, Giovanni; Lampronti, Ilaria; Borgatti, Monica; Manzini, Paolo; Gambari, Roberto; Chilin, Adriana

    2015-08-01

    Simplified analogues of previously reported NF-κB interaction inhibitors, lacking the furan moiety, were synthesized and evaluated by performing experiments based on electrophoretic mobility shift assay (EMSA). The synthetic modifications led to simpler coumarin derivatives with lower activity allowing to better understand the minimal structural requirement for the binding to NF-κB. PMID:25869956

  5. Discovery of novel phenoxazinone derivatives as DKK1/LRP6 interaction inhibitors: Synthesis, biological evaluation and structure-activity relationships.

    PubMed

    Thysiadis, Savvas; Mpousis, Spyros; Avramidis, Nicolaos; Katsamakas, Sotirios; Balomenos, Athanasios; Remelli, Rosaria; Efthimiopoulos, Spyros; Sarli, Vasiliki

    2016-03-01

    Amino derivatives of NCI8642 were synthesized and evaluated as inhibitors of DKK1/LRP6 interactions. The new inhibitors were able to activate the Wnt signaling pathway as indicated by the increased levels of β-catenin, and decrease the DKK1-induced Tau phosphorylation at serine 396. PMID:26819000

  6. 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

  7. The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes.

    PubMed

    Kawaoka, Shinpei; Hayashi, Nobumitsu; Suzuki, Yutaka; Abe, Hiroaki; Sugano, Sumio; Tomari, Yukihide; Shimada, Toru; Katsuma, Susumu

    2009-07-01

    Genetic studies and large-scale sequencing experiments have revealed that the PIWI subfamily proteins and PIWI-interacting RNAs (piRNAs) play an important role in germ line development and transposon control. Biochemical studies in vitro have greatly contributed to the understanding of small interfering RNA (siRNA) and microRNA (miRNA) pathways. However, in vitro analyses of the piRNA pathway have been thus far quite challenging, because their expression is largely restricted to the germ line. Here we report that Bombyx mori ovary-derived cultured cell line, BmN4, endogenously expresses two PIWI subfamily proteins, silkworm Piwi (Siwi) and Ago3 (BmAgo3), and piRNAs associated with them. Siwi-bound piRNAs have a strong bias for uridine at their 5' end and BmAgo3-bound piRNAs are enriched for adenine at position 10. In addition, Siwi preferentially binds antisense piRNAs, whereas BmAgo3 binds sense piRNAs. Moreover, we identified many pairs in which Siwi-bound antisense and BmAgo3-bound sense piRNAs are overlapped by precisely 10 nt at their 5' ends. These signatures are known to be important for secondary piRNA biogenesis in other organisms. Taken together, BmN4 is a unique cell line in which both primary and secondary steps of piRNA biogenesis pathways are active. This cell line would provide useful tools for analysis of piRNA biogenesis and function. PMID:19460866

  8. Microenvironment-derived IL-1 and IL-17 interact in the control of lung metastasis.

    PubMed

    Carmi, Yaron; Rinott, Gal; Dotan, Shahar; Elkabets, Moshe; Rider, Peleg; Voronov, Elena; Apte, Ron N

    2011-03-15

    Inflammatory cytokines modulate immune responses in the tumor microenvironment during progression/metastasis. In this study, we have assessed the role of IL-1 and IL-17 in the control of antitumor immunity versus progression in a model of experimental lung metastasis, using 3LL and B16 epithelial tumor cells. The absence of IL-1 signaling or its excess in the lung microenvironment (in IL-1β and IL-1R antagonist knockout [KO] mice, respectively) resulted in a poor prognosis and reduced T cell activity, compared with WT mice. In IL-1β KO mice, enhanced T regulatory cell development/function, due to a favorable in situ cytokine network and impairment in APC maturation, resulted in suppressed antitumor immunity, whereas in IL-1R antagonist KO mice, enhanced accumulation and activity of myeloid-derived suppressor cells were found. Reduced tumor progression along with improved T cell function was found in IL-17 KO mice, compared with WT mice. In the microenvironment of lung tumors, IL-1 induces IL-17 through recruitment of γ/δ T cells and their activation for IL-17 production, with no involvement of Th17 cells. These interactions were specific to the microenvironment of lung tumors, as in intrafootpad tumors in IL-1/IL-17 KO mice, different patterns of invasiveness were observed and no IL-17 could be locally detected. The results highlight the critical and unique role of IL-1, and cytokines induced by it such as IL-17, in determining the balance between inflammation and antitumor immunity in specific tumor microenvironments. Also, we suggest that intervention in IL-1/IL-17 production could be therapeutically used to tilt this balance toward enhanced antitumor immunity. PMID:21300825

  9. Interactive initialization of heat flux parameters for numerical models using satellite temperature measurements. [Kansas and Indiana

    NASA Technical Reports Server (NTRS)

    Carlson, T. N. (Principal Investigator)

    1982-01-01

    A method for obtaining patterns of moisture availability (and net evaporation) from satellite infrared measurements employs Carlson's boundary layer model and a variety of image processing routines executed by a minicomputer. To test the method with regard to regional scale moisture analyses, two case studies were chosen because of the availability of HCMM data and because of the presence of a large horizontal gradient in antecedent precipitation and crp moisture index. Results show some correlation in both cases between antecedent precipitation and derived moisture availability. Apparently, regional-scale moisture availability patterns can be determined with some degree of fidelity but the values themselves may be useful only in the relative sense and significant to within plus or minus one category of dryness over a range of 4 or 5 categories between absolutely dry and field saturation. Preliminary results suggest that the derived moisture values correlate best with longer-term precipitation totals, suggesting that the infrared temperatures respond more sensitively to a relatively deep substrate layer.

  10. 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.

  11. Using Isothermal Titration Calorimetry to Determine Thermodynamic Parameters of Protein–Glycosaminoglycan Interactions

    PubMed Central

    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. PMID:25325962

  12. 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

  13. 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

  14. Insecticide resistance and nutrition interactively shape life-history parameters in German cockroaches.

    PubMed

    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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Excited-state quantum phase transitions in the interacting boson model: Spectral characteristics of 0+ states and effective order parameter

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Zuo, Yan; Pan, Feng; Draayer, J. P.

    2016-04-01

    The spectral characteristics of the Lπ=0+ excited states in the interacting boson model are systematically investigated. It is found that various types of excited-state quantum phase transitions may widely occur in the model as functions of the excitation energy, which indicates that the phase diagram of the interacting boson model can be dynamically extended along the direction of the excitation energy. It has also been justified that the d -boson occupation probability ρ (E ) is qualified to be taken as the effective order parameter to identify these excited-state quantum phase transitions. In addition, the underlying relation between the excite-state quantum phase transition and the chaotic dynamics is also stated.

  2. Determination of the interaction parameters of ions from a rarefied plasma flow with electrically conducting surfaces using thermoanemometric probes

    SciTech Connect

    Shuvalov, V.A.; Gubin, V.V.; Kostenko, V.S.; Reznichenko, N.P.

    1985-05-01

    A method is proposed for measuring a combination of parameters associated with the interaction of ions from a rarefied plasma with electrically conducting surfaces using thermoanemometric probes. Results of measurements of the ion-electron secondary emission coefficients and of the accommodation coefficients for the energy and the normal and tangential momenta of inert gas and molecular nitrogen ions on the surfaces of commercial materials are presented. Empirical approximations are given for the dependences of the energy and normal momentum accommodation coefficients on the orientation of the probe-target with respect to the velocity vector of the flow.

  3. Dynamic calibration of higher eigenmode parameters of a cantilever in atomic force microscopy by using tip–surface interactions

    DOE PAGESBeta

    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.

  4. 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.

  5. Effects of lactoferrin, a protein present in the female reproductive tract, on parameters of human sperm capacitation and gamete interaction.

    PubMed

    Zumoffen, C M; Massa, E; Caille, A M; Munuce, M J; Ghersevich, S A

    2015-11-01

    In a recent study, lactoferrin (LF) was detected in human oviductal secretion. The protein was able to bind to oocytes and sperm, and modulated gamete interaction. The aim of the present study was to investigate the effect of LF on parameters related to human sperm capacitation and sperm-zona pellucida interaction. Semen samples were obtained from healthy normozoospermic donors (n = 7). Human follicular fluids and oocytes were collected from patients undergoing in vitro fertilization. Motile sperm obtained by swim-up were incubated for 6 or 22 h under capacitating conditions with LF (0-100 μg/mL). After incubations, viability, motility, presence of α-d-mannose receptors (using a fluorescent probe on mannose coupled to bovine serum albumin), spontaneous and induced acrosome reaction (assessed with Pisum sativum agglutinin conjugated to fluorescein isothiocyanate), and tyrosine phosphorylation of sperm proteins were evaluated. Sperm-zona pellucida interaction in the presence of LF was investigated using the hemizone assay. The presence of LF did not affect sperm viability or motility, but caused a dose-dependent significant decrease in sperm α-d-mannose-binding sites, and the effect was already significant with the lowest concentration of the protein used after 22 h incubation. Dose-dependent significant increases in both induced acrosome reaction and tyrosine phosphorylation of sperm proteins were observed in the presence of LF. The present data indicate that LF modulates parameters of sperm function. The inhibition of gamete interaction by LF could be partially explained by the decrease in sperm d-mannose-binding sites. The presence of the LF promoted sperm capacitation in vitro. PMID:26445132

  6. 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

  7. 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

  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. Redox and complexation interactions of neptunium(V) with quinonoid-enriched humic derivatives.

    PubMed

    Shcherbina, Natalia S; Perminova, Irina V; Kalmykov, Stepan N; Kovalenko, Anton N; Haire, Richard G; Novikov, Alexander P

    2007-10-15

    Actinides in their higher valence states (e.g., MO2+ and MO2(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 regardsto 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(-6) (parent humic acid) to 1.06 x 10(-5) sec(-1) (derivative with maximum hydroquinone content). Stability constants for Np(V)-humic complexes calculated from spectroscopic data produce corresponding Logbeta 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 are the most useful for addressing

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. Evaluation of Interactive Visualization on Mobile Computing Platforms for Selection of Deep Brain Stimulation Parameters.

    PubMed

    Butson, Christopher R; Tamm, Georg; Jain, Sanket; Fogal, Thomas; Krüger, Jens

    2013-01-01

    In recent years, there has been significant growth in the use of patient-specific models to predict the effects of neuromodulation therapies such as deep brain stimulation (DBS). However, translating these models from a research environment to the everyday clinical workflow has been a challenge, primarily due to the complexity of the models and the expertise required in specialized visualization software. In this paper, we deploy the interactive visualization system ImageVis3D Mobile, which has been designed for mobile computing devices such as the iPhone or iPad, in an evaluation environment to visualize models of Parkinson's disease patients who received DBS therapy. Selection of DBS settings is a significant clinical challenge that requires repeated revisions to achieve optimal therapeutic response, and is often performed without any visual representation of the stimulation system in the patient. We used ImageVis3D Mobile to provide models to movement disorders clinicians and asked them to use the software to determine: 1) which of the four DBS electrode contacts they would select for therapy; and 2) what stimulation settings they would choose. We compared the stimulation protocol chosen from the software versus the stimulation protocol that was chosen via clinical practice (independent of the study). Lastly, we compared the amount of time required to reach these settings using the software versus the time required through standard practice. We found that the stimulation settings chosen using ImageVis3D Mobile were similar to those used in standard of care, but were selected in drastically less time. We show how our visualization system, available directly at the point of care on a device familiar to the clinician, can be used to guide clinical decision making for selection of DBS settings. In our view, the positive impact of the system could also translate to areas other than DBS. PMID:22450824

  16. Exploring medical diagnostic performance using interactive, multi-parameter sourced receiver operating characteristic scatter plots.

    PubMed

    Moore, Hyatt E; Andlauer, Olivier; Simon, Noah; Mignot, Emmanuel

    2014-04-01

    Determining diagnostic criteria for specific disorders is often a tedious task that involves determining optimal diagnostic thresholds for symptoms and biomarkers using receiver-operating characteristic (ROC) statistics. To help this endeavor, we developed softROC, a user-friendly graphic-based tool that lets users visually explore possible ROC tradeoffs. The software requires MATLAB installation and an Excel file containing threshold symptoms/biological measures, with corresponding gold standard diagnoses for a set of patients. The software scans the input file for diagnostic and symptom/biomarkers columns, and populates the graphical-user-interface (GUI). Users select symptoms/biomarkers of interest using Boolean algebra as potential inputs to create diagnostic criteria outputs. The software evaluates subtests across the user-established range of cut-points and compares them to a gold standard in order to generate ROC and quality ROC scatter plots. These plots can be examined interactively to find optimal cut-points of interest for a given application (e.g. sensitivity versus specificity needs). Split-set validation can also be used to set up criteria and validate these in independent samples. Bootstrapping is used to produce confidence intervals. Additional statistics and measures are provided, such as the area under the ROC curve (AUC). As a testing set, softROC is used to investigate nocturnal polysomnogram measures as diagnostic features for narcolepsy. All measures can be outputted to a text file for offline analysis. The softROC toolbox, with clinical training data and tutorial instruction manual, is provided as supplementary material and can be obtained online at http://www.stanford.edu/~hyatt4/software/softroc or from the open source repository at http://www.github.com/informaton/softroc. PMID:24561350

  17. Closed string Ramond-Ramond proposed higher derivative interactions on fermionic amplitudes in IIB

    NASA Astrophysics Data System (ADS)

    Hatefi, Ehsan

    2014-03-01

    The complete form of the amplitude of one closed string Ramond-Ramond (RR), two fermionic strings and one scalar field in IIB superstring theory has been computed in detail. Deriving by using suitable gauge fixing, we discover some new vertices and their higher derivative corrections. We investigate both infinite gauge and scalar u-channel poles of this amplitude. In particular, by using the fact that the kinetic term of fermion fields has no correction, employing Born-Infeld action, the Wess-Zumino terms and their higher derivative corrections, we discover all infinite t,s-channel fermion poles. The couplings between one RR and two fermions and all their infinite higher derivative corrections have been explored. In order to look for all infinite (s+t+u)-channel scalar/gauge poles for p+2=n, p=n cases, we obtain the couplings between two fermions-two scalars and two fermions, one scalar and one gauge field as well as all their infinite higher derivative corrections in type IIB. Specifically we make various comments based on arXiv:1205.5079 in favor of universality conjecture for all order higher derivative corrections (with or without low energy expansion) and the relation of open/closed string that is responsible for all superstring scattering amplitudes in IIA, IIB.

  18. 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

  19. 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

  20. Towards Improving our Understanding on the Retrievals of Key Parameters Characterising Land Surface Interactions from Space: Introduction & First Results from the PREMIER-EO Project

    NASA Astrophysics Data System (ADS)

    Ireland, Gareth; North, Matthew R.; Petropoulos, George P.; Srivastava, Prashant K.; Hodges, Crona

    2015-04-01

    Acquiring accurate information on the spatio-temporal variability of soil moisture content (SM) and evapotranspiration (ET) is of key importance to extend our understanding of the Earth system's physical processes, and is also required in a wide range of multi-disciplinary research studies and applications. The utility and applicability of Earth Observation (EO) technology provides an economically feasible solution to derive continuous spatio-temporal estimates of key parameters characterising land surface interactions, including ET as well as SM. Such information is of key value to practitioners, decision makers and scientists alike. The PREMIER-EO project recently funded by High Performance Computing Wales (HPCW) is a research initiative directed towards the development of a better understanding of EO technology's present ability to derive operational estimations of surface fluxes and SM. Moreover, the project aims at addressing knowledge gaps related to the operational estimation of such parameters, and thus contribute towards current ongoing global efforts towards enhancing the accuracy of those products. In this presentation we introduce the PREMIER-EO project, providing a detailed overview of the research aims and objectives for the 1 year duration of the project's implementation. Subsequently, we make available the initial results of the work carried out herein, in particular, related to an all-inclusive and robust evaluation of the accuracy of existing operational products of ET and SM from different ecosystems globally. The research outcomes of this project, once completed, will provide an important contribution towards addressing the knowledge gaps related to the operational estimation of ET and SM. This project results will also support efforts ongoing globally towards the operational development of related products using technologically advanced EO instruments which were launched recently or planned be launched in the next 1-2 years. Key Words: PREMIER

  1. 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. PMID:26924329

  2. A statistical analysis of sounding derived indices and parameters for extreme and non-extreme thunderstorm events over Cyprus

    NASA Astrophysics Data System (ADS)

    Savvidou, K.; Orphanou, A.; Charalambous, D.; Lingis, P.; Michaelides, S.

    2010-06-01

    The main purpose of this study is to provide a simple statistical analysis of several stability indices and parameters for extreme and non-extreme thunderstorm events during the period 1997 to 2001 in Cyprus. For this study, radiosonde data from Athalassa station (35°1´ N, 33°4´ E) were analyzed during the aforementioned period. The stability indices and parameters set under study are the K index, the Total Totals (TT) index, the Convective Available Potential Energy related parameters such as Convective Available Potential Energy (CAPE), Downdraft CAPE (DCAPE) and the Convective Inhibition (CIN), the Vorticity Generator Parameter (VGP), the Bulk Richardson Number (BRN), the BRN Shear and the Storm Relative Helicity (SRH). An event is categorized as extreme, if primarily, CAPE was non zero and secondary, if values of both the K and the TotalTotals (TT) indices exceeded 26.9 and 50, respectively. The cases with positive CAPE but lower values of the other indices, were identified as non-extreme. By calculating the median, the lower and upper limits, as well as the lower and upper quartiles of the values of these indices, the main characteristics of their distribution were determined.

  3. Productivity, Respiration, and Light-Response Parameters of World Grassland and Agroecosystems Derived From Flux-Tower Measurements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grasslands and agroecosystems occupy one-third of the terrestrial area, but their contribution to the global carbon cycle remains uncertain. We used a set of 316 site-years of CO2 exchange measurements to quantify gross primary productivity, respiration, and light-response parameters of grasslands, ...

  4. A Bayesian approach to incorporating maximum entropy-derived signal parameter statistics into the receiver operating characteristic (ROC) curves

    NASA Astrophysics Data System (ADS)

    Culver, R. Lee; Sibul, Leon H.; Bradley, David L.; Ballard, Jeffrey A.; Camin, H. John

    2005-09-01

    Our goal is to develop a probabilistic sonar performance prediction methodology that can make use of limited knowledge of random or uncertain environment, target, and sonar system parameters, but does not make unwarranted assumptions. The maximum entropy method (MEM) can be used to construct probability density functions (pdfs) for relevant environmental and source parameters, and an ocean acoustic propagation model can use those pdfs to predict the variability of received signal parameter. At this point, the MEM can be used once again to produce signal parameter pdfs. A Bayesian framework allows these pdfs to be incorporated into the signal processor to produce ROC curves in which, for example, the signal-to-noise ratio (SNR) is a random variable for which a pdf has been calculated. One output of such a processor could be a range-dependent probability of detection for fixed probability of false alarm, which would be more useful than the conventional range of the day that is still in use in some areas. [Work supported by ONR Code 321US.

  5. Relativistic effects in the intermolecular interaction-induced nuclear magnetic resonance parameters of xenon dimer.

    PubMed

    Hanni, Matti; Lantto, Perttu; Ilias, Miroslav; Jensen, Hans Jorgen Aagaard; Vaara, Juha

    2007-10-28

    Relativistic effects on the (129)Xe nuclear magnetic resonance shielding and (131)Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe(2) system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift delta, the anisotropy of the shielding tensor Deltasigma, and the NQC constant along the internuclear axis chi( parallel) are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Moller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for delta and Deltasigma by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for delta and Deltasigma in Xe(2). For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For chi( parallel), the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the (129)Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the

  6. Vacuum-vapor-deposited thin films of benzo[a]phenoxazone-5 derivatives as photoresist layers: properties versus deposition parameters

    NASA Astrophysics Data System (ADS)

    Agabekov, Vladimir E.; Gudimenko, Yurii I.; Ignasheva, Olga E.

    1992-08-01

    The phisico-chemical properties of the benzo [a] phenoxazone-5 derivatives and their vacuum-deposited thin films (optical absorption, phase and chemical compositions, free surface energies of the films, and their supermolecular structures) have been studied. Changes in the vapor phase ratio of the dye derivatives have been investigated dependent on the boat- evaporator temperature, and chemical structures of the transformation products have been established. The films of different structure phase states have been obtained dependent on the formation conditions. Thin films of 9-diethylamino-3-methacryloyloxy-5H-benzo [a] phenoxaz-5-dicyanmethylene display good light-sensitive and masking properties and are suitable for submicron patterning under UV-exposure with (lambda) equals 266 nm.

  7. 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.

  8. 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.

  9. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1.

    PubMed

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-01-01

    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. PMID:26689258

  10. 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

  11. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1

    PubMed Central

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-01-01

    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. PMID:26689258

  12. Killing of melanoma cells and their metastases by human lactoferricin derivatives requires interaction with the cancer marker phosphatidylserine.

    PubMed

    Riedl, Sabrina; Rinner, Beate; Schaider, Helmut; Lohner, Karl; Zweytick, Dagmar

    2014-10-01

    Despite favorable advancements in therapy cancer is still not curative in many cases, which is often due to inadequate specificity for tumor cells. In this study derivatives of a short cationic peptide derived from the human host defense peptide lactoferricin were optimized in their selective toxicity towards cancer cells. We proved that the target of these peptides is the negatively charged membrane lipid phosphatidylserine (PS), specifically exposed on the surface of cancer cells. We have studied the membrane interaction of three peptides namely LF11-322, its N-acyl derivative 6-methyloctanoyl-LF11-322 and its retro repeat derivative R(etro)-DIM-P-LF11-322 with liposomes mimicking cancerous and non-cancerous cell membranes composed of PS and phosphatidylcholine (PC), respectively. Calorimetric and permeability studies showed that N-acylation and even more the repeat derivative of LF11-322 leads to strongly improved interaction with the cancer mimic PS, whereas only the N-acyl derivative also slightly affects PC. Tryptophan fluorescence of selective peptide R-DIM-P-LF11-322 revealed specific peptide penetration into the PS membrane interface and circular dichroism showed change of its secondary structure by increase of proportion of β-sheets just in the presence of the cancer mimic. Data correlated with in vitro studies with cell lines of human melanomas, their metastases and melanocytes, revealing R-DIM-P-LF11-322 to exhibit strongly increased specificity for cancer cells. This indicates the need of high affinity to the target PS, a minimum length and net positive charge, an adequate but moderate hydrophobicity, and capability of adoption of a defined structure exclusively in presence of the target membrane for high antitumor activity. PMID:24838743

  13. 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.

  14. 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

  15. 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.

  16. 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. PMID:25133257

  17. 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

  18. Relationship between sounding derived parameters and the strength of tornadoes in Europe and the USA from reanalysis data

    NASA Astrophysics Data System (ADS)

    Grünwald, S.; Brooks, H. E.

    2011-06-01

    Proximity soundings from reanalysis data for tornado events in Europe for the years 1958 to 1999 and in the US for the years 1991 to 1999 have been used for generating distributions of parameter combinations important for severe convection. They include parcel updraft velocity (WMAX) and deep-layer shear (DLS), lifting condensation level (LCL) and deep-layer shear (DLS), and LCL and shallow-layer shear (LLS) for weak and significant tornadoes. We investigate how well they discriminate between weak and significant tornadoes. For Europe, these distributions have been generated for unrated, F0 and F1 tornadoes as well to discover if the unrated tornadoes can be associated with the weak tornadoes. The pattern of parameter combination distributions for unrated tornadoes in Europe strongly resembles the pattern of F0 tornadoes. Thus, the unrated tornadoes are likely to consist of mostly F0 tornadoes. Consequently, the unrated tornadoes have been included into the weak tornadoes and distributions of parameter combinations have been generated for these. In Europe, none of the three combinations can discriminate well between weak and significant tornadoes, but all can discriminate if the unrated tornadoes are included with the weak tornadoes (unrated/weak). In the US, the combinations of LCL and either of the shear parameters discriminate well between weak and significant tornadoes, with significant tornadoes occurring at lower LCL and higher shear values than the weak ones. In Europe, the shear shows the same behavior, but the LCL behaves differently, with significant tornadoes occurring at higher LCL than the unrated/weak ones. The combination of WMAX and DLS is a good discriminator between unrated/weak and significant tornadoes in Europe, but not in the US, with significant tornadoes occurring at a higher WMAX and DLS than the unrated/weak tornadoes.

  19. 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.

  20. Analytic derivative couplings between configuration-interaction-singles states with built-in electron-translation factors for translational invariance

    NASA Astrophysics Data System (ADS)

    Fatehi, Shervin; Alguire, Ethan; Shao, Yihan; Subotnik, Joseph E.

    2011-12-01

    We present a method for analytically calculating the derivative couplings between a pair of configuration-interaction-singles (CIS) excited states obtained in an atom-centered basis. Our theory is exact and has been derived using two completely independent approaches: one inspired by the Hellmann-Feynman theorem and the other following from direct differentiation. (The former is new, while the latter is in the spirit of existing approaches in the literature.) Our expression for the derivative couplings incorporates all Pulay effects associated with the use of an atom-centered basis, and the computational cost is minimal, roughly comparable to that of a single CIS energy gradient. We have validated our method against CIS finite-difference results and have applied it to the lowest lying excited states of naphthalene; we find that naphthalene derivative couplings include Pulay contributions sufficient to have a qualitative effect. Going beyond standard problems in analytic gradient theory, we have also constructed a correction, based on perturbative electron-translation factors, for including electronic momentum and eliminating spurious components of the derivative couplings that break translational symmetry. This correction is general and can be applied to any level of electronic structure theory.

  1. 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.

  2. 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)...

  3. 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

  4. 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.

  5. Assessing the relationship between urban parameters and the LST derived by satellite and aerial imageries in a GIS environment: the case of Bari (Italy).

    NASA Astrophysics Data System (ADS)

    Caprioli, Mauro; Ceppi, Claudia; Falchi, Ugo; Mancini, Francesco; Scarano, Mario

    2014-05-01

    The use of thermal remote sensing to estimate the phenomenon of urban heat islands (UHI) and development of climate anomalies in urban context represents a consolidated approach. In the current scientific literature a widespread case studies were focused on the estimation of the relationship between features related to the urban environment and the Land Surface Temperatures (LST). The latter is a basic starting observation in the investigation on the UHI phenomenon . However, the evaluation of these relationships is rather difficult. This is due to deficiencies in the detailed knowledge of parameters able to describe geometric and qualitative properties of land covers. These properties are very often not repeatable and not easily transferable in other contexts. In addition, many of the relevant parameters are difficult to be determined at the required spatial resolution and analyses are affected by a lack in the amount of quantitative parameters used. In addition to the LST, several useful indicators are introduced by the literature in the investigation of such phenomena. The objective of this work is to study the relationship between the LST and a set of variables that characterize the anthropic and natural domains of the urban areas, such as urban morphology, the Normalized Differenced Vegetation Index (NDVI), the Sky View Factor (SVF) and other morphometric parameters implemented within a GIS environment. The study case is the city of Bari (Southern Italy) where several recognizable morphologies exhibit a different thermal behavior. The LST parameter was derived from a collection of satellite ASTER images collected within a period spanning from July 2001 and July 2006, whereas aerial thermal imageries were acquired on September 2013. The basic data used for the determination of the descriptive parameters of the urban environmental are derived from digital maps(Geographic Information System of the Apulia Region), Digital Elevation Model and Land Use. The analysis

  6. 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.

  7. Relation between coda-Q and stress loaded to an elastic body ~state parameters derived by stochastic measurement~

    NASA Astrophysics Data System (ADS)

    Okamoto, K.; Mikada, H.; Goto, T.; Takekawa, J.

    2009-12-01

    Coda-wave is the summation of the scattered waves caused by scatterers such as cracks and medium inhomogeneities in the rock. Coda-wave is composed of P-wave, S-wave and variety of other waves. When the spatial scale of inhomogeneities become comparable with seismic wavelength, it becomes very difficult to analyze the coda-wave quantitatively in terms of the location of scatterers, scattering mechanisms, etc. As a consequence, it is very hard in general to apply a method of deterministic structural analysis to use coda waves. For inhomogeneous meda, it is natural to deal with stochastic methdologies to interpret seismic data. In this regard, coda-Q, i.e., parameters of attenuation or decay of energy scattered by medium inhomogeneities, has been frequently used as a stochastic measure of the medium in which seismic waves propagate. Since objectives of recent structural surveys include spatiotemporal or time-lapse variation of physical properties of underground medium, we would like to exploit the stochastic parameters if these parameters reflect any changes of physical state of the medium. The purpose of this study is to relate this parameter to non-stochastic propertyies of the underground property. In this study, we performed a simulation on seismic wave propagation in an elastic medium using a two-dimensional finite difference method. In our numerical calculatoins, seismic scatters were randomly placed in the simulation model. Coda-Q values are estimated using simulated waveforms for a set of various loading stresses that was applied to the model. Since the scatters are displaced due to loaded stresses, Coda-Q values are obtained against loading stresses and directions. In order to estimate the magnitude of stress and the direction of the principal stress, we used a variation of the envelope of coda-wave. Analysis of coda-wave revealed proportional relations between the loading stress and attenuation factor of the envelope. For the direction of the principal

  8. 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

  9. 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

  10. Studies on intermolecular interaction on binary mixtures of methyl orange-water system: excess molar functions of ultrasonic parameters at different concentrations and at different temperatures.

    PubMed

    Thanuja, B; Kanagam, Charles; Sreedevi, S

    2011-11-01

    Density (ρ), viscosity (η) and ultrasonic velocity (u) of binary mixtures of methyl orange and water were measured at different concentrations and at different temperatures; several useful parameters such as excess volume, excess velocity, and excess adiabatic compressibility have been calculated. These parameters are used to explain the nature of intermolecular interactions taking place in the binary mixture. The above study is helpful in understanding the dye/solvent interaction at different concentration and temperatures. PMID:21596612

  11. Ab initio study of hyperfine interaction parameters in C14 Hf and Zr Laves-phase compounds

    NASA Astrophysics Data System (ADS)

    Belošević-Čavor, Jelena; Koteski, V.; Radaković, J.; Cekić, B.

    2009-05-01

    Using ab initio density-functional theory approach the electric field gradients (EFGs) and hyperfine magnetic fields (HMFs) for the isostructural C14 Laves-phase compounds HfCr2 , HfFe2 , HfMn2 , ZrCr2 , and ZrMn2 are calculated and compared with the available experimental data from time differential perturbed angular-correlation (TDPAC) spectroscopy. In addition, supercell calculations of the hyperfine interaction parameters at the nucleus of the substitutional Ta impurity are used to elucidate the role played by the Ta probe in the TDPAC measurements of Hf and Zr C14 Laves phases and solve the controversy related to the origin of the HMF in the C14 HfFe2 compound.

  12. Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameters.

    PubMed

    Vardevanyan, Poghos O; Antonyan, Ara P; Parsadanyan, Marine A; Torosyan, Margarita A; Karapetian, Armen T

    2016-07-01

    Large amount of data of experimental and theoretical studies have shown that ethidium bromide (EtBr) and methylene blue (MB) may bind to nucleic acids via three modes: intercalation between two adjacent base pairs, insertion into the plane between neighboring bases in the same strand (semi-intercalation), and outside binding with negatively charged backbone phosphate groups. The aim of the given research is to examine the behavior of these two ligands at both separate and joint DNA binding. The obtained experimental data show that the effect of simultaneous binding of EtBr and MB on double-stranded DNA has a non-additive effect of separate binding. The analyses of the melting thermodynamic parameters of DNA complexes with two bound ligands suggest competitive mechanism of interaction. PMID:26239502

  13. 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

  14. Cooperative Self-Assembly of Carbazole Derivatives Driven by Multiple Dipole-Dipole Interactions.

    PubMed

    Ikeda, Toshiaki; Iijima, Tatsuya; Sekiya, Ryo; Takahashi, Osamu; Haino, Takeharu

    2016-08-01

    Carbazole possessing phenylisoxazoles self-assembled in a cooperative manner in decalin. X-ray crystal structure analysis revealed that the isoxazole dipoles align in a head-to-tail fashion. DFT calculations suggested that the linear array of dipoles induced the polarization of each dipole, leading to an increase in dipole-dipole interactions. This dipole polarization resulted in cooperative assembly. PMID:27391525

  15. 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…

  16. 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)

  17. Allosteric interactions of quaternary strychnine and brucine derivatives with muscarinic acetylcholine receptors.

    PubMed

    Gharagozloo, P; Lazareno, S; Popham, A; Birdsall, N J

    1999-02-11

    The affinity and allosteric properties of 22 quaternary derivatives of strychnine and brucine at the m1-m4 subtypes of muscarinic receptors have been analyzed and compared. The subtype selectivity, in terms of affinity, was in general m2 > m4 > m1 > m3. The highest affinities were found for N-benzyl, N-2-naphthylmethyl, and N-4-biphenylylmethyl strychnine (13, 14, and 18, respectively). All the strychnine and brucine derivatives were positively cooperative with the antagonist, N-methylscopolamine, at m2 receptors and, in the case of the strychnine analogues, were positively cooperative with N-methylscopolamine at least at one other subtype. The strychnine analogues were negatively cooperative with the neurotransmitter, acetylcholine, at all subtypes whereas brucine and five of the six derivatives examined were positively cooperative with acetylcholine at one or more subtypes (m1-m5) and exhibited different patterns of subtype selectivity. The ability to generate subtype-selective allosteric enhancers of acetylcholine binding and function may be of use in the development of drugs for the treatment of Alzheimer's disease. PMID:9986715

  18. Experimental and calculated structural parameters of 5-trihalomethyl-4,5-dihydro-1 H-pyrazole derivatives, novel analgesic agents

    NASA Astrophysics Data System (ADS)

    Machado, Pablo; Campos, Patrick T.; Lima, Glauber R.; Rosa, Fernanda A.; Flores, Alex F. C.; Bonacorso, Helio G.; Zanatta, Nilo; Martins, Marcos A. P.

    2009-01-01

    The crystal structures of four novel analgesic agents, methyl 5-hydroxy-3- or 4-methyl-5-trichloro[trifluoro]methyl-4,5-dihydro-1 H-pyrazole-1-carboxylate, have been determined by X-ray diffractometry. The data demonstrated that the molecular packing was stabilized mainly by O sbnd H⋯O hydrogen bonds of the 5-hydroxy and 1-carboxymethyl groups. The 4,5-dihydro-1 H-pyrazole rings were obtained as almost planar structures showing RMS deviation at a range of 0.0052-0.0805 Å. Additionally, computational investigation using semi-empirical AM1 and PM3 methods were performed to find a correlation between experimental and calculated geometrical parameters. The data obtained suggest that the structural data furnished by the AM1 method is in better agreement with those experimentally determined for the above compounds.

  19. 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.

  20. Investigation on interaction and sonodynamic damage of fluorescein derivants to bovine serum albumin (BSA) under ultrasonic irradiation

    NASA Astrophysics Data System (ADS)

    Zou, Mingming; Zhang, Lei; Wang, Jun; Wang, Qi; Gao, Jingqun; Fan, Ping

    2013-06-01

    The fluorescein derivants (Fluorescein: (2-(6-Hydroxy-3-oxo-(3H)-xanthen-9-yl) benzoic acid), Fluorescein-DA: (Bis [N,N-bis (carboxymethyl) aminomethyl] fluorescein) and Fluorescein-DAsbnd Fe(III): (Bis [N,N-bis (carboxymethyl) aminomethyl] fluoresceinsbnd Ferrous(III)) with a tricyclic plane structure were used to study the interaction and sonodynamic damage to bovine serum albumin (BSA) under ultrasonic irradiation through fluorospectrometry and UV-vis spectrophotometry. Besides, because of the existence of Fe(III) ion in Fluorescein-DAsbnd Fe(III), under ultrasonic irradiation the sonocatalytic activity in the damage of BSA molecules was also found. Three-dimensional fluorescence spectra and three-dimensional fluorescence contour profile spectra were mentioned to determine the fluorescence quenching and the conformation change of BSA in the absence and presence of these fluorescein derivants. As judged from the experimental results, the fluorescence quenching of BSA in aqueous solution caused by these fluorescein derivants were all attributed to static quenching process. The damage degree and mode were related to some factors such as ultrasonic irradiation time, fluorescein derivant concentration and ionic strength. Finally, several quenchers were used to determine the amount and kind of generated reactive oxygen species (ROS) during sonodynamic and sonocatalytic reaction processes. It suggests that these fluorescein derivants induce protein damage via various ROS, at least, including singlet oxygen (1O2) and hydroxyl radicals (rad OH). Perhaps, this paper may offer some important subjects for broadening the application of these fluorescein derivants in sonodynamic therapy (SDT) and sonocatalytic therapy (SCT) technologies for tumor treatment.

  1. 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

  2. Social Anxiety, Acute Social Stress, and Reward Parameters Interact to Predict Risky Decision-Making among Adolescents

    PubMed Central

    Richards, Jessica M.; Patel, Nilam; Daniele, Teresa; MacPherson, Laura; Lejuez, C.W.; Ernst, Monique

    2014-01-01

    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 to 18 yo), characterized as having high or low social anxiety, participated in a 2-day study, 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

  3. 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+). PMID:23257345

  4. 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. PMID:26809976

  5. Derivative couplings and analytic gradients for diabatic states, with an implementation for Boys-localized configuration-interaction singles

    NASA Astrophysics Data System (ADS)

    Fatehi, Shervin; Alguire, Ethan; Subotnik, Joseph E.

    2013-09-01

    We demonstrate that Boys-localized diabatic states do indeed exhibit small derivative couplings, as is required of quasidiabatic states. In doing so, we present a general formalism for calculating derivative couplings and analytic gradients for diabatic states. We then develop additional equations specific to the case of Boys-localized configuration-interaction singles (CIS)—in particular, the analytic gradient of the CIS dipole matrix—and we validate our implementation against finite-difference results. In a forthcoming paper, we will publish additional algorithmic and computational details and apply our method to the Closs energy-transfer systems as a further test of the validity of Boys-localized diabatic states.

  6. 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

  7. 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.

  8. Technical note: Monte Carlo derivation of TG-43 dosimetric parameters for radiation therapy resources and 3M Cs-137 sources.

    PubMed

    Pérez-Calatayud, J; Granero, D; Ballester, F; Casal, E; Cases, R; Agramunt, S

    2005-08-01

    In clinical brachytherapy dosimetry, a detailed dose rate distribution of the radioactive source in water is needed in order to plan for quality treatment. Two Cs-137 sources are considered in this study; the Radiation Therapy Resources 67-800 source (Radiation Therapy Resources Inc., Valencia, CA) and the 3M model 6500/6D6C source. A complete dosimetric dataset for both sources has been obtained by means of the Monte Carlo GEANT4 code. Dose rate distributions are presented in two different ways; following the TG43 formalism and in a 2D rectangular dose rate table. This 2D dose rate table is helpful for the TPS quality control and is fully consistent with the TG43 dose calculation formalism. In this work, several improvements to the previously published data for these sources have been included: the source asymmetries were taken explicitly into account in the MC calculations, TG43 data were derived directly from MC calculations, the data radial range was increased, the angular grid in the anisotropy function was increased, and TG43 data is now consistent with the along and away dose rate table as recommended by the TG43 update. PMID:16193775

  9. Technical note: Monte Carlo derivation of TG-43 dosimetric parameters for radiation therapy resources and 3M Cs-137 sources

    SciTech Connect

    Perez-Calatayud, J.; Granero, D.; Ballester, F.; Casal, E.; Cases, R.; Agramunt, S.

    2005-08-15

    In clinical brachytherapy dosimetry, a detailed dose rate distribution of the radioactive source in water is needed in order to plan for quality treatment. Two Cs-137 sources are considered in this study; the Radiation Therapy Resources 67-800 source (Radiation Therapy Resources Inc., Valencia, CA) and the 3M model 6500/6D6C source. A complete dosimetric dataset for both sources has been obtained by means of the Monte Carlo GEANT4 code. Dose rate distributions are presented in two different ways; following the TG43 formalism and in a 2D rectangular dose rate table. This 2D dose rate table is helpful for the TPS quality control and is fully consistent with the TG43 dose calculation formalism. In this work, several improvements to the previously published data for these sources have been included: the source asymmetries were taken explicitly into account in the MC calculations, TG43 data were derived directly from MC calculations, the data radial range was increased, the angular grid in the anisotropy function was increased, and TG43 data is now consistent with the along and away dose rate table as recommended by the TG43 update.

  10. 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.

  11. 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.

  12. 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

  13. Surface functionalization and electronic interactions of ZnO nanorods with a porphyrin derivative.

    PubMed

    Klaumünzer, Martin; Kahnt, Axel; Burger, Alexandra; Mačković, Mirza; Münzel, Corinna; Srikantharajah, Rubitha; Spiecker, Erdmann; Hirsch, Andreas; Peukert, Wolfgang; Guldi, Dirk M

    2014-05-14

    To optimize electron transfer and optoelectronic properties in nanoparticulate thin films for electronics we show the surface functionalization of ZnO nanorods by means of replacing surface active 2-[2-(2-methoxyethoxy)ethoxy]acetic acid (TODA) by a redoxactive organic component, that is, 5,10,15,20-(phenoxyacetat)-porphyrin bearing four carboxylic acids as possible ZnO anchors. Microscopy-transmission electron microscopy-and spectroscopy-optical spectroscopy-verifies the successful and homogenous integration of the porphyrin onto the surface of ZnO nanorods, a process that is facilitated by the four anchoring groups. Photophysical investigations based on emission and absorption spectroscopy prompt to distinct electronic interactions between ZnO nanorods and the porphyrins. Consequently, we performed further photophysical studies flanked by pulse radiolysis assays to corroborate the nature of the electronic interactions. PMID:24665864

  14. Secondary phases formed during nuclear waste glass-water interactions: Thermodynamic and derived properties

    SciTech Connect

    McKenzie, W.F.

    1992-08-01

    The thermodynamic properties of secondary phases observed to form during nuclear waste glass-water interactions are of particular interest as it is with the application of these properties together with the thermodynamic properties of other solid phases, fluid phases, and aqueous species that one may predict the environmental consequences of introducing radionuclides contained in the glass into groundwater at a high-level nuclear waste repository. The validation of these predicted consequences can be obtained from laboratory experiments and field observations at natural analogue sites. The purpose of this report is to update and expand the previous compilation (McKenzie, 1991) of thermodynamic data retrieved from the literature and/or estimated for secondary phases observed to form (and candidate phases from observed chemical compositions) during nuclear waste glass-water interactions. In addition, this report includes provisionally recommended thermodynamic data of secondary phases.

  15. 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

  16. 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.

  17. Selective interaction of a soluble pentacene derivative with metallic single-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Liu, Cai-Hong; Liu, Yi-Yang; Zhang, Yong-Hui; Wei, Rui-Rui; Li, Bing-Rui; Zhang, Hao-Li; Chen, Yong

    2009-03-01

    We report a soluble pentacene derivative, 6,13-bis(2-(trimethylsilyl)ethynyl)pentacene, can be used for efficient extraction of metallic single-walled carbon nanotubes (SWCNTs), which is proven by resonance Raman spectroscopy (RRS), Vis-NIR absorption spectroscopy and conductivity measurements. RRS studies reveal that the separation is solvent-dependent and is more efficient for small diameter tubes. Theoretical simulation suggests that the adsorption of pentacene on (7, 7) metallic SWCNT is about 34% more favorable than that on (13, 0) semiconducting SWCNT. This work provides a new direction in seeking reagents to facilitate high efficiency and nondestructive separation of metallic and semiconducting SWCNTs.

  18. 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

  19. 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

  20. 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".

  1. 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.

  2. Shuttle derived atmospheric density model. Part 1: Comparisons of the various ambient atmospheric source data with derived parameters from the first twelve STS entry flights, a data package for AOTV atmospheric development

    NASA Technical Reports Server (NTRS)

    Findlay, J. T.; Kelly, G. M.; Troutman, P. A.

    1984-01-01

    The ambient atmospheric parameter comparisons versus derived values from the first twelve Space Shuttle Orbiter entry flights are presented. Available flights, flight data products, and data sources utilized are reviewed. Comparisons are presented based on remote meteorological measurements as well as two comprehensive models which incorporate latitudinal and seasonal effects. These are the Air Force 1978 Reference Atmosphere and the Marshall Space Flight Center Global Reference Model (GRAM). Atmospheric structure sensible in the Shuttle flight data is shown and discussed. A model for consideration in Aero-assisted Orbital Transfer Vehicle (AOTV) trajectory analysis, proposed to modify the GRAM data to emulate Shuttle experiments.

  3. Formation of Neuronal Circuits by Interactions between Neuronal Populations Derived from Different Origins in the Drosophila Visual Center.

    PubMed

    Suzuki, Takumi; Hasegawa, Eri; Nakai, Yasuhiro; Kaido, Masako; Takayama, Rie; Sato, Makoto

    2016-04-19

    A wide variety of neurons, including populations derived from different origins, are precisely arranged and correctly connected with their partner to establish a functional neural circuit during brain development. The molecular mechanisms that orchestrate the production and arrangement of these neurons have been obscure. Here, we demonstrate that cell-cell interactions play an important role in establishing the arrangement of neurons of different origins in the Drosophila visual center. Specific types of neurons born outside the medulla primordium migrate tangentially into the developing medulla cortex. During their tangential migration, these neurons express the repellent ligand Slit, and the two layers that the neurons intercalate between express the receptors Robo2 and Robo3. Genetic analysis suggests that Slit-Robo signaling may control the positioning of the layer cells or their processes to form a path for migration. Our results suggest that conserved axon guidance signaling is involved in the interactions between neurons of different origins during brain development. PMID:27068458

  4. Relation between Coda-Q and stress loaded to an elastic body. -parameters of material conditions derived by stochastic measurement-

    NASA Astrophysics Data System (ADS)

    Okamoto, K.; Mikada, H.; Goto, T.; Takekawa, J.

    2010-12-01

    Seismic coda is formed by superposed signals caused by scatterers. When heterogeneous condition is changed due to crustal deformations, coda-Q should vary reflecting the physical state if the materials. When the spatial scale of scatters in a medium becomes comparable with or smaller then the wavelength of seismic waves traveling through, it becomes very difficult to analyze the coda-wave quantitatively in terms of the location of scatterers, scattering mechanisms, etc. For inhomogeneous medium, it is natural to deal with stochastic methodologies to interpret seismic data. In this regard coda-Q has been frequently used as a stochastic measure of the medium in which seismic waves propagate. Since objectives of recent structural surveys include spatiotemporal or time-lapse variation of physical properties of underground medium, we propose a new geophysical monitoring method using the stochastic parameters if these parameters reflect changes of physical state of the medium. Several observed examples are reported that the relationship between the coda-Q and the number of earthquakes (e.g., Aki,2004). Aki (2004) said that the interrelation between the coda-Q and the number of earthquakes might be a key to understand the change in the state of crustal stress field. Here, we hypothesize that the change of the coda- Q reflects that of the stress magnitude and direction and try to focus on the relationship between the coda-Q and loaded stress which could cause earthquakes. The purpose of this study is to relate this relationship to non-stochastic quantity of the underground physical state, i.e., the stress to test our hypothesis. We employ two methods to achieve our objectives. One is Finite Difference Method (FDM), and the other is Boundary Integral Equation Method (BIEM). FDM is superior in the calculation of large field and saving calculation time. BIEM is superior in the free shape of boundaries. These two methods are applied to a numerical model of elastic body

  5. Correlation between optical coherence tomography-derived assessments of lower tear meniscus parameters and clinical features of dry eye disease

    PubMed Central

    Nguyen, Pho; Huang, David; Li, Yan; Sadda, Srinivas R.; Ramos, Sylvia; Pappuru, Rajeev R.; Yiu, Samuel C.

    2011-01-01

    Purpose To measure the correlation between subjective symptom score, conventional clinical tests, and Fourier-domain optical coherence tomography (FD-OCT) of lower tear meniscus parameters in patients with dry eye disease. Methods Eighteen patients with dry eye disease requiring medical therapy and/or punctal occlusion were recruited for this prospective, nonrandomized, observational case series. Severity of symptoms of dry eye disease was assessed using the Indiana Dry Eye Questionnaire 2002. Clinical assessments were completed using slit-lamp biomicroscopy, rose bengal dye staining, fluorescein tear break-up time (TBUT), and 5-minute Schirmer’s test with topical anesthesia. The lower tear meniscus was imaged using a FD-OCT system with 5-μm axial resolution and measured manually by a masked grader using computer calipers. Correlation was assessed using Spearman’s correlation coefficient (ρ). Results The mean scaled symptom score was 58 ± 21 (±SD), with a range of 0 to 100. Vital staining test averaged 1.7 ± 3.4, TBUT averaged 4.4 ± 1.8 seconds, and Schirmer’s tests averaged 10.2 ± 8.1 mm. As determined by OCT, the meniscus height was 228 ± 153 μm, depth was 127 ± 79 μm, and cross-sectional area was 0.018 ± 0.021 mm2. OCT meniscus area was negatively correlated with the symptom questionnaire score (P < 0.01) and positively correlated with Schirmer’s test results (P < 0.01). There was no significant correlation between symptom score and rose bengal staining, TBUT, or Schirmer’s test results (P > 0.01). Conclusions Lower tear meniscus measurement with FD-OCT is an objective, noninvasive test that correlates well with symptoms of dry eye disease and the Schirmer’s test. PMID:22378111

  6. Quantifying the uncertainty of Landsat tm derived energy balance parameters in the discontinuous permafrost zone: A Monte Carlo approach

    NASA Astrophysics Data System (ADS)

    Johnson, A.; Stoy, P.; Ewing, S. A.

    2013-12-01

    High latitude regions are proving to be highly sensitive to climatic change as indicated by shifts in plant communities and other surface properties. Such transitions in the vegetated surface result in differences in the absorption and partitioning of incident solar radiation with uncertain consequences for regional climate. Simple descriptions of surface and subsurface changes over time in the discontinuous permafrost zone often remain elusive because of the complex spatial patterning of vegetated surface. The analysis of remote sensing data to determine the spatial extent and location of different surface features, and their changes, provides a means to track the temporal changes that have occurred since the dawn of of the remote sensing data record. Here, we evaluate the uncertainties associated with generating albedo from Landsat tm. There are two primary sources of uncertainty in the albedo product generated from Landsat; uncertainty associated with coefficients assigned to Landsat bands for generating albedo, and uncertainty in the raw digital remote sensing values. We employed a Monte Carlo method of random parameter generation and implementation of these coefficients to characterize changes to and uncertainty in Landsat albedo in an area of pronounced thaw in the discontinuous permafrost zone in west-central Alaska. The motivation for the uncertainty analysis is to quantify significant changes to land surface properties over time. Results indicate that the overall variability in the albedo layer is not strongly impacted by the coefficients applied to the Landsat data bands, and more affected by the variance within the Landsat data (Figure 1). Changes in albedo over the past 40 years tend to be concentrated along the edges of existing features, especially lakes.

  7. 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.

  8. Huntingtin-associated Protein-1 Interacts with Pro-brain-derived Neurotrophic Factor and Mediates Its Transport and Release*

    PubMed Central

    Wu, Linda Lin-yan; Fan, Yongjun; Li, Shihua; Li, Xiao-Jiang; Zhou, Xin-Fu

    2010-01-01

    Brain-derived neurotrophic factor (BDNF) plays a pivotal role in brain development and synaptic plasticity. It is synthesized as a precursor (pro-BDNF), sorted into the secretory pathway, transported along dendrites and axons, and released in an activity-dependent manner. Mutant Huntingtin with expanded polyglutamine (polyQ) and the V66M polymorphism of BDNF reduce the dendritic distribution and axonal transport of BDNF. However, the mechanism underlying this defective transport remains unclear. Here, we report that Huntingtin-associated protein-1 (HAP1) interacts with the prodomain of BDNF and that the interaction was reduced in the presence of polyQ-expanded Huntingtin and BDNF V66M. Consistently, there was reduced coimmunoprecipitation of pro-BDNF with HAP1 in the brain homogenate of Huntington disease. Pro-BDNF distribution in the neuronal processes and its accumulation in the proximal and distal segments of crushed sciatic nerve and the activity-dependent release of pro-BDNF were abolished in HAP1−/− mice. These results suggest that HAP1 may participate in axonal transport and activity-dependent release of pro-BDNF by interacting with the BDNF prodomain. Accordingly, the decreased interaction between HAP1 and pro-BDNF in Huntington disease may reduce the release and transport of BDNF. PMID:19996106

  9. 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

  10. Inhibition of Human Aldehyde Oxidase Activity by Diet-Derived Constituents: Structural Influence, Enzyme-Ligand Interactions, and Clinical Relevance

    PubMed Central

    Barr, John T.; Jones, Jeffrey P.; Oberlies, Nicholas H.

    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 O6-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 (r2 = 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

  11. 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

  12. 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.

  13. Pharmacokinetic characteristics of N7-substituted theophylline derivatives and their interaction with quinolone in rats.

    PubMed

    Hasegawa, T; Nadai, M; Apichartpichean, R; Muraoka, I; Nabeshima, T; Takagi, K

    1991-10-01

    Disposition of diprophylline (DPP) and proxyphylline (PXP) and the effect of enoxacin on their disposition were investigated in rats. Concentrations of the two drugs in plasma and urine were measured by HPLC. The pharmacokinetic parameters of the two drugs were estimated by model-independent methods. Although the chemical structures of the two drugs are very similar, remarkable differences in the disposition of the two drugs were observed. Total body clearance (CLT) of DPP was 1.77 L/h/kg, which was sevenfold greater than that of PXP (0.26 L/h/kg). Diprophylline was excreted in an almost completely unchanged form in the urine, but only 50% of PXP was excreted. However, no binding of either drug to proteins in rat plasma was observed. The DPP renal clearance (CLR) was 1.75 L/h/kg, approximately 13-fold the CLR for PXP (0.13 L/h/kg) and sevenfold the rat glomerular filtration rate. This study indicates that in rats, DPP is mainly excreted by active tubular secretion and that renal tubular reabsorption contributes to renal excretion of PXP with glomerular filtration. No significant changes in any pharmacokinetic parameters of the two drugs were observed when they were coadministered with enoxacin, compared with the drug administered alone, suggesting that enoxacin had no effect on the pharmacokinetics of either drug. PMID:1664467

  14. In vitro interaction of Stenotrophomonas maltophilia with human monocyte-derived dendritic cells

    PubMed Central

    Roscetto, Emanuela; Vitiello, Laura; Muoio, Rosa; Soriano, Amata A.; Iula, Vita D.; Vollaro, Antonio; Gregorio, Eliana De; 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. PMID:26236302

  15. More on closed string induced higher derivative interactions on D-branes

    NASA Astrophysics Data System (ADS)

    Hatefi, Ehsan; Park, I. Y.

    2012-06-01

    In our continued efforts of matching full string computations with the corresponding effective field theory computations, we evaluate string theory correlators in closed forms. In particular, we consider a correlator between three super Yang-Mills vertex operators and one Ramond-Ramond C-field vertex operator: ⟨VCVϕVAVA⟩. We show that the infinite number of massless poles of this amplitude can be reproduced by the Born-Infeld action, the Wess-Zumino terms, and their higher derivative corrections. More specifically, we find, up to an on-shell ambiguity, two scalar field and two gauge field couplings to all orders in α' such that the infinite number of massless poles of the field theory amplitude exactly match the infinite number of massless poles of the S-matrix elements of ⟨VCVϕVAVA⟩. We comment on the close intertwinedness of an open string and a closed string that must be behind the matching.

  16. 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

  17. Tumor response parameters for head and neck cancer derived from tumor-volume variation during radiation therapy

    SciTech Connect

    Chvetsov, Alexei V.

    2013-03-15

    -and-neck squamous cell carcinoma (SCC) is equal to 3.8 mean potential doubling times, which agrees with 4.0 mean potential doubling times obtained previously for lung SCC. Conclusions: The distribution of cell survival fractions obtained in this study support the hypothesis that the tumor-volume variation during radiotherapy treatment for head and neck cancer can be described by the two-level cell population tumor-volume model. This model can be used for in vivo evaluation of patient-specific radiobiological parameters that are needed for tumor-control probability evaluation.

  18. The fluorescent interactions between amphiphilic chitosan derivatives and water-soluble quantum dots.

    PubMed

    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. PMID:26232578

  19. 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

  20. Prevention of thermally induced aggregation of IgG antibodies by noncovalent interaction with poly(acrylate) derivatives.

    PubMed

    Martin, Nicolas; Ma, Dewang; Herbet, Amaury; Boquet, Didier; Winnik, Françoise M; Tribet, Christophe

    2014-08-11

    Prevention of thermal aggregation of antibodies in aqueous solutions was achieved by noncovalent association with hydrophobically modified poly(acrylate) copolymers. Using a polyclonal immunoglobin G (IgG) as a model system for antibodies, we have studied the mechanisms by which this multidomain protein interacts with polyanions when incubated at physiological pH and at temperatures below and above the protein unfolding/denaturation temperature, in salt-free solutions and in 0.1 M NaCl solutions. The polyanions selected were sodium poly(acrylates), random copolymers of sodium acrylate and N-n-octadecylacrylamide (3 mol %), and a random copolymer of sodium acrylate, N-n-octylacrylamide (25 mol %), and N-isopropylacrylamide (40 mol %). They were derived from two poly(acrylic acid) parent chains of Mw 5000 and 150000 g·mol(-1). The IgG/polyanion interactions were monitored by static and dynamic light scattering, fluorescence correlation spectroscopy, capillary zone electrophoresis, and high sensitivity differential scanning calorimetry. In salt-free solutions, the hydrophilic PAA chains form complexes with IgG upon thermal unfolding of the protein (1:1 w/w IgG/PAA), but they do not interact with native IgG. The complexes exhibit a remarkable protective effect against IgG aggregation and maintain low aggregation numbers (average degree of oligomerization <12 at a temperature up to 85 °C). These interactions are screened in 0.1 M NaCl and, consequently, PAAs lose their protective effect. Amphiphilic PAA derivatives (1:1 w/w IgG/polymer) are able to prevent thermal aggregation (preserving IgG monomers) or retard aggregation of IgG (formation of oligomers and slow growth), revealing the importance of both hydrophobic interactions and modulation of the Coulomb interactions with or without NaCl present. This study leads the way toward the design of new formulations of therapeutic proteins using noncovalent 1:1 polymer/protein association that are transient and require a

  1. 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

  2. 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

  3. 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.

  4. Missing derivative discontinuity of the exchange-correlation energy for attractive interactions: The charge Kondo effect

    NASA Astrophysics Data System (ADS)

    Perfetto, E.; Stefanucci, G.

    2012-08-01

    We show that the energy functional of ensemble density functional theory (DFT) [Perdew , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.49.1691 49, 1691 (1982)] in systems with attractive interactions is a convex function of the fractional particle number N and is given by a series of straight lines joining a subset of ground-state energies. As a consequence the exchange-correlation (XC) potential is not discontinuous for all N. We highlight the importance of this exact result in the ensemble-DFT description of the negative-U Anderson model. In the atomic limit the discontinuity of the XC potential is missing for odd N while for finite hybridizations the discontinuity at even N is broadened. We demonstrate that the inclusion of these properties in any approximate XC potential is crucial to reproduce the characteristic signatures of the charge-Kondo effect in the conductance and charge susceptibility.

  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. Analysis of expressed sequence tags derived from a compatible Mycosphaerella fijiensis-banana interaction.

    PubMed

    Portal, Orelvis; Izquierdo, Yovanny; De Vleesschauwer, David; Sánchez-Rodríguez, Aminael; Mendoza-Rodríguez, Milady; Acosta-Suárez, Mayra; Ocaña, Bárbara; Jiménez, Elio; Höfte, Monica

    2011-05-01

    Mycosphaerella fijiensis, a hemibiotrophic fungus, is the causal agent of black leaf streak disease, the most serious foliar disease of bananas and plantains. To analyze the compatible interaction of M. fijiensis with Musa spp., a suppression subtractive hybridization (SSH) cDNA library was constructed to identify transcripts induced at late stages of infection in the host and the pathogen. In addition, a full-length cDNA library was created from the same mRNA starting material as the SSH library. The SSH procedure was effective in identifying specific genes predicted to be involved in plant-fungal interactions and new information was obtained mainly about genes and pathways activated in the plant. Several plant genes predicted to be involved in the synthesis of phenylpropanoids and detoxification compounds were identified, as well as pathogenesis-related proteins that could be involved in the plant response against M. fijiensis infection. At late stages of infection, jasmonic acid and ethylene signaling transduction pathways appear to be active, which corresponds with the necrotrophic life style of M. fijiensis. Quantitative PCR experiments revealed that antifungal genes encoding PR proteins and GDSL-like lipase are only transiently induced 30 days post inoculation (dpi), indicating that the fungus is probably actively repressing plant defense. The only fungal gene found was induced 37 dpi and encodes UDP-glucose pyrophosphorylase, an enzyme involved in the biosynthesis of trehalose. Trehalose biosynthesis was probably induced in response to prior activation of plant antifungal genes and may act as an osmoprotectant against membrane damage. PMID:21279642

  7. 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

  8. 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

  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. Physiochemical characterization of the nisin-membrane interaction with liposomes derived from Listeria monocytogenes.

    PubMed Central

    Winkowski, K; Ludescher, R D; Montville, T J

    1996-01-01

    Mechanistic information about the bacteriocin nisin was obtained by examining the efflux of 5(6)-carboxy-fluorescein from Listeria monocytogenes-derived liposomes. The initial leakage rate (percentage of efflux per minute) of the entrapped dye was dependent on both nisin and lipid concentrations. At all nisin concentrations tested, 5(6)-carboxyfluorescein efflux plateaued before all of the 5(6)-carboxyfluorescein was released (suggesting that pore formation was transient), but efflux resumed when more nisin was added. Isotherms for the binding of nisin to liposomes constructed on the basis of the Langmuir isotherm gave an apparent binding constant of 6.2 x 10(5)M(-1) at pH 6.0. The critical number of nisin molecules required to induce efflux from liposomes at pH 6.0 was approximately 7,000 molecules per liposome. The pH affected the 5(6)-carboxyfluorescein leakage rates, with higher pH values resulting in higher leakage rates. The increased leakage rate observed at higher pH values was not due to an increase in the binding affinity of the nisin molecules towards the liposomal membrane. Rather, the critical number of nisin molecules required to induce activity was decreased (approximately 1,000 nisin molecules per liposome at pH 7.0). These data are consistent with a poration mechanism in which the ionization state of histidine residues in nisin plays an important role in membrane permeabilization. PMID:8593036

  12. 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.

  13. 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.

  14. Influence of aminopyrimidyl derivatives on the supramolecular architectures and abundant nonvalent interactions of silver 5-nitroisophthalate coordination polymers

    NASA Astrophysics Data System (ADS)

    Sun, Di; Luo, Geng-Geng; Zhang, Na; Wei, Zhan-Hua; Yang, Cheng-Feng; Xu, Qin-Juan; Huang, Rong-Bin; Zheng, Lan-Sun

    2010-04-01

    Two 5-nitroisophthalate silver(I) coordination polymers with 2-aminopyrimidyl derivatives, namely [Ag 2(apym) 1.5(nipa)·H 2O] n ( 1) and [Ag 2(dmapym) 2(nipa)] n ( 2) were synthesized and characterized by single-crystal X-ray analysis (apym = 2-aminopyrimidine, dmapym = 2-amino-4,6-dimethylprimidine, H 2nipa = 5-nitroisophthalic acid). Complex 1 possesses a one-dimensional (1D) structure built from rhombic [Ag 4(apym) 2(nipa) 2] second building units (SBUs). The uncoordinated O nitro is involved in the significant lone-pair (lp)⋯π interaction with the benzene ring of nipa. Complex 2 possesses a two-dimensional (2D) structure in which dmapym ligands show two different coordination modes, monodentate and bidentate, respectively. Moreover, 2 shows abundant nonvalent interactions, such as lp(O carboxyl)⋯π, π⋯π, C-H⋯π interactions and hydrogen-bonding simultaneously. 1 and 2 also exhibit diverse structure motifs due to the effects of substituent methyl groups. The photoluminescence properties of these complexes also were examined.

  15. Epigenetic and epistatic interactions between serotonin transporter and brain-derived neurotrophic factor genetic polymorphism: insights in depression.

    PubMed

    Ignácio, Z M; Réus, G Z; Abelaira, H M; Quevedo, J

    2014-09-01

    Epidemiological studies have shown significant results in the interaction between the functions of brain-derived neurotrophic factor (BDNF) and 5-HT in mood disorders, such as major depressive disorder (MDD). The latest research has provided convincing evidence that gene transcription of these molecules is a target for epigenetic changes, triggered by stressful stimuli that starts in early childhood and continues throughout life, which are subsequently translated into structural and functional phenotypes culminating in depressive disorders. The short variants of 5-HTTLPR and BDNF-Met are seen as forms which are predisposed to epigenetic aberrations, which leads individuals to a susceptibility to environmental adversities, especially when subjected to stress in early life. Moreover, the polymorphic variants also feature epistatic interactions in directing the functional mechanisms elicited by stress and underlying the onset of depressive disorders. Also emphasized are works which show some mediators between stress and epigenetic changes of the 5-HTT and BDNF genes, such as the hypothalamic-pituitary-adrenal (HPA) axis and the cAMP response element-binding protein (CREB), which is a cellular transcription factor. Both the HPA axis and CREB are also involved in epistatic interactions between polymorphic variants of 5-HTTLPR and Val66Met. This review highlights some research studying changes in the epigenetic patterns intrinsic to genes of 5-HTT and BDNF, which are related to lifelong environmental adversities, which in turn increases the risks of developing MDD. PMID:24972302

  16. Two new isoforms of the human hepatoma-derived growth factor interact with components of the cytoskeleton.

    PubMed

    Nüße, Jessica; Mirastschijski, Ursula; Waespy, Mario; Oetjen, Janina; Brandes, Nadine; Rebello, Osmond; Paroni, Federico; Kelm, Sørge; Dietz, Frank

    2016-05-01

    Hepatoma-derived growth factor (HDGF) is involved in diverse, apparently unrelated processes, such as cell proliferation, apoptosis, DNA-repair, transcriptional control, ribosome biogenesis and cell migration. Most of the interactions of HDGF with diverse molecules has been assigned to the hath region of HDGF. In this study we describe two previously unknown HDGF isoforms, HDGF-B and HDGF-C, generated via alternative splicing with structurally unrelated N-terminal regions of their hath region, which is clearly different from the well described isoform, HDGF-A. In silico modeling revealed striking differences near the PHWP motif, an essential part of the binding site for glycosaminoglycans and DNA/RNA. This observation prompted the hypothesis that these isoforms would have distinct interaction patterns with correspondingly diverse roles on cellular processes. Indeed, we discovered specific associations of HDGF-B and HDGF-C with cytoskeleton elements, such as tubulin and dynein, suggesting previously unknown functions of HDGF in retrograde transport, site directed localization and/or cytoskeleton organization. In contrast, the main isoform HDGF-A does not interact directly with the cytoskeleton, but via RNA with messenger ribonucleoprotein (mRNP) complexes. In summary, the discovery of HDGF splice variants with their discrete binding activities and subcellular distributions opened new avenues for understanding its biological function and importance. PMID:26845719

  17. 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

  18. 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

  19. Interaction of neutrophils with vascular smooth muscle: identification of a neutrophil-derived relaxing factor.

    PubMed

    Rimele, T J; Sturm, R J; Adams, L M; Henry, D E; Heaslip, R J; Weichman, B M; Grimes, D

    1988-04-01

    Experiments were designed to study the interaction of rat peritoneal neutrophils with the vascular smooth muscle of the rat aorta. Rings of aorta, suspended in 10-ml organ chambers containing a physiologic salt solution, were precontracted with phenylephrine. Neutrophils (1 X 10(5) -4 X 10(7) cells/organ chamber) caused a cell number-dependent relaxation of the rat aorta that was augmented by superoxide dismutase (100 U/ml) or changing the oxygen content from 95 to 21%. The neutrophil-induced smooth muscle relaxation occurred in rings with and without endothelium and in rings precontracted with increasing concentrations of phenylephrine, prostaglandin F2 alpha or KCI. Catalase (1000 U/ml) and mannitol (1 X 10(-3) M) did not block the neutrophil-induced relaxation, whereas phenazine methosulfate (1 X 10(-5) M), hydroquinone (3 X 10(-5) M) and methylene blue (1 X 10(-5) M) reversed the neutrophil-induced relaxation. Pre-exposure of endothelium-rubbed rings to neutrophils (2 X 10(7) cells/organ chamber; 15 min) depressed the subsequent concentration-response curve to phenylephrine but augmented the relaxation induced by the phosphodiesterase inhibitor zaprinast (1 X 10(-5) M). The effluent from a column restraining the neutrophils induced a relaxation of endothelium-rubbed aortic rings that was prevented by methylene blue (1 X 10(-5) M). These results demonstrate that rat neutrophils release a factor that has a pharmacologic profile similar to that previously reported for the relaxing factor released from the vascular endothelium. PMID:3129547

  20. 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

  1. 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

  2. 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.

  3. 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

  4. A structural study of the interaction between the Dr haemagglutinin DraE and derivatives of chloramphenicol

    SciTech Connect

    Pettigrew, David M.; Roversi, Pietro; Davies, Stephen G.; Russell, Angela J.; Lea, Susan M.

    2009-06-01

    The structures of two Dr adhesin (DraE) complexes with chloramphenicol derivatives, namely chloramphenicol succinate and bromamphenicol, have been solved. The structures reveal important functional groups for small-molecule binding and imply possible modifications to the molecule that would permit a more wide-ranging interaction without the toxic side effects associated with chloramphenicol. Dr adhesins are expressed on the surface of uropathogenic and diffusely adherent strains of Escherichia coli. The major adhesin subunit (DraE/AfaE) of these organelles mediates attachment of the bacterium to the surface of the host cell and possibly intracellular invasion through its recognition of the complement regulator decay-accelerating factor (DAF) and/or members of the carcinoembryonic antigen (CEA) family. The adhesin subunit of the Dr haemagglutinin, a Dr-family member, additionally binds type IV collagen and is inhibited in all its receptor interactions by the antibiotic chloramphenicol (CLM). In this study, previous structural work is built upon by reporting the X-ray structures of DraE bound to two chloramphenicol derivatives: chloramphenicol succinate (CLS) and bromamphenicol (BRM). The CLS structure demonstrates that acylation of the 3-hydroxyl group of CLM with succinyl does not significantly perturb the mode of binding, while the BRM structure implies that the binding pocket is able to accommodate bulkier substituents on the N-acyl group. It is concluded that modifications of the 3@@hydroxyl group would generate a potent Dr haemagglutinin inhibitor that would not cause the toxic side effects that are associated with the normal bacteriostatic activity of CLM.

  5. 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

  6. 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.

  7. 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

  8. In vitro inhibition of beta-haematin formation, DNA interactions, antiplasmodial activity, and cytotoxicity of synthetic neocryptolepine derivatives.

    PubMed

    Van Miert, Sabine; Jonckers, Tim; Cimanga, Kanyanga; Maes, Louis; Maes, Bert; Lemière, Guy; Dommisse, Roger; Vlietinck, Arnold; Pieters, Luc

    2004-01-01

    Neocryptolepine, a minor alkaloid of Cryptolepis sanguinolenta, was investigated as a lead for new antiplasmodial agents, because of its lower cytotoxicity than cryptolepine, the major alkaloid. Synthetic 2- or 3-substituted neocryptolepine derivatives were evaluated for their biological activity. In addition to the antiplasmodial activity (Plasmodium falciparum chloroquine-sensitive and -resistant) also the cytotoxicity (MRC-5 cells) was determined. Several compounds such as 2-bromoneocryptolepine showing higher and more selective antiplasmodial activity than neocryptolepine were obtained. Several functional assays and in vitro tests were used to obtain additional information on the mechanism of action, i.e., the beta-haematin formation inhibitory assay (detoxification of haem) and the DNA-methylgreen displacement assay (interaction with DNA). It could be demonstrated that the 2- or 3-substituted neocryptolepine derivatives investigated here have about the same potency to inhibit the beta-haematin formation as chloroquine, indicating that inhibition of haemozoin formation makes at least an important contribution to their antiplasmodial activity, although their in vitro antiplasmodial activity is still less than chloroquine. PMID:15582513

  9. Climate parameters of Estonia and the Baltic Sea region derived from the high-resolution reanalysis database BaltAn65+

    NASA Astrophysics Data System (ADS)

    Männik, Aarne; Zirk, Marko; Rõõm, Rein; Luhamaa, Andres

    2015-10-01

    The high-resolution reanalysis data-base BaltAn65+ covers the period of 1965-2005. Here, this dataset is used to derive essential climate parameters for the Baltic Sea region and Estonia. In particular, monthly mean temperature and total precipitation are calculated and a trend analysis is performed to analyze the temporal evolution of these climatological parameters during the reanalysis period. Monthly, seasonal, and annual maps of the climate characteristics, including trend maps, are created for the Baltic Sea region. Time series of monthly and annually averaged temperature and precipitation sum are presented over the Baltic Sea and Estonian domains together with fitted linear trends and trend significance analysis. Then, comparison with an observational database is performed to assess the quality of the reanalysis database. Additionally, the time series are compared with official climate normals for the period of 1971-2000, as calculated by the Estonian Environment Agency (EtEA). Findings of other publications in the scientific literature dealing with the climate of similar time period for Estonia and the Baltic Sea region are discussed. The quality of the BaltAn65+ reanalysis is found to be generally good for temperature but weak for precipitation.

  10. Synthesis, cytotoxicity assessment, and interaction and docking of novel palladium(II) complexes of imidazole derivatives with human serum albumin.

    PubMed

    Eslami Moghadam, Mahboube; Divsalar, Adeleh; Abolhosseini Shahrnoy, Abdolghafar; Saboury, Ali Akbar

    2016-08-01

    Imidazole analogs are the agents that attract both bioinorganic chemist and drug designer. Numerous methods have been proposed for synthesis of imidazole derivatives. In this study, a series of heterocyclic system with p-conjugated system such as 2-aryl-imidazo[4,5-f][1,10]phenanthroline analogs were synthesized. Then, three new palladium(II) complexes containing 2-(Furan-2-yl)-1H-Imidazo[4,5-f][1,10]Phenanthroline (FIP) and 2-(thiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (TIP) ligands were synthesized. The structures of the compounds, [Pd(Phen)(TIP)](NO3)2, [Pd(Phen)(FIP)](NO3)2, and [Pd(FIP)2]Cl were determined by spectroscopic methods and elemental analysis. Biological activity of the complexes synthesized was assessed against chronic myelogenous leukemia cell line, K562. Also, the interactions of human serum albumin with complexes were investigated using isothermal titration in the Tris buffer, pH 7.4. According to the results obtained, it was found that there is a set of six binding sites for these complexes on HSA with positive cooperativity in the binding process. Docking technique was also applied to confirm the experimental results. The results showed that smaller complexes have higher interaction affinity. PMID:26338667

  11. Competitive Interactions of Collagen and a Jararhagin-derived Disintegrin Peptide with the Integrin α2-I Domain*

    PubMed Central

    Lambert, Lester J.; Bobkov, Andrey A.; Smith, Jeffrey W.; Marassi, Francesca M.

    2008-01-01

    Integrin α2β1 is a major receptor required for activation and adhesion of platelets, through the specific recognition of collagen by the α2-I domain (α2-I), which binds fibrillar collagen via Mg2+-bridged interactions. The crystal structure of a truncated form of the α2-I domain, bound to a triple helical collagen peptide, revealed conformational changes suggestive of a mechanism where the ligand-bound I domain can initiate and propagate conformational change to the full integrin complex. Collagen binding by α2-I and fibrinogen-dependent platelet activity can be inhibited by snake venom polypeptides. Here we describe the inhibitory effect of a short cyclic peptide derived from the snake toxin metalloprotease jararhagin, with specific amino acid sequence RKKH, on the ability of α2-I to bind triple helical collagen. Isothermal titration calorimetry measurements showed that the interactions of α2-I with collagen or RKKH peptide have similar affinities, and NMR chemical shift mapping experiments with 15N-labeled α2-I, and unlabeled RKKH peptide, indicate that the peptide competes for the collagen-binding site of α2-I but does not induce a large scale conformational rearrangement of the I domain. PMID:18417478

  12. PfCRT and PfMDR1 modulate interactions of artemisinin derivatives and ion channel blockers.

    PubMed

    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 Ca(2+) 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

  13. 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

  14. 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

  15. 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

  16. 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. PMID:24522406

  17. Fourier transform infrared spectroscopic and theoretical study of water interactions with glycine and its N-methylated derivatives.

    PubMed

    Panuszko, Aneta; Śmiechowski, Maciej; Stangret, Janusz

    2011-03-21

    In this study we attempt to explain the molecular aspects of amino acids' hydration. Glycine and its N-methylated derivatives: N-methylglycine, N,N-dimethylglycine, and N,N,N-trimethylglycine were used as model solutes in aqueous solution, applying FT-IR spectroscopy as the experimental method. The quantitative version of the difference spectra method enabled us to obtain the solute-affected HDO spectra as probes of influenced water. The spectral results were confronted with density functional theory calculated structures of small hydration complexes of the solutes using the polarizable continuum model. It appears that the hydration of amino acids in the zwitterionic form can be understood allowing a synchronized fluctuation of hydrogen bonding between the solute and the water molecules. This effect is caused by a noncooperative interaction of water molecules with electrophilic groups of amino acid and by intramolecular hydrogen bond, allowing proton transfer from the carboxylic to the amine group, accomplishing by the chain of two to four water molecules. As a result, an instantaneous water-induced asymmetry of the carboxylate and the amino group of amino acid molecule is observed and recorded as HDO band splitting. Water molecules interacting with the carboxylate group give component bands at 2543 ± 11 and 2467 ± 15 cm(-1), whereas water molecules interacting with protons of the amine group give rise to the bands at 2611 ± 15 and 2413 ± 12 cm(-1). These hydration effects have not been recognized before and there are reasons to expect their validity for other amino acids. PMID:21428668

  18. 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

  19. 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

  20. 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.

  1. ODPEVP: A program for computing eigenvalues and eigenfunctions and their first derivatives with respect to the parameter of the parametric self-adjoined Sturm-Liouville problem

    NASA Astrophysics Data System (ADS)

    Chuluunbaatar, O.; Gusev, A. A.; Vinitsky, S. I.; Abrashkevich, A. G.

    2009-08-01

    A FORTRAN 77 program is presented for calculating with the given accuracy eigenvalues, eigenfunctions and their first derivatives with respect to the parameter of the parametric self-adjoined Sturm-Liouville problem with the parametric third type boundary conditions on the finite interval. The program calculates also potential matrix elements - integrals of the eigenfunctions multiplied by their first derivatives with respect to the parameter. Eigenvalues and matrix elements computed by the ODPEVP program can be used for solving the bound state and multi-channel scattering problems for a system of the coupled second-order ordinary differential equations with the help of the KANTBP programs [O. Chuluunbaatar, A.A. Gusev, A.G. Abrashkevich, A. Amaya-Tapia, M.S. Kaschiev, S.Y. Larsen, S.I. Vinitsky, Comput. Phys. Commun. 177 (2007) 649-675; O. Chuluunbaatar, A.A. Gusev, S.I. Vinitsky, A.G. Abrashkevich, Comput. Phys. Commun. 179 (2008) 685-693]. As a test desk, the program is applied to the calculation of the potential matrix elements for an integrable 2D-model of three identical particles on a line with pair zero-range potentials, a 3D-model of a hydrogen atom in a homogeneous magnetic field and a hydrogen atom on a three-dimensional sphere. Program summaryProgram title: ODPEVP Catalogue identifier: AEDV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 3001 No. of bytes in distributed program, including test data, etc.: 24 195 Distribution format: tar.gz Programming language: FORTRAN 77 Computer: Intel Xeon EM64T, Alpha 21264A, AMD Athlon MP, Pentium IV Xeon, Opteron 248, Intel Pentium IV Operating system: OC Linux, Unix AIX 5.3, SunOS 5.8, Solaris, Windows XP RAM: depends on the number and order of finite

  2. Estimation of the effective parameter of spinorbital interaction of electrons in intermetallic Er-In system compounds from the kinetic and magnetic properties

    NASA Astrophysics Data System (ADS)

    Kuvandikov, O. K.; Hamraev, N. S.; Razhabov, R. M.; Éshkulov, A. A.

    2012-05-01

    Normal, R 0 and anomalous, R S components of the Hall coefficient are determined from the results of experimental investigations of temperature dependences of the Hall coefficient, magnetic susceptibility, and specific electrical resistance for intermetallic Er2In, ErIn, and Er3In5 compounds. Effective parameters of spinorbital interaction λSO of intermetallic compounds are calculated from anomalous components RS of the Hall coefficient and specific electrical resistance. The results calculated for the band parameters and effective parameters of spin-orbital interaction λSO for Er-In system intermetallides coincide by orders of magnitude with the results obtained in [4,7,8] from the optical spectra of pure rare-earth metals.

  3. 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

  4. Interaction of PiB-derivative metal complexes with beta-amyloid peptides: selective recognition of the aggregated forms.

    PubMed

    Martins, André F; Dias, David M; Morfin, Jean-François; Lacerda, Sara; Laurents, Douglas V; Tóth, Éva; Geraldes, Carlos F G C

    2015-03-27

    Metal complexes are increasingly explored as imaging probes in amyloid peptide related pathologies. We report the first detailed study on the mechanism of interaction between a metal complex and both the monomer and the aggregated form of Aβ1-40 peptide. We have studied lanthanide(III) chelates of two PiB-derivative ligands (PiB=Pittsburgh compound B), L(1) and L(2), differing in the length of the spacer between the metal-complexing DO3A macrocycle (DO3A=1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid) and the peptide-recognition PiB moiety. Surface plasmon resonance (SPR) and saturation transfer difference (STD) NMR spectroscopy revealed that they both bind to aggregated Aβ1-40 (KD =67-160 μM), primarily through the benzothiazole unit. HSQC NMR spectroscopy on the (15) N-labeled, monomer Aβ1-40 peptide indicates nonsignificant interaction with monomeric Aβ. Time-dependent circular dichroism (CD), dynamic light scattering (DLS), and TEM investigations of the secondary structure and of the aggregation of Aβ1-40 in the presence of increasing amounts of the metal complexes provide coherent data showing that, despite their structural similarity, the two complexes affect Aβ fibril formation distinctly. Whereas GdL(1), at higher concentrations, stabilizes β-sheets, GdL(2) prevents