Science.gov

Sample records for derived interaction parameters

  1. Theoretical derivation of solute-solvent interaction parameter in binary solution: case of the deviation from Raoult's law.

    PubMed

    Liron, Z; Srebrenik, S; Martin, A; Cohen, S

    1986-05-01

    In a binary mixture, partial vapor pressure may show either a positive or negative deviation from the predicted value of an ideal solution. In this report we derive the deviation from Raoult's law from the heat of mixing, delta H mix, and the molal volume, V, of each of the components of a binary solution. This derivation is then tested for seven sets of combinations of two different solvents, taken at random from the literature. Each set consists of several different ratios of solute-solvent. The correlation between the reported experimental values of the partial vapor pressure of a given component, P1, and the theoretically derived values is excellent. The same derivation is further applied to calculate the solute-solvent interaction parameter, beta 12, independently from the geometric mean assumption of regular solution theory. In a number of cases, especially in hydrocarbon-alcohol mixtures, beta 12 proves to be significantly different from the calculated geometric mean square root beta 11 beta 22 or from the Walker interaction parameter term, K. PMID:3735084

  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 individual experiment with respect to the solid of interest. The calculation of aqueous speciation and saturation indices was repeated by adjusting β(0), β(1), and Cφ in the database until the values are found that make the sum of squared saturation indices smallest for the given number of experiments. Preliminary results indicated that Mg2+ and FeCitrate- exhibit an insignificant interaction. The interaction of other pairs in the system are being investigated.

  3. Consequences of dark matter-dark energy interaction on cosmological parameters derived from type Ia supernova data

    SciTech Connect

    Amendola, Luca; Campos, Gabriela Camargo; Rosenfeld, Rogerio

    2007-04-15

    Models where the dark matter component of the Universe interacts with the dark energy field have been proposed as a solution to the cosmic coincidence problem, since in the attractor regime both dark energy and dark matter scale in the same way. In these models the mass of the cold dark matter particles is a function of the dark energy field responsible for the present acceleration of the Universe, and different scenarios can be parametrized by how the mass of the cold dark matter particles evolves with time. In this article we study the impact of a constant coupling {delta} between dark energy and dark matter on the determination of a redshift dependent dark energy equation of state w{sub DE}(z) and on the dark matter density today from SNIa data. We derive an analytical expression for the luminosity distance in this case. In particular, we show that the presence of such a coupling increases the tension between the cosmic microwave background data from the analysis of the shift parameter in models with constant w{sub DE} and SNIa data for realistic values of the present dark matter density fraction. Thus, an independent measurement of the present dark matter density can place constraints on models with interacting dark energy.

  4. The angular overlap model applied to the calculation of nuclear quadrupole interactions. Derivation of partial nuclear quadrupole interaction parameters for biological relevant ligands in cadmium complexes

    NASA Astrophysics Data System (ADS)

    Bauer, R.; Jensen, S. J.; Schmidt-Nielsen, B.

    1988-07-01

    By the application of the angular overlap model to the calculation of nuclear quadrupole interactions (NQI), it is shown that it is possible to predict the NQI for the111Cd nucleus in a cadmium complex with known coordination geometry. This fact makes it relevant to apply such calculations to nuclear quadrupole interaction data for111Cd substituted zinc enzymes. It is demonstrated that with an approximate knowledge about the geometry and type of protein ligands from X-ray diffractions, it is possible to extract knowledge about type and geometry of nonprotein ligands in zinc enzymes, such as coordination of water, anions, or substrate molecules.

  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. 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.

  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. Interactions between SH2 domains and tyrosine-phosphorylated platelet-derived growth factor beta-receptor sequences: analysis of kinetic parameters by a novel biosensor-based approach.

    PubMed Central

    Panayotou, G; Gish, G; End, P; Truong, O; Gout, I; Dhand, R; Fry, M J; Hiles, I; Pawson, T; Waterfield, M D

    1993-01-01

    The interaction between SH2 domains and phosphotyrosine-containing sequences was examined by real-time measurements of kinetic parameters. The SH2 domains of the p85 subunit of the phosphatidylinositol 3-kinase as well as of other signaling molecules were expressed in bacteria as glutathione S-transferase fusion proteins. Phosphotyrosine-containing peptides, corresponding to two autophosphorylation sites on the human platelet-derived growth factor beta-receptor that are responsible for phosphatidylinositol 3-kinase binding, were synthesized and used as capturing molecules, immobilized on a biosensor surface. The association and dissociation rate constants for binding to both sites were determined for intact p85 and the recombinant SH2 domains. High association rates were found to be coupled to very fast dissociation rates for all interactions studied. A binding specificity was observed for the two SH2 domains of p85, with the N-terminal SH2 binding with high affinity to the Tyr-751 site but not to the Tyr-740 site, and the C-terminal SH2 interacting strongly with both sites. This approach should be generally applicable to the study of the specificity inherent in the assembly of signaling complexes by activated protein-tyrosine kinase receptors. PMID:8388538

  9. 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 trajectory benchmark testing assessments with parachute inflation parameters, drag area, and reefing cutter timing used by CPAS.

  10. π-π interaction of quinacridone derivatives.

    PubMed

    Huang, Zhaowei; Sun, Hui; Zhang, Houyu; Wang, Yue; Li, Fei

    2011-07-30

    The π–π stacking interactions play an important role in molecular assemblies of quinacridone derivatives (QAs). In our previous work (Sun et al., J Phys Chem A 2008, 112, 11382), we have shown that quinacridone derivatives can be self-associated as dimers in solution by means of NMR study. Herein, we perform theoretical studies on the molecular interaction in the dimers of QAs to illustrate π–π interactions in terms of their strength, geometrical preference, substituent effect, and physical nature. Density functional theory (DFT-D) was adopted to calculate potential energy surfaces. The detailed analysis on the intermolecular interaction in diversity of dimeric configurations reveals that the displaced conformations with specific geometries in both parallel and antiparallel stacking manners can be stabilized, which are in agreement with NMR experimental findings. PMID:21541951

  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. 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.

  13. ParaGlide: interactive parameter space partitioning for computer simulations.

    PubMed

    Bergner, Steven; Sedlmair, Michael; Möller, Torsten; Abdolyousefi, Sareh Nabi; Saad, Ahmed

    2013-09-01

    In this paper, we introduce ParaGlide, a visualization system designed for interactive exploration of parameter spaces of multidimensional simulation models. To get the right parameter configuration, model developers frequently have to go back and forth between setting input parameters and qualitatively judging the outcomes of their model. Current state-of-the-art tools and practices, however, fail to provide a systematic way of exploring these parameter spaces, making informed decisions about parameter configurations a tedious and workload-intensive task. ParaGlide endeavors to overcome this shortcoming by guiding data generation using a region-based user interface for parameter sampling and then dividing the model's input parameter space into partitions that represent distinct output behavior. In particular, we found that parameter space partitioning can help model developers to better understand qualitative differences among possibly high-dimensional model outputs. Further, it provides information on parameter sensitivity and facilitates comparison of models. We developed ParaGlide in close collaboration with experts from three different domains, who all were involved in developing new models for their domain. We first analyzed current practices of six domain experts and derived a set of tasks and design requirements, then engaged in a user-centered design process, and finally conducted three longitudinal in-depth case studies underlining the usefulness of our approach. PMID:23846095

  14. Paraglide: Interactive Parameter Space Partitioning for Computer Simulations.

    PubMed

    Bergner, Steven; Sedlmair, Michael; Moller, Torsten; Nabi Abdolyousefi, Sareh; Saad, Ahmed

    2013-02-28

    In this paper we introduce ParaGlide, a visualization system designed for interactive exploration of parameter spaces of multi-dimensional simulation models. To get the right parameter configuration, model developers frequently have to go back and forth between setting input parameters and qualitatively judging the outcomes of their model. Current state-of-the-art tools and practices, however, fail to provide a systematic way of exploring these parameter spaces, making informed decisions about parameter configurations a tedious and workload-intensive task. ParaGlide endeavors to overcome this shortcoming by guiding data generation using a region-based user interface for parameter sampling and then dividing the model's input parameter space into partitions that represent distinct output behavior. In particular, we found that parameter space partitioning can help model developers to better understand qualitative differences among possibly high-dimensional model outputs. Further, it provides information on parameter sensitivity and facilitates comparison of models. We developed ParaGlide in close collaboration with experts from three different domains, who all were involved in developing new models for their domain. We first analyzed current practices of six domain experts and derived a set of tasks and design requirements, then engaged in a user-centered design process, and finally conducted three longitudinal in-depth case studies underlining the usefulness of our approach. PMID:23459287

  15. Comparison of ionospheric peak parameters derived from different modeling approaches

    NASA Astrophysics Data System (ADS)

    Mahdi Alizadeh, M.; Schuh, Harald

    2014-05-01

    Due to the fact that Ionosphere is a dispersive medium, microwave signals travelling through this medium are affected proportional to their frequencies. This effect allows gaining information about the parameters of the ionosphere in terms of Total Electron Content (TEC) or the electron density. There are different approaches for modeling these parameters. Some models are based on physical properties such as the Global Assimilative Ionospheric Model (GAIM). Some are empirical models, e.g. the International Reference Ionosphere (IRI), the NeQuick model, or the Neustrelitz TEC Model (NTCM). Finally some models are based on purely mathematical/statistical approaches. In the mathematical models, the corresponding model parameters are calculated using measurements from different space geodetic techniques or the ionosonde data. This study investigates different approaches for computing the electron density along the ray path. First the mathematical approach developed at Technical University of Berlin (TUB) for global 3D reconstruction of the ionospheric F2-peak parameters is presented. In this approach, the F2-peak parameters, i.e. the maximum electron density and its corresponding height are represented as a function of geographic or geomagnetic longitude, latitude, and height with two sets of spherical harmonic expansions of degree and order 15, which correspond to a spatial resolution of 5° in longitude and 2.5° in latitude. To assess this modeling approach, the estimated F2-peak parameters are compared with the peak parameters derived from several other modeling approaches.

  16. 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.

  17. Deriving the microstructural parameters of sea foam from experimental measurements

    NASA Astrophysics Data System (ADS)

    Chan, Wai Soen; Lee, Hon Ping; Yu, Kin Wah

    2014-03-01

    We have studied the effective dielectric constant of sea foam by exploiting its spectral structure. We have considered sea foam as a two-phase composite containing air and sea water, at scale where the quasi-static limit is valid. McPhedran and co-workers derived tight bounds of the structural parameters of such composite when a set of measured data is given. However, determining the exact structural parameters have not been successful. We have performed an inverse algorithm, attempted to determine the structure of the foam given measured data of dielectric constant. We model the sea foam by a multilayered Hashin-Shtrikman structure consisting of air embedded in sea water with decreasing air volume fraction from the top to bottom. We first express the effective permittivity of the foam using spectral representation as proposed by Bergman and Milton. Then, by an optimization approach, we determine the spectral parameters, namely the zeros and poles. Next, we convert these spectral parameters into structural parameters by an algorithm proposed by Sun and Yu. Hence the structure of foam could be determined. The inverse problem of determining the sea foam structure is important in marine science. Sea surface wind speed and salinity could be determined from properties of sea foam.

  18. 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

  19. Analytic partial derivatives for estimating low-thrust parameters.

    NASA Technical Reports Server (NTRS)

    Cunningham, G. W.

    1972-01-01

    Analytic partial derivatives for estimating orbital low-thrust parameters via differential correction are developed and compared with two different numerical methods. The formulation is independent of the particular thrust model used and is applicable to all physically possible elliptic orbits. The starting point for the development is the set of variational equations of the elliptic orbital elements in the form due to Lagrange. The first time derivatives of the elements are transformed to derivatives with respect to the space variable, true anomaly, and integrated to first order in closed form in a straightforward general perturbations approach, with one exception: particular attention is given to the mean anomaly as influenced by thrust perturbations in the semimajor axis so that the complete first-order effect is included. The partials of the elements are then taken with respect to any given thrust parameter. Two comparisons are made with numerical methods for computing these thrust partials: numerical quotients and numerical integration of the variational equations for thrust.

  20. Satellite observation of atmosphere and surface interaction parameters

    NASA Technical Reports Server (NTRS)

    Chahine, Moustafa T.; Haskins, Robert D.; Susskind, Joel; Reuter, Dennis

    1987-01-01

    Atmosphere and ocean surface parameters are being derived from weather satellite data acquired by the High Resolution Infrared Sounder and the Microwave Sounding Unit. In this paper, the global distribution and accuracy of the derived parameters are described, and the satellite-derived skin surface temperature is compared with available shelter temperature. Seasonal and interannual changes are examined to study the response time of large-scale atmospheric changes to changes in surface conditions.

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

    NASA Astrophysics Data System (ADS)

    Weigand, M.; Kemna, A.

    2016-03-01

    Spectral induced polarisation (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 polarisation 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 % 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.

  2. Antisense DNA parameters derived from next-nearest-neighbor analysis of experimental data

    PubMed Central

    2010-01-01

    Background The enumeration of tetrameric and other sequence motifs that are positively or negatively correlated with in vivo antisense DNA effects has been a useful addition to the arsenal of information needed to predict effective targets for antisense DNA control of gene expression. Such retrospective information derived from in vivo cellular experiments characterizes aspects of the sequence dependence of antisense inhibition that are not predicted by nearest-neighbor (NN) thermodynamic parameters derived from in vitro experiments. However, quantitation of the antisense contributions of motifs is problematic, since individual motifs are not isolated from the effects of neighboring nucleotides, and motifs may be overlapping. These problems are circumvented by a next-nearest-neighbor (NNN) analysis of antisense DNA effects in which the overlapping nature of nearest-neighbors is taken into account. Results Next-nearest-neighbor triplet combinations of nucleotides are the simplest that include overlapping sequence effects and therefore can encompass interactions beyond those of nearest neighbors. We used singular value decomposition (SVD) to fit experimental data from our laboratory in which phosphorothioate-modified antisense DNAs (S-DNAs) 20 nucleotides long were used to inhibit cellular protein expression in 112 experiments involving four gene targets and two cell lines. Data were fitted using a NNN model, neglecting end effects, to derive NNN inhibition parameters that could be combined to give parameters for a set of 49 sequences that represents the inhibitory effects of all possible overlapping triplet interactions in the cellular targets of these antisense S-DNAs. We also show that parameters to describe subsets of the data, such as the mRNAs being targeted and the cell lines used, can be included in such a derivation. While NNN triplet parameters provided an adequate model to fit our data, NN doublet parameters did not. Conclusions The methodology presented illustrates how NNN antisense inhibitory information can be derived from in vivo cellular experiments. Subsequent calculations of the antisense inhibitory parameters for any mRNA target sequence automatically take into account the effects of all possible overlapping combinations of nearest-neighbors in the sequence. This procedure is more robust than the tallying of tetrameric motifs that have positive or negative antisense effects. The specific parameters derived in this work are limited in their applicability by the relatively small database of experiments that was used in their derivation. PMID:20470414

  3. 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 extensions of the stochastic model is recommended.

  4. Chromatic parameters derived from increment spectral sensitivity functions

    NASA Astrophysics Data System (ADS)

    Diaconu, Vasile; Faubert, Jocelyn

    2006-11-01

    We propose a mathematical model to derive the chromatic parameters from increment spectral sensitivity functions. This model was applied to determine the effective red, green, blue, and yellow mechanism contribution to the detection of the spectral stimuli of five normal trichromatic subjects. Detection thresholds were measured for a 300 ms, 1.2 circular test flash presented on a 100 cd/m2 white background for spectral wavelengths between 410 and 660 nm. The model analysis confirmed that in the red-green wavelength area, the detection of our chosen stimuli was mediated by two distinct (L-M) antagonistic mechanisms: a red-green and a yellow, from the blue-yellow system. We inferred that the red-green mechanism receptive fields consisted of a single L- or M-cone center with a homogeneous or heterogeneous surround devoid of S-cone projections. For the receptive fields of the yellow half of the blue-yellow mechanism, we propose a similar configuration but with S-cone projections present in the surround. This proposal is not concordant with what is currently understood regarding retinal physiology. However, two L-M antagonistic mechanisms in the red-green wavelengths as proposed by our results predict what would appear as an intuitive yellow mechanism with a maximal sensitivity at the 578 nm wavelength, where the red-green mechanism sensitivity is null.

  5. 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.

  6. 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

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

    PubMed Central

    Manjunatha, H. C.

    2014-01-01

    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 (Nel) 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), Zeff and Nel 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

  8. 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.

  9. 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.

  10. 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 and throughput for interactive graphical work, and problems relating to graphical interfaces.

  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. 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...

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Jasinski, M. F.; Borak, J. S.; Crago, R. D.

    2005-05-01

    Most numerical atmospheric simulation models and land surface hydrology models used today require knowledge of aerodynamic roughness in the parameterization of surface fluxes. In this paper, the bulk parameters associated with the absorption of surface momentum by vegetated landscapes are theoretically estimated within the context of Raupach's roughness sublayer formulation and the canopy area index. The estimated parameters include the bulk plant drag coefficient, maximum u*/uh, sheltering coefficient, and canopy area density at onset of sheltering. The test case includes the U.S. Southern Great Plains, that includes four principal IGBP land classes; Evergreen needleleaf, grassland, crops, and savanna/shrub. The estimation approach uses the Method of Moments and roughness data from several international field experiments and other published data. The above procedure provides a physically based approach for estimating roughness length for seasonally variable vegetation fields using satellite data.

  15. Uniformly Derived Orbital Parameters of Exo-planets using EXOFIT

    NASA Astrophysics Data System (ADS)

    Balan, S. T.; Lever, G.; Lahav, O.

    2010-10-01

    We present the results from a new systematic study of the radial velocity data of more than 200 planets using the Keplerian orbital fitting program EXOFIT. Based on a Bayesian framework, EXOFIT uses Markov Chain Monte Carlo method to simulate the full posterior distribution of the orbital parameters of extrasolar planets. We discuss the disparity in the eccentricity values obtained by EXOFIT with the published values and the possible reasons for the lower estimates of eccentricity obtained by the EXOFIT. The full details of this work, including an online catalogue of exo-planets with the posterior distributions and the radial velocity plots will appears in Balan, Lever and Lahav (in preparation).

  16. 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.

  17. 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.

  18. The effects of binary interactions on parameter determinations for early-type galaxies

    NASA Astrophysics Data System (ADS)

    Yu, Zhang

    2015-08-01

    Based on stellar population models without (SSP) and with (BSP) binary interactions, we investigate the effects of binary interactions on parameter determinations for early-type galaxies (ETGs).We present photometric redshift (photo-z), age and spectral type for photometric data sample by fitting observed magnitudes with the SSP and BSP models. Our results show that binary interactions have no effect on photo-z estimation. Once we neglect binary interactions, the age of ETGs will be underestimated, by contrast, the effects on the age estimations can be negligible for other type of galaxies. For ETG sample, we derive their properties by fitting their spectra with the SSP and BSP models. When comparing these galaxy properties, we find no variation of the overall metallicities for ETGs among the SSP and BSP models. Moreover, the inclusion of binary interactions can affect age and star formation history estimations.

  19. 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 celestial pole with periods of about a year and less. We make an estimate of the systematic changes introduced in the orbital parameters in the case if erroneous tidal model is kept fixed in the processing.

  20. Interacting quintessence from a variational approach. II. Derivative couplings

    NASA Astrophysics Data System (ADS)

    Böhmer, Christian G.; Tamanini, Nicola; Wright, Matthew

    2015-06-01

    We consider an original variational approach for building new models of quintessence interacting with dark or baryonic matter. The coupling is introduced at the Lagrangian level using a variational formulation for relativistic fluids, where the interacting term generally depends on both the dynamical degrees of freedom of the theory and their spacetime derivatives. After deriving the field equations from the action, we consider applications in the context of cosmology. Two simple models are studied using dynamical system techniques showing the interesting phenomenology arising in this framework. We find that these models contain dark energy dominated late-time attractors with early-time matter dominated epochs and also obtain a possible dynamical crossing of the phantom barrier. The formulation and results presented here complete and expand the analysis exposed in the first part of this work, where only algebraic couplings, without spacetime derivatives, were considered.

  1. 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.

  2. 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.

  3. 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.

  4. Synthesis, characterization and DNA interaction studies of new triptycene derivatives

    PubMed Central

    Chakraborty, Sourav; Mondal, Snehasish; Kumari, Rina; Bhowmick, Sourav; Das, Prolay

    2014-01-01

    Summary A facile and efficient synthesis of a new series of triptycene-based tripods is being reported. Using 2,6,14- or 2,7,14-triaminotriptycenes as synthons, the corresponding triazidotriptycenes were prepared in high yield. Additionally, we report the transformation of 2,6,14- or 2,7,14-triaminotriptycenes to the corresponding ethynyl-substituted triptycenes via their tribromo derivatives. Subsequently, derivatization of ethynyl-substituted triptycenes was studied to yield the respective propiolic acid and ethynylphosphine derivatives. Characterization of the newly functionalized triptycene derivatives and their regioisomers were carried out using FTIR and multinuclear NMR spectroscopy, mass spectrometry, and elemental analyses techniques. The study of the interaction of these trisubstituted triptycenes with various forms of DNA revealed interesting dependency on the functional groups of the triptycene core to initiate damage or conformational changes in DNA. PMID:24991281

  5. 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

  6. 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 thinnest of these at less than 3nm, i.e. 1/300 of the laser wavelength, are even thinner than the plasma skin depth. This drastically changes the laser-matter interaction physics leading to the emergence of new particle acceleration mechanisms, like Break-Out Afterburner (BOA) Acceleration, driven by a relativistic, kinetic plasma instability or Radiation Pressure Acceleration (RPA), driven by stabilized charge separation. Furthermore, these interactions also produce relativistic high harmonics in forward direction as well as mono-en,ergetic electron pulses which might lend itself as a source for fully coherent Thomson scattering in the mulit-keV regime. In this talk I will present an overview over the laser developments leading to this paradigm change as well as over the theoretical and experimental results following from it. Specifically we were able for the first time to demonstrate BOA acceleration of Carbon ions to up to 0.5 GeV using a laser pulse with {approx}10{sup 20} W/cm{sup 2} intensity and showing the scalability of this mechanism into regimes relevant for Hadron Therapy. We were further able to demonstrate mono-energetic electron break-out from ultrathin targets, as a first step towards a flying mirror.

  7. 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.

  8. 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.

  9. 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 organic aerosol) we present first mass-based measurements of water uptake over a wide range of relative humidity (1-99.4%) obtained with a new filter-based differential hygroscopicity analyzer (FDHA) technique. For these samples the concentration dependence of κm can be described by a simple KIM model equation based on observable mass growth factors and a total of only six fit parameters summarizing the combined effects of the dilute hygroscopicity parameters, self- and cross-interaction parameters, and solubilities of all involved chemical components. One of the fit parameters represents κm0 and can be used to predict critical dry diameters for the activation of cloud condensation nuclei (CCN) as a function of water vapor supersaturation according to Köhler theory. For sodium chloride and ammonium sulfate reference particles as well as for pristine rainforest aerosols consisting mostly of secondary organic matter, we obtained good agreement between the KIM predictions and measurement data of CCN activation. The application of KIM and mass-based measurement techniques shall help to bridge gaps in the current understanding of water uptake by atmospheric aerosols: (1) the gap between hygroscopicity parameters determined by hygroscopic growth measurements under sub-saturated conditions and by CCN activation measurements at water vapor supersaturation, and (2) the gap between the results of simplified single parameter models widely used in atmospheric or climate science and the results of complex multi-parameter ion- and molecule-interaction models frequently used in physical chemistry and solution thermodynamics (e.g., AIM, E-AIM, ADDEM, UNIFAC, AIOMFAC).

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

    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. 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 intrinsic hygroscopicity parameter (κm,∞) and additional self- and cross-interaction parameters describing non-ideal solution behavior and concentration dependencies of single- and multi-component systems. For sodium chloride, the κm-interaction model (KIM) captures the 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). For atmospheric aerosol samples collected from boreal rural air and from pristine tropical rainforest air (secondary organic aerosol) we present first mass-based measurements of water uptake over a wide range of relative humidity (1-99%) obtained with a new filter-based differential hygroscopicity analyzer (FDHA) technique. By application of KIM to the measurement data we can distinguish three different regimes of hygroscopicity in the investigated aerosol samples: (I) A quasi-eutonic regime at low relative humidity (~60% RH) where the solutes co-exist in an aqueous and non-aqueous phase; (II) a gradually deliquescent regime at intermediate humidity (~60%-90% RH) where different solutes undergo gradual dissolution in the aqueous phase; and (III) a dilute regime at high humidity (≳90% RH) where the solutes are fully dissolved approaching their dilute intrinsic hygroscopicity. The characteristic features of the three hygroscopicity regimes are similar for both samples, while the RH threshold values vary as expected for samples of different chemical composition. In each regime, the concentration dependence of κm can be described by a simple KIM model equation based on observable mass growth factors and six fit parameters summarizing the combined effects of the dilute intrinsic hygroscopicity and interaction parameters of all involved chemical components. One of the fit parameters represents κm,∞ and can be used to predict CCN activation diameters as a function of water vapor supersaturation. For sodium chloride reference particles as well as for pristine rainforest aerosols consisting mostly of secondary organic matter, we obtained good agreement between the predicted and measured critical diameters of CCN activation. The application of KIM and mass-based measurement techniques shall help to bridge gaps in the current understanding of water uptake by atmospheric aerosols: (1) the gap between hygroscopicity parameters determined by HTDMA (hygroscopicity tandem differential mobility analyzer) or FDHA measurements under sub-saturated conditions and by CCN measurements at water vapor supersaturation, and (2) the gap between the results of simplified single parameter models widely used in atmospheric or climate science and the results of complex multi-parameter ion- and molecule-interaction models frequently used in physical chemistry and thermodynamics (AIM, E-AIM, UNIFAC, AIOMFAC etc.).

  11. 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:26428406

  12. Solubility and interaction parameters as references for solution properties II: precipitation and aggregation of asphaltene in organic solvents.

    PubMed

    Johansson, Bjarne; Friman, Rauno; Hakanpää-Laitinen, Hannele; Rosenholm, Jarl B

    2009-01-01

    The total combinatory Gibbs free energy was successfully used to model the solubility of two purified asphaltenes in pure and mixed solvents, as well as the precipitation of asphaltenes from mixed solvents. Intrinsic viscosity and aggregate size both sensitively reflected the state of the asphaltenes in homogeneous solution and were used for determining the solubility parameters of the asphaltenes. Phase separation was clearly reflected by a dramatic increase in aggregate size. The interaction parameter was subdivided into enthalpy and entropy contributions. All parameters indicate an extensive association or phase transition when the phase boundary was followed by simultaneously varying the temperature and the solubility parameter of the solvent. However, the interaction parameter is frequently derived in two ways. We show that, depending on the definition, the enthalpy and entropy contributions lead to conflicting results. These were evaluated on thermodynamic grounds. PMID:19019320

  13. Interaction between proteins and polyphosphazene derivatives having a galactose moiety.

    PubMed

    Heyde, Mieke; Claeyssens, Marc; Schacht, Etienne H

    2008-02-01

    For tissue engineering applications, it is necessary to balance the need for specific biological interactions with the need to prevent unfavorable nonspecific interactions. For this purpose, novel poly[(organo)phosphazenes] were synthesized having galactose and/or poly(ethylene glycol) (PEG) side chains. The synthesis was described previously. Here, we investigate the human serum albumin (HSA) adhesion to these polymers using surface plasmon resonance (SPR). We could conclude that the incorporation of PEG reduced the protein adsorption. The influence of the galactose moieties was investigated using SPR and a sugar-lectin binding assay. The interaction between a lectin (Peanut agglutinin, PNA or Ricinus communis-agglutinin, RCA) and the polyphosphazene derivatives was evaluated. Type IIA polymers, having aminohexyl-galactose, phenylalanine ethyl ester, and glycine ethyl ester side chains, were capable of binding with the lectin. As the amount of galactose was increased, the extent of the galactose specific lectin binding was also increased (higher RU or absorbance). PEG containing polymers failed to bind specifically with the lectin. The presence of PEG, either as a spacer or as additional chains, interfered with the establishment of contact between the galactose and the binding site on the lectin. The adsorption of PNA or RCA to these types of polymers was attributed to nonspecific interactions. SPR was also used to determine rate and equilibrium constants. In addition the effect of the addition of water soluble polyphosphazenes on the enzymatic cleavage of o-nitrophenyl-beta-D-galactopyranoside was investigated. The galactose moieties were not available as inhibitors because of the presence of PEG. PMID:18208315

  14. The effects of binary interactions on parameter determinations for early-type galaxies

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Liu, Jinzhong; Zhang, Fenghui

    2015-05-01

    Based on stellar population models without (SSP) and with (BSP) binary interactions, we investigate the effects of binary interactions on parameter determinations for early-type galaxies (ETGs). We present photometric redshift (photo-z), age and spectral type for photometric data sample by fitting observed magnitudes with the SSP and BSP models. Our results show that binary interactions have no effect on photo-z estimation. Once we neglect binary interactions, the age of ETGs will be underestimated, by contrast, the effects on the age estimations can be negligible for other type of galaxies. For ETG sample, we derive their properties by fitting their spectra with the SSP and BSP models. When comparing these galaxy properties, we find no variation of the overall metallicities for ETGs among the SSP and BSP models. Moreover, the inclusion of binary interactions can affect age estimations. Our results show that the BSP-fitted ages in ˜33.3 per cent of ETG sample are around 0.5-1.0 Gyr larger than the SSP-fitted ages; ˜44.2 per cent are only 0.1 - 0.5 Gyr larger; the rest ˜22.5 per cent are approximately equal. By comparisons, we find the difference of the star formation rate between the SSP and BSP models is large at the late evolution stage.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    PubMed

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

    2015-07-01

    Star polymers provide model architectures to understand the dynamic and rheological effects of chain confinement for a range of complex topological structures like branched polymers, colloids, and micelles. It is important to describe the structure of such macromolecular topologies using small-angle neutron and x-ray scattering to facilitate understanding of their structure-property relationships. Modeling of scattering from linear, Gaussian polymers, such as in the melt, has applied the random phase approximation using the Debye polymer scattering function. The Flory-Huggins interaction parameter can be obtained using neutron scattering by this method. Gaussian scaling no longer applies for more complicated chain topologies or when chains are in good solvents. For symmetric star polymers, chain scaling can differ from ν=0.5(d(f)=2) due to excluded volume, steric interaction between arms, and enhanced density due to branching. Further, correlation between arms in a symmetric star leads to an interference term in the scattering function first described by Benoit for Gaussian chains. In this work, a scattering function is derived which accounts for interarm correlations in symmetric star polymers as well as the polymer-solvent interaction parameter for chains of arbitrary scaling dimension using a hybrid Unified scattering function. The approach is demonstrated for linear, four-arm and eight-arm polyisoprene stars in deuterated p-xylene. PMID:26274195

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. Deriving temporal and spatial variation in ecosystem parameters from FLUXNET data

    NASA Astrophysics Data System (ADS)

    Groenendijk, M.; Dolman, H.

    2007-12-01

    To understand the global variation in carbon and water balances and to predict the ecosystem responses to climate changes it is important to identify the processes driving the differences and thus make progress beyond the simple regressions end empirical relationships that have been found. This study presents a method using the FLUXNET data and a simple ecosystem model to obtain five model parameters. Two parameters (reference respiration and activation energy) are related to ecosystem respiration and three parameters (carboxylation capacity, water use efficiency and light use efficiency) to photosynthesis and transpiration. The model is constrained by both the observed carbon and water fluxes, and determines the parameter uncertainty from the uncertainty in the observations. The main question is how the parameters are varying in time and space and if this can be related to environmental variations. The parameters are derived for four European forests. Annual parameter values are significantly different between sites and years, with no overlap in parameter space, taking into account the uncertainty. These site year parameters are very useful for comparing sites. The carboxylation capacity and light use efficiency are lowest for dry Mediterranean sites, while here the water use efficiency is highest. The light use efficiency is higher for the more northern sites. Adaptation to the environment may explain most of this, because sites are generally water limited in the south and light limited in the north of Europe. Whereas the parameter values appear meaningful when the model is applied on an annual basis, the correlation between observations and simulations improves when the model is applied on smaller time scales, but noise increases. The change in performance raises the interesting question how the different time scales are related. Improvement of the model could, for instance, be including this relation between time scales constrained by the environment.

  2. Structure of p-shell Nuclei with Interactions Derived from Chiral Effective-Field Theory

    NASA Astrophysics Data System (ADS)

    Ormand, W. E.; Gueorguiev, V. G.; Navratil, P.; Vary, J. P.

    2006-04-01

    Traditional realistic nucleon-nucleon (NN) interactions based on precision fits to 2-body data have not produced high-quality descriptions of light nuclei. Effective-Field theories (EFT) based on chiral-perturbation theory provide a natural scheme to derive inter-nucleon interactions and predict a three-nucleon interaction at next-to-next-to-leading order (N2LO). A key feature of these EFT potentials is a set of parameters; some of which are determined by the EFT NN couplings, while others are chosen to reproduce the binding energies of A=3 and 4 nuclei. We have developed the tools to utilize EFT-based potentials, including the NNN terms, in the ab initio no-core shell model (NCSM). We have also improved our shell-model codes to increase the scope of our calculations with three-nucleon interactions to the point where model spaces up to 6 φ are accessible for all p-shell nuclei. We will show results of large-basis NCSM calculations for light p-shell nuclei, especially masses A =10, 11, 12, 13 and highlight the impact the N2LO TNI and its parameters on their structure. Support from LDRD contract No. 04-ERD-058 and DOE grant SCW0498 is acknowledged.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. The impact parameter dependence of swift electron-matter interactions

    SciTech Connect

    Ritchie, R.H.

    1988-01-01

    In quantal collision theories, momentum and energy are usually taken to be good quantal variables. Classical collision theory, on the other hand, uses position and time to describe interactions between a probe and a target. In modern physics one may wish to express quantal theories in terms of spacelike variables. For example, experiments are now common in which one measures, by means of a narrowly focused beam of swift electrons, the distribution in energy of losses experienced in a very small region of space. Also, in experiments with channeled ions, and in microdosimetry, one is interested in the spatial coherence of unlocalized excitations created by swift ions and electrons, and their ultimate localization through transfer of energy to, e.g., single-particle excitations. In this lecture the author describes work, done in part in collaboration with Professor Howie, on some aspects of the spatial dependence of inelastic interactions between a charged particle and a condensed matter target. 6 refs., 1 fig.

  9. Photon interaction parameters of dosimetric interest in bone.

    PubMed

    Manjunatha, H C; Rudraswamy, B

    2012-09-01

    The effective atomic numbers (Z(eff)) and electron densities (N(el)) of cortical and compact bone have been computed for total and partial photon interactions (photoelectric absorption, coherent scattering, incoherent scattering, pair production in a nuclear field, pair production in an electronic field, and sum of non-coherent scattering) by computing the molecular, atomic, and electronic cross section in the wide energy range of 1 keV-100 GeV using WinXCom. The variations of effective atomic number and electron density with energy are shown graphically for all photon interactions. The effective atomic numbers (ZPEA(eff)) for photon energy absorption are also calculated from mass energy absorption coefficients in the energy range 1 keV-20 MeV. The kerma values of bone relative to air are also computed. Additionally, computed tomography (CT) numbers of bone for photon interaction and energy absorption are also computed. The computed Z(eff) and N(el) may be useful in choosing a substitute composite material in place of bone. The estimated mass energy absorption coefficient may be used to evaluate dose and determine the surviving fraction (S) for bone. The usefulness of computed data in the simulation of tissue substitutes is also discussed. PMID:22850239

  10. 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. A simple Web front end of SP_Ace can be found at http://dc.g-vo.org/SP_ACE while the source code will be published soon. Full Tables D.1-D.3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/587/A2

  11. 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.

  12. 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.

  13. 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.

  14. Monofunctional polymers in liquid adsorption chromatography: determination of the interaction parameter in the range of weak interaction.

    PubMed

    Trathnigg, Bernd; Malik, Muhammad Imran; Cuong, Nguyen Viet; Skvortsov, Alexander M

    2008-10-17

    The main physical characteristics of monofunctionals in adsorption chromatography - the adsorption interaction parameter of the repeat units c and the interaction parameter of specific end group q - are discussed. Both parameters are independent on column dimensions and pore diameter, and depend on mobile phase composition. In a plot of elution volumes V(n) vs. the difference DeltaV=V(n)-V(n-1) in elution volumes of consecutive non-functional or monofunctional oligomers, straight lines with the same slope are obtained for sufficiently high molar masses. The intercept of these lines yield the accessible volumes of functionalized and non-functionalized oligomers. In the range of weak interaction, the interaction parameter of the repeat unit can be determined using monofunctional chains with strongly adsorbing end group. Scope and limitations of this approach are studied using monoalkyl ethers of polypropylene glycol as model polymers. PMID:18760416

  15. Quality assessment and derivation of hydrological relevant parameters from Shuttle Radar Topography Mission data

    NASA Astrophysics Data System (ADS)

    Hochschild, V.; Wolf, M.

    2003-04-01

    The aim of the paper is to demonstrate the value of Shuttle Radar Topography Mission (SRTM, X-Band) derived Digital Elevation Model (DEM) Data for hydrological applications. The quality assessment results are compared with other remote sensing derived elevation data, namely a photogrammetrically derived Digital Terrain Model (DTM) of the Thuringian Survey Agency, ERS Tandem Mission data (C-Band) and a high resolution Experimental SAR (E-SAR) DEM. The analysis carried out in three testsites in Thuringia (Biosphere Conservation Area Rhön Mountains, Ilm-Catchment and Zeulenroda Reservoir Area) comprises difference images between several DTMs and DEMs, statistical analysis and quality estimations as well as the derivation of secondary DEM products like slope, aspect, curvature, catchment area, river density, flow direction, flow accumulation, evaporation, transport capacity, etc. These parameters are used as spatial input for distributed hydrological models. Finally the suitability of the SRTM-DEMs for hydrological models (water balance and solute transport models) is assessed on the comparison of simulation results with measured runoff curves.

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

    NASA Astrophysics Data System (ADS)

    Morse, Peter K.; Corwin, Eric I.

    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.

  17. 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.

  18. 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.

  19. 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.

  20. Determination of phenological parameters from MODIS derived NDVI data using hidden Markov models

    NASA Astrophysics Data System (ADS)

    García, Miguel A.; Moutahir, Hassane; Bautista, Susana; Rodríguez, Francisco

    2014-08-01

    The phenological characteristics of the vegetation are key elements for understanding vegetation responses in different climate change scenarios, as well as indicators of ongoing processes of increasing aridity. Determination of phenological parameters for different types of vegetation in large areas help evaluate current and future impacts of climate change in ecosystems, specially in those more vulnerable. Moderate resolution remote sensing data, as provided by MODIS, has already been used to extract phenological characteristics from time series data of vegetation indices, most usually by data smoothing and fitting of polynomial models. In this work, we use hidden Markov models (HMMs) to define phenological parameters from MODIS derived NDVI time series data in a semiarid Mediterranean region. Different types of HMMs are applied in selected areas with well-defined vegetation communities, and their potentials for automatic phenological analysis at large scale are discussed.

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

    PubMed

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

    2014-05-01

    The U.S. Department of Energy Order 458.1 states that the compliance with the 1 mSv annual dose constraint to a member of the public may be demonstrated by calculating dose to the maximally exposed individual (MEI) or to a representative person. Historically, the MEI concept was used for dose compliance at the Savannah River Site (SRS) using adult dose coefficients and adult male usage parameters. For future compliance, SRS plans to use the representative person concept for dose estimates to members of the public. The representative person dose will be based on the reference person dose coefficients from the U.S. DOE Derived Concentration Technical Standard and on usage parameters specific to SRS for the reference and typical person. Usage parameters and dose coefficients were determined for inhalation, ingestion and external exposure pathways. The reference intake for air, water, meat, dairy, freshwater fish, saltwater invertebrates, produce (fruits and vegetables), and grains for the 95th percentile are 17.4 m d, 2.19 L d, 220.6 g d, 674 cm d, 66.4 g d, 23.0 g d, 633.4 g d (448.5 g dand 631.7 g d) and 251.3 g d, respectively. For the 50th percentile: 13.4 m d, 0.809 L d, 86.4 g d, 187 cm d, 8.97 g d, 3.04 g d, 169.5 g d (45.9 g d and 145.6 g d), 101.3 g d, respectively. These parameters for the representative person were used to calculate and tabulate SRS-specific derived concentration standards (DCSs) for the pathways not included in DOE-STD-1196-2011. PMID:24667386

  2. 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

  3. Aerosol hygroscopicity parameter derived from the light scattering enhancement factor measurements in the North China Plain

    NASA Astrophysics Data System (ADS)

    Chen, J.; Zhao, C. S.; Ma, N.; Yan, P.

    2014-08-01

    The relative humidity (RH) dependence of aerosol light scattering is an essential parameter for accurate estimation of the direct radiative forcing induced by aerosol particles. Because of insufficient information on aerosol hygroscopicity in climate models, a more detailed parameterization of hygroscopic growth factors and resulting optical properties with respect to location, time, sources, aerosol chemistry and meteorology are urgently required. In this paper, a retrieval method to calculate the aerosol hygroscopicity parameter, κ, is proposed based on the in situ measured aerosol light scattering enhancement factor, namely f(RH), and particle number size distribution (PNSD) obtained from the HaChi (Haze in China) campaign. Measurements show that f(RH) increases sharply with increasing RH, and that the time variance of f(RH) is much greater at higher RH. A sensitivity analysis reveals that the f(RH) is more sensitive to the aerosol hygroscopicity than PNSD. f(RH) for polluted cases is distinctly higher than that for clean periods at a specific RH. The derived equivalent κ, combined with the PNSD measurements, is applied in the prediction of the cloud condensation nuclei (CCN) number concentration. The predicted CCN number concentration with the derived equivalent κ agrees well with the measured ones, especially at high supersaturations. The proposed calculation algorithm of κ with the f(RH) measurements is demonstrated to be reasonable and can be widely applied.

  4. 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.

  5. 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.

  6. 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 ...

  7. 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

    We discuss reactor antineutrino oscillations with non-standard interactions (NSIs) at the neutrino production and detection processes. The neutrino oscillation probability is calculated with a parametrization of the NSI parameters by splitting them into the averages and differences of the production and detection processes respectively. The average parts induce constant shifts of the neutrino mixing angles from their true values, and the difference parts can generate the energy (and baseline) dependent corrections to the initial mass-squared differences. We stress that only the shifts of mass-squared differences are measurable in reactor antineutrino experiments. Taking Jiangmen Underground Neutrino Observatory (JUNO) as an example, we analyze how NSIs influence the standard neutrino measurements and to what extent we can constrain the NSI parameters. Long baseline reactor antineutrino experiments, such as KamLAND [10,11]. The aim of these experiments is to observe the slow oscillation with ?21 and measure the corresponding oscillation parameters ?m212 and ?12. Short baseline reactor antineutrino experiments, such as Daya Bay [1-3], Double CHOOZ [4], RENO [5]. They are designed to observe the fast oscillation with ?31 and ?32 (or equivalently, ?ee[3]) and measure the corresponding oscillation parameters ?mee2, ?13. Medium baseline reactor antineutrino experiments. They stand for the next generation experiments of reactor antineutrinos, with typical representatives of Jiangmen Underground Neutrino Observatory (JUNO) [12] and RENO-50 [13]. They can determine the neutrino mass ordering (m1interactions (NSIs) [14,15]. 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.

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

    PubMed Central

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

    2014-01-01

    Background There is a need for simple clinical tools that can objectively assess fall risk in people with dementia. Wearable sensors seem to have potential for fall prediction, however, there has been limited work performed in this important area. Objective To explore the validity of sensor-derived physical activity (PA) parameters for predicting future falls in people with dementia. To compare sensor-based fall risk assessment with conventional fall risk measures. Methods A cohort study of people with confirmed dementia discharged from a geriatric rehabilitation ward. PA was quantified using 24-hour motion-sensor monitoring at the beginning of the study. PA parameters (percentage of walking, standing, sitting, lying; duration of single walking, standing, and sitting bouts) were extracted using specific algorithms. Conventional assessment included performance-based tests (Timed-up-and-go test, Performance-Oriented-Mobility-Assessment, 5-chair stand) and questionnaires (cognition, ADL-status, fear of falling, depression, previous faller). Outcome measures were fallers (at least one fall in the 3-month follow-up period) versus non-fallers. Results Seventy-seven people were included in the study (age 81.8 ± 6.3; community dwelling 88%, institutionalized 12%). Surprisingly, fallers and non-fallers did not differ on any conventional assessment (p= 0.069–0.991), except for ‘previous faller’ (p= 0.006). Interestingly, several PA parameters discriminated between groups. The ‘walking bouts average duration’, ‘longest walking bout duration’ and ‘walking bouts duration variability’ were lower in fallers, compared to non-fallers (p= 0.008–0.027). The ‘standing bouts average duration’ was higher in fallers (p= 0.050). Two variables, ‘walking bouts average duration’ [odds ratio (OR) 0.79, p= 0.012] and ‘previous faller’ [OR 4.44, p= 0.007] were identified as independent predictors for falls. The OR for a ‘walking bouts average duration’ of less than 15 seconds for predicting fallers was 6.30 (p= 0.020). Combining ‘walking bouts average duration’ and ‘previous faller’ improved fall prediction [OR 7.71, p< 0.001, sensitivity/specificity 72%/76%]. Discussion Results demonstrate that sensor-derived PA parameters are independent predictors of fall risk and may have higher diagnostic accuracy in persons with dementia compared to conventional fall risk measures. Our findings highlight the potential of telemonitoring technology for estimating fall risk. Results should be confirmed in a larger study and by measuring PA over a longer time period. PMID:25171300

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

    SciTech Connect

    Jannik, T.

    2013-03-14

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

  10. Derivation of the switch-on parameters in the dual channel double heterostructure optoelectronic switch

    NASA Astrophysics Data System (ADS)

    Taylor, G. W.; Opper, H.; Cai, J.; Garber, B.; Basilica, R.

    2004-12-01

    The switching mechanism in the dual channel double heterostructure optoelectronic switch is investigated using a mathematically precise definition to describe the conditions at the transition between the off state and negative resistance regions on the thyristor I-V curve. Analytical expressions of quantum well density, voltage, and current parameters at switching are found for both three terminal electrical injection and optical input. Agreement is found to be within 2% of full numerical simulation. Using derivatives of the analytic functions to determine the various current gains, the classic thyristor switching equations due to avalanching are found to be inaccurate and that instead switching is more appropriately determined by the rate of change of charge populations in the control regions compared to the other charges in the device. This analysis is supported by measurements of three terminal thyristor operation of the thyristor device.

  11. Deriving an estimate for the Fried parameter in mobile optical transmission scenarios.

    PubMed

    Giggenbach, Dirk

    2011-01-10

    Measuring the Fried parameter r(0) (atmospheric optical coherence length) in optical link scenarios is crucial to estimate a receiver's telescope performance or to dimension atmospheric mitigation techniques, such as in adaptive optics. The task of measuring r(0) is aggravated in mobile scenarios, when the receiver itself is prone to mechanical vibrations (e.g., when mounted on a moving platform) or when the receiver telescope has to track a fast-moving signal source, such as, in our case, a laser transmitter on board a satellite or aircraft. We have derived a method for estimating r(0) that avoids the influence of angle-of-arrival errors by only using short-term tilt-removed focal intensity speckle patterns. PMID:21221148

  12. Nonlinear Interaction of Zero Sound with the Order Parameter Collective Modes in Superfluid HELIUM-3-BORON.

    NASA Astrophysics Data System (ADS)

    McKenzie, Ross Hugh

    A brief overview of past experimental and theoretical investigations of the linear and nonlinear interaction of zero sound with the order parameter collective modes in superfluid ^3He-B is given before introducing the quasiclassical (QC) theory of superfluid ^3He. A new approach to calculating the linear and nonlinear response is presented. The QC propagator is calculated by expanding the low energy Dyson's equation in powers of the nonequilibrium self energy. The expression given for the expansion coefficients, involving products of pairs of equilibrium Green's functions, has a simple diagrammatic representation, and establishes a connection between the QC theory and other theoretical formalisms which have been used to investigate the collective modes. It is shown that the expansion coefficients satisfy Onsager-like relations and some identities required by gauge and galilean invariance. Consequently, this new approach to deriving dynamical equations for the collective modes is more efficient and transparent than solving the QC transport equations. This new approach is used to investigate the linear coupling of zero sound to the order parameter collective modes in weakly inhomogeneous superfluid ^3 He. It makes tractable the treatment of (nonlinear) parametric processes involving zero sound and the collective modes. It is shown that the approximate particle-hole symmetry of the ^3He Fermi liquid determines important selection rules for nonlinear acoustic processes, just as it is well known to do for linear processes. Analogues with nonlinear optics guide the derivation, solution and interpretation of the dynamical equations for a three-wave resonance between two zero sound waves and the J = 2 ^+ order parameter collective mode. It is shown that stimulated Raman scattering and two phonon absorption of zero sound by the J = 2^+ collective mode should be observable when the pump sound wave has energy density larger than about one percent of the superfluid condensation energy density. Generation of anti-Stokes waves and third harmonics should also be observable if the sound path length is small enough to reduce the interference effects of dispersion. Finally, the feasibility of using nonlinear acoustics in ^3He-B to observe quantum mechanical properties of sound is considered.

  13. 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

  14. 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.

  15. 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    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 m2/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.

  18. Optimizing Performance Parameters of Chemically-Derived Graphene/p-Si Heterojunction Solar Cell.

    PubMed

    Batra, Kamal; Nayak, Sasmita; Behura, Sanjay K; Jani, Omkar

    2015-07-01

    Chemically-derived graphene have been synthesized by modified Hummers method and reduced using sodium borohydride. To explore the potential for photovoltaic applications, graphene/p-silicon (Si) heterojunction devices were fabricated using a simple and cost effective technique called spin coating. The SEM analysis shows the formation of graphene oxide (GO) flakes which become smooth after reduction. The absence of oxygen containing functional groups, as observed in FT-IR spectra, reveals the reduction of GO, i.e., reduced graphene oxide (rGO). It was further confirmed by Raman analysis, which shows slight reduction in G-band intensity with respect to D-band. Hall effect measurement confirmed n-type nature of rGO. Therefore, an effort has been made to simu- late rGO/p-Si heterojunction device by using the one-dimensional solar cell capacitance software, considering the experimentally derived parameters. The detail analysis of the effects of Si thickness, graphene thickness and temperature on the performance of the device has been presented. PMID:26373050

  19. A numerical model to improve the derivation of aerosols optical parameters from elastic backscatter lidar data

    NASA Astrophysics Data System (ADS)

    Nicolae, Doina; Talianu, Camelia; Nemuc, Anca; Carstea, Emil; Ciuciu, Jeni; Cristescu, Constantin

    2006-09-01

    LIDAR systems have demonstrated their ability to map aerosol variations throughout the atmospheric column and therefore they have has become a central technology in current strategies for tropospheric aerosol research. Its use is complicated, however, by the fact that the lidar signal contains a convolution of two basic optical properties of the aerosol particles: the backscatter coefficient and the extinction coefficient. A quantitative retrieval of either property requires knowledge of their relationship along the laser path which is referred as lidar ratio. If the lidar ratio can not be measured by high spectral resolution lidar, or Raman lidar, then either an assumed value of LR a must be used in the lidar retrieval, leading to very large uncertainties in light extinction , or models can be used for determination of LR a profile. Our research refers to the development of an iterative hybrid regularization technique for elastic backscatter lidar data processing and retrieval of the aerosols optical parameters using the atmospheric model, Mie model and Fernald-Klett, but also Ackermann algorithm for lidar ratio calculation based on relative humidity profile. This study focuses on a numerical investigation about the lidar ratio of tropospheric aerosols characterizing Romanian atmosphere. The model can be also used for other type of atmosphere in order to improve the derivation of aerosols optical parameters from elastic backscatter lidar data when no other information than meteorological data are available.

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

    PubMed

    Jakobsen, Sofie; Jensen, Frank

    2014-12-01

    We assess the accuracy of force field (FF) electrostatics at several levels of approximation from the standard model using fixed partial charges to conformational specific multipole fits including up to quadrupole moments. Potential-derived point charges and multipoles are calculated using least-squares methods for a total of ∼1000 different conformations of the 20 natural amino acids. Opposed to standard charge fitting schemes the procedure presented in the current work employs fitting points placed on a single isodensity surface, since the electrostatic potential (ESP) on such a surface determines the ESP at all points outside this surface. We find that the effect of multipoles beyond partial atomic charges is of the same magnitude as the effect due to neglecting conformational dependency (i.e., polarizability), suggesting that the two effects should be included at the same level in FF development. The redundancy at both the partial charge and multipole levels of approximation is quantified. We present an algorithm which stepwise reduces or increases the dimensionality of the charge or multipole parameter space and provides an upper limit of the ESP error that can be obtained at a given truncation level. Thereby, we can identify a reduced set of multipole moments corresponding to ∼40% of the total number of multipoles. This subset of parameters provides a significant improvement in the representation of the ESP compared to the simple point charge model and close to the accuracy obtained using the complete multipole parameter space. The selection of the ∼40% most important multipole sites is highly transferable among different conformations, and we find that quadrupoles are of high importance for atoms involved in π-bonding, since the anisotropic electric field generated in such regions requires a large degree of flexibility. PMID:26583232

  1. Spin and spin-isospin instabilities and Landau parameters of Skyrme interactions with tensor correlations

    SciTech Connect

    Cao Ligang; Colo, Gianluca; Sagawa, Hiroyuki

    2010-04-15

    The Landau parameters of Skyrme interactions in the spin and spin-isospin channels are studied using various Skyrme effective interactions with and without tensor correlations. We focus on the role of the tensor terms on the spin and spin-isospin instabilities that can occur in nuclear matter above saturation density. We point out that these instabilities are realized in nuclear matter at the critical density of about two times the saturation density for all the adopted parameter sets. The critical density is shown to be very much dependent not only on the choice of the Skyrme parameter set, but also on the inclusion of the tensor terms.

  2. 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

  3. 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.

  4. The ILIUM forward modelling algorithm for multivariate parameter estimation and its application to derive stellar parameters from Gaia spectrophotometry

    NASA Astrophysics Data System (ADS)

    Bailer-Jones, C. A. L.

    2010-03-01

    I introduce an algorithm for estimating parameters from multidimensional data based on forward modelling. It performs an iterative local search to effectively achieve a non-linear interpolation of a template grid. In contrast to many machine-learning approaches, it avoids fitting an inverse model and the problems associated with this. The algorithm makes explicit use of the sensitivities of the data to the parameters, with the goal of better treating parameters which only have a weak impact on the data. The forward modelling approach provides uncertainty (full covariance) estimates in the predicted parameters as well as a goodness-of-fit for observations, thus providing a simple means of identifying outliers. I demonstrate the algorithm, ILIUM, with the estimation of stellar astrophysical parameters (APs) from simulations of the low-resolution spectrophotometry to be obtained by Gaia. The AP accuracy is competitive with that obtained by a support vector machine. For zero extinction stars covering a wide range of metallicity, surface gravity and temperature, ILIUM can estimate Teff to an accuracy of 0.3 per cent at G = 15 and to 4 per cent for (lower signal-to-noise ratio) spectra at G = 20, the Gaia limiting magnitude (mean absolute errors are quoted). [Fe/H] and logg can be estimated to accuracies of 0.1-0.4dex for stars with G <= 18.5, depending on the magnitude and what priors we can place on the APs. If extinction varies a priori over a wide range (0-10mag) - which will be the case with Gaia because it is an all-sky survey - then logg and [Fe/H] can still be estimated to 0.3 and 0.5dex, respectively, at G = 15, but much poorer at G = 18.5. Teff and AV can be estimated quite accurately (3-4 per cent and 0.1-0.2mag, respectively, at G = 15), but there is a strong and ubiquitous degeneracy in these parameters which limits our ability to estimate either accurately at faint magnitudes. Using the forward model, we can map these degeneracies (in advance) and thus provide a complete probability distribution over solutions. Additional information from the Gaia parallaxes, other surveys or suitable priors should help reduce these degeneracies.

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

    PubMed

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

    2013-06-01

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

  6. Interaction of cinnamic acid derivatives with serum albumins: A fluorescence spectroscopic study

    NASA Astrophysics Data System (ADS)

    Singh, T. Sanjoy; Mitra, Sivaprasad

    2011-03-01

    Cinnamic acid (CA) derivatives are known to possess broad therapeutic applications including anti-tumor activity. The present study was designed to determine the underlying mechanism and thermodynamic parameters for the binding of two CA based intramolecular charge transfer (ICT) fluorescent probes, namely, 4-(dimethylamino) cinnamic acid (DMACA) and trans-ethyl p-(dimethylamino) cinnamate (EDAC), with albumins by fluorescence spectroscopy. Stern-Volmer analysis of the tryptophan fluorescence quenching data in presence of the added ligand reveals fluorescence quenching constant ( κq), Stern-Volmer constant ( KSV) and also the ligand-protein association constant ( Ka). The thermodynamic parameters like enthalpy (Δ H) and entropy (Δ S) change corresponding to the ligand binding process were also estimated. The results show that the ligands bind into the sub-domain IIA of the proteins in 1:1 stoichiometry with an apparent binding constant value in the range of 10 4 dm 3 mol -1. In both the cases, the spontaneous ligand binding to the proteins occur through entropy driven mechanism, although the interaction of DMACA is relatively stronger in comparison with EDAC. The temperature dependence of the binding constant indicates the induced change in protein secondary structure.

  7. Interaction of cinnamic acid derivatives with serum albumins: a fluorescence spectroscopic study.

    PubMed

    Singh, T Sanjoy; Mitra, Sivaprasad

    2011-03-01

    Cinnamic acid (CA) derivatives are known to possess broad therapeutic applications including anti-tumor activity. The present study was designed to determine the underlying mechanism and thermodynamic parameters for the binding of two CA based intramolecular charge transfer (ICT) fluorescent probes, namely, 4-(dimethylamino) cinnamic acid (DMACA) and trans-ethyl p-(dimethylamino) cinnamate (EDAC), with albumins by fluorescence spectroscopy. Stern-Volmer analysis of the tryptophan fluorescence quenching data in presence of the added ligand reveals fluorescence quenching constant (κ(q)), Stern-Volmer constant (K(SV)) and also the ligand-protein association constant (K(a)). The thermodynamic parameters like enthalpy (ΔH) and entropy (ΔS) change corresponding to the ligand binding process were also estimated. The results show that the ligands bind into the sub-domain IIA of the proteins in 1:1 stoichiometry with an apparent binding constant value in the range of 10(4) dm(3) mol(-1). In both the cases, the spontaneous ligand binding to the proteins occur through entropy driven mechanism, although the interaction of DMACA is relatively stronger in comparison with EDAC. The temperature dependence of the binding constant indicates the induced change in protein secondary structure. PMID:21247795

  8. 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 exclude source of artifacts. At the moment of writing, the atlas has reached version 2.0, and most likely it will be updated by fall with an improved version. Moreover, the current number of 56 maps will increase as soon as new parameters, or a combination of them, will be added to the atlas.

  9. 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…

  10. 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.

  11. 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.

  12. 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.

  13. Spatial probabilistic approach on landslide susceptibility assessment from high resolution sensors derived parameters

    NASA Astrophysics Data System (ADS)

    Aman, S. N. A.; Abd Latif, Z.; Pradhan, B.

    2014-02-01

    Landslide occurrence depends on various interrelating factors which consequently initiate to massive mass of soil and rock debris that move downhill due to the gravity action. LiDAR has come with a progressive approach in mitigating landslide by permitting the formation of more accurate DEM compared to other active space borne and airborne remote sensing techniques. The objective of this research is to assess the susceptibility of landslide in Ulu Klang area by investigating the correlation between past landslide events with geo environmental factors. A high resolution LiDAR DEM was constructed to produce topographic attributes such as slope, curvature and aspect. These data were utilized to derive second deliverables of landslide parameters such as topographic wetness index (TWI), surface area ratio (SAR) and stream power index (SPI) as well as NDVI generated from IKONOS imagery. Subsequently, a probabilistic based frequency ratio model was applied to establish the spatial relationship between the landslide locations and each landslide related factor. Factor ratings were summed up to obtain Landslide Susceptibility Index (LSI) to construct the landslide susceptibility map.

  14. Azimuthal angle dependence of the Coulomb barrier parameters for the interaction between two deformed nuclei

    SciTech Connect

    Ismail, M.; Adel, A.

    2011-09-15

    The azimuthal angle ({phi}) dependence of the Coulomb barrier parameters (height V{sub b} and position R{sub b}) are studied in the framework of the double-folding model with the realistic M3Y nucleon-nucleon interaction. Different pairs of axially symmetric, deformed nuclei are considered. For the interaction between medium and heavy nuclei, the maximum percentage of {phi} dependence is studied as a function of relative orientations of the interacting nuclei. It appreciably increases as the values of the deformation parameters increase and is sensitive to the hexadecapole deformation. The smallest {phi} variation is found for the relative orientations {theta}{sub P}={theta}{sub T}=90 deg. The {phi} variation of the Coulomb barrier parameters, as calculated in the present paper, is completely different in both magnitude and behavior from those deduced in the widely used proximity approach.

  15. A data base for polymer chromatography: temperature dependence of interaction parameters in liquid adsorption chromatography.

    PubMed

    Trathnigg, Bernd; Cuong, Nguyen Viet; Ahmed, Hasnat

    2009-09-01

    The temperature dependence of retention behaviour of polyethylene glycol (PEG) and its mono- and dimethyl ethers was studied on various RP columns in different mobile phases. The accessible volumes and the interaction parameters were determined from slope and intercept in a plot of the elution volumes of the oligomers of a polymer homologous series as a function of the difference of the elution volumes of consecutive oligomers. A quite different dependence of the interaction parameters was observed in the different mobile phases. While in methanol-water the interaction parameter decreases with increasing temperature, the opposite effect is observed in acetonitrile (ACN)-water. In acetone-water, the temperature dependence is almost negligible. PMID:19714653

  16. 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 .

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  18. Some special derived radar parameters and their development during the life cycle of different thunderstorm types

    NASA Astrophysics Data System (ADS)

    Neuper, Malte; Handwerker, Jan; Beheng, Klaus D.

    2014-05-01

    Data from a C-Band Doppler Radar - located in Southwestern Germany - was used to track different isolated thunderstorms in order to investigate their 4-dimensional developments. This study concentrates especially on the development of some bulk properties, which were calculated from the reflectivity data points that are supposed to represent the thunderstorm. In order to separate the reflectivity data of the investigated thunderstorm from the background and to obtain this data in subsequent datasets the tracking algorithm TRACE3D was used. TRACE3D thereby identifies thunderstorms as continuous regions of strong reflectivities and tracks them in time, giving access to the total life cycle of observed storms. For a further investigation of the development of the storms we defined - next to 'often' used properties like the total volume, the maximum reflectivity, the velocity of a storms' reference point, the total liquid water content and others - some abstract properties like a 'reflectivity mass' as a reflectivity weighted volume, the height of the center of gravity of the thunderstorms' volume and reflectivity mass and some special ratios. These last parameters are also evaluated in relation to some specific, the convective environment representing heights like the level of free convection (LFC), the 0°C and the -10°C level, which were extracted from data of operational upper air rawind soundings. In this presentation the development of the special derived radar parameters of a strong multicell storm and a damaging hail developing supercell are compared. The track of the multicell storm lasted 130 min. and covered a distance of 65 km, whereas the examined track of the supercell lasted for 170 min. and covered a distance of 109 km. Especially the parameters, that are related to the levels of isotherms (0°C, 10°C) as well as to the LFC showed distinct differences. It was found, for example, that for the supercell thunderstorms the height of the center of gravity of the thunderstorms' volume and reflectivity mass were located during the entire period above the 0°C level and showed just a slight oscillation. In the case of the thunderstorms' volume the height was even located above the -10°C level for a considerably long period (after which - by the way - large hail was reported). The multicell thunderstorm on the other hand indicated a pronounced oscillation of the parameters over significantly greater distances and only relatively short crossings of different levels of isotherms by a new updraft pulse within the regular multicell life cycle. It thus seems that the height of the center of gravity above a specific level and the time it remains there can serve as a distinction between the storm types and indicate a short-term development.

  19. 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 (these 3 sections, a) b) c) represent the first one centimeter of the specimen from the bottom); d) and the fourth and top section, which shows no influence by the effect of urine capillary absorption. The obtained results showed, from bottom to top, the following crystallized salts: a) abundant prismatic crystals enriched in P and Ca (calcium phosphate); b) amorphous round-shaped potassium sulfate crystals and cubic sodium chloride crystals embedded in an organic matrix; d) cubic sodium chloride crystals are dominant. In the unaffected area, no other crystals were detected different from the carbonate minerals forming the rock. These results are in accordance to which has already been published by the authors in granitic materials (Cámara et al 2014). Acknowledgements: to Geomateriales 2 programme (S2013/MIT-2914) funded by the Community of Madrid. Cámara B., Alvarez de Buergo, M.; Fort, R.; Ascaso, C. de los Rios, A.; Gomez-Heras, M. 2014. Another source of soluble salts in urban environments due to recent social behaviour pattern in historical centres. In: Science, Technology and Cultural Heritage (edited by M.A. Rogerio-Candelera), 89-94. CRC Press-Balkema, Taylor and Francis. ISBN 9781138027442 - CAT# K25502

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  1. 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.

  2. 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.

  3. 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.

  4. SEVEN-YEAR WILKINSON MICROWAVE ANISOTROPY PROBE (WMAP ) OBSERVATIONS: POWER SPECTRA AND WMAP-DERIVED PARAMETERS

    SciTech Connect

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

    2011-02-01

    The WMAP mission has produced sky maps from seven years of observations at L2. We present the angular power spectra derived from the seven-year maps and discuss the cosmological conclusions that can be inferred from WMAP data alone. With the seven-year data, the temperature (TT) spectrum measurement has a signal-to-noise ratio per multipole that exceeds unity for l < 919; and in band powers of width {Delta}l = 10, the signal-to-noise ratio exceeds unity up to l = 1060. The third acoustic peak in the TT spectrum is now well measured by WMAP. In the context of a flat {Lambda}CDM model, this improvement allows us to place tighter constraints on the matter density from WMAP data alone, {Omega}{sub m} h {sup 2} = 0.1334{sup +0.0056}{sub -0.0055}, and on the epoch of matter-radiation equality, z{sub eq} = 3196{sup +134}{sub -133}. The temperature-polarization (TE) spectrum is detected in the seven-year data with a significance of 20{sigma}, compared to 13{sigma} with the five-year data. We now detect the second dip in the TE spectrum near l {approx} 450 with high confidence. The TB and EB spectra remain consistent with zero, thus demonstrating low systematic errors and foreground residuals in the data. The low-l EE spectrum, a measure of the optical depth due to reionization, is detected at 5.5{sigma} significance when averaged over l = 2-7: l(l + 1)C {sup EE}{sub l}/(2{pi}) = 0.074{sup +0.034}{sub -0.025} {mu}K{sup 2} (68% CL). We now detect the high-l, 24 {<=} l {<=} 800, EE spectrum at over 8{sigma}. The BB spectrum, an important probe of gravitational waves from inflation, remains consistent with zero; when averaged over l = 2-7, l(l + 1)C {sup BB}{sub l}/(2{pi}) < 0.055 {mu}K{sup 2} (95% CL). The upper limit on tensor modes from polarization data alone is a factor of two lower with the seven-year data than it was using the five-year data. The data remain consistent with the simple {Lambda}CDM model: the best-fit TT spectrum has an effective {chi}{sup 2} of 1227 for 1170 degrees of freedom, with a probability to exceed of 9.6%. The allowable volume in the six-dimensional space of {Lambda}CDM parameters has been reduced by a factor of 1.5 relative to the five-year volume, while the {Lambda}CDM model that allows for tensor modes and a running scalar spectral index has a factor of three lower volume when fit to the seven-year data. We test the parameter recovery process for bias and find that the scalar spectral index, n{sub s} , is biased high, but only by 0.09{sigma}, while the remaining parameters are biased by <0.15{sigma}. The improvement in the third peak measurement leads to tighter lower limits from WMAP on the number of relativistic degrees of freedom (e.g., neutrinos) in the early universe: N{sub eff}>2.7(95%CL). Also, using WMAP data alone, the primordial helium mass fraction is found to be Y{sub He} = 0.28{sup +0.14}{sub -0.15}, and with data from higher-resolution cosmic microwave background experiments included, we now establish the existence of pre-stellar helium at >3{sigma}. These new WMAP measurements provide important tests of big bang cosmology.

  5. 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 characteristics, such as, onset time, duration and size of hail. The results of the analysis for the time evolution of the storm cells properties enabled the identification of the following key signatures for hail-producing cells: storm volume varying between at least 250 km3 and 1850 km3; average speed of more than 50 km/h; FOKR and POH indices with values between 3 and 4 and 0,8 to 1, respectively, observed at the same time as hail was reported to have fallen on the ground; HMA parameters (mass of hail accumulated aloft) peaking between 80 tons and 808 tons, preceding the time of the hail observed on the ground. The onset of hail, indicated in the reports, corroborates the time near the observed collapse of the cell indicated by a decreasing value of the severity indices provided by TITAN. This ongoing research will add more cases to include not only hail-producing cells, but also those associated with extreme winds and flash floods, to contribute towards the improvement of IPMet's radar bulletins issued routinely by the operational sector for the private and public sector, like the Civil Defense Authorities of the state of São Paulo.

  6. 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

  7. 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 ?. We have investigated the ? 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 ? 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 ? 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 ? parameter predicted from solubility parameter theory. Our study complements prior work investigating the interactions between polystyrene and short-chain polyacrylates (n ? 10). To our knowledge, this is the first study to explore the thermodynamic interactions between polystyrene and long-chain poly(n-alkyl acrylates) with n > 10. This work lays the groundwork for the development of multicomponent structured systems (i.e., blends and copolymers) in this class of sustainable materials. PMID:26020581

  8. DATA BASE ANALYZER AND PARAMETER ESTIMATOR (DBAPE) INTERACTIVE COMPUTER PROGRAM--USER'S MANUAL

    EPA Science Inventory

    The Data Base Analyzer and Parameter Estizator (DBAPE) is an interactive computer progran that provides a link between two of EPA's development products--an environmental model and a data base. BAPE was created to encourage and support the use of the RUSTIC model, a newly develop...

  9. 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 NPP and EVI-derived APAR into the Monteith equation. Results indicate spatial variability in LUE values across Iowa and Illinois. Northern regions of both Iowa and Illinois have higher LUE values than southern regions. This trend is reflected in NPP estimates. Results also show that corn has higher LUE values than soybean, resulting in higher NPP for corn than for soybean. Current NPP estimates were compared with NPP estimates from MOD17A3 product and with county inventory-based NPP estimates. Results indicate that current NPP estimates closely agree with inventory-based estimates, and that current NPP estimates are higher than those of the MOD17A3 product. It was also found that when mixed pixels were substituted with nearest pure pixels, revised NPP estimates were improved showing better agreement with inventory-based estimates.

  10. Upper-crustal scattering parameters as derived from induced micro-seismicity and acoustic log data

    NASA Astrophysics Data System (ADS)

    Fielitz, Daniel; Wegler, Ulrich

    2013-04-01

    In deterministic seismology it is assumed, that each inhomogeneity within the traversed medium causes a travel time shift and/or special phase in the observed seismogram. This information may then be used to analyze the properties of the inhomogeneity (e.g. location, size). However, this method is only successful for inhomogeneities larger than the station separation, the Fresnel zone and the wavelength. In the Earth's curst there exist many small-scale heterogeneities. Stochastic models can be used to determine the most important statistical parameters of the small-scale inhomogeneities neglecting their exact locations. In high-frequency seismograms (> 1 Hz) information on heterogeneity and seismic absorption is reflected by wave trains following the direct wave featuring decreasing amplitude with increasing lapse time, know as Coda waves. Since seismic wave propagation through a heterogeneous and absorbing medium is an extremely complex process, it has become common practice to use seismogram envelopes instead of complete waveforms to gain insight in the attenuation properties. Besides the manifestation in high-frequency seismograms information on heterogeneity can be extracted from well-logs. Borehole measurements provide detailed 1D information on the distribution of elastic properties within the upper crust at scales from about one meter to several kilometers. Strong random fluctuations in seismic velocity having short wavelengths superposed on a step-like structure represent here the deterministic and stochastic components of the crustal structure. These observations suggest a description of the crust as a random medium with a broad spectrum of heterogeneity. In the framework of developing techniques for the estimation of attenuation properties in geothermal reservoirs, as part of the German research program Geothermal Energy and High-performance Drilling (gebo), seismogram envelope inversion and statistical analysis of acoustic logs have been applied to data from the German Continental Deep Drilling (KTB) project. In the present research a passive seismic data set is considered which was acquired during a long-term hydraulic fracturing treatment at the KTB in 2000. Induced seismicity was recorded with a temporal seismic network, consisting of 40 stations, at epicentral distances less than 20 km. Processed seismic events have magnitudes Ml ˜ 1.0. Acoustic log data comprise the P- and S-wave velocity distribution logged in two boreholes. In the pilot borehole continuous data reach from the surface (28 m) to a depth of approx. 4000 m, while for the main borehole coherent logs are available between 285 m and 7160 m. Scattering and intrinsic attenuation, derived from micro-seismic events at the KTB, reasonably match regional attenuation models for Southern Germany. In contrast, scattering strength estimated from acoustic log data exceeds the regional attenuation models by one order of magnitude. The scattering coefficient shows weak but almost identical frequency dependence for both types of analysis that is best-described by a power-law form. From the frequency dependence it can be inferred that a von Kármán-type of random medium is a good model for representing the fractured geothermal reservoir at the KTB. The estimated Hurst exponent, related to the scattering coefficient, is also in good agreement with reference values derived for the upper crust.

  11. 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.

  12. 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.

  13. Determination of the accessible volume and the interaction parameter in the adsorption mode of liquid chromatography.

    PubMed

    Trathnigg, Bernd; Skvortsov, Alexander

    2006-09-15

    The main physical parameters in liquid chromatography of oligomers-the accessible volume and the adsorption interaction parameter-are discussed. It is shown, that in liquid adsorption chromatography (LAC) there is a linear relation between elution volume and the distance of two subsequent peaks of a homologous series. From the intercept of the regression lines in such a plot the accessible volume can be easily determined at any mobile phase in LAC (corresponding to conditions of weak or strong adsorption) without any information about the molar mass of the peaks. From the slope of this dependence the adsorption interaction parameter of a given repeat unit can be obtained. The accurate determination of the accessible volume and the adsorption interaction parameter in the LAC regime is presented for PEG, PPG and fatty alcohols on various reversed phase columns with different pore size in methanol-water or acetone-water mobile phases. The difference between the void volume, the dead volume or hold-up volume (from the solvent peak position) and the accessible volume (obtained by this procedure) is discussed. PMID:16806253

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

    PubMed

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

    2012-11-01

    Recent work indicates that the interaction between body-size-dependent demographic processes can generate macroecological patterns such as the scaling of population density with body size. In this study, we evaluate this possibility for grazing protists and also test whether demographic parameters in these models are correlated after controlling for body size. We compiled data on the body-size dependence of consumer-resource interactions and population density for heterotrophic protists grazing algae in laboratory studies. We then used nested dynamic models to predict both the height and slope of the scaling relationship between population density and body size for these protists. We also controlled for consumer size and assessed links between model parameters. Finally, we used the models and the parameter estimates to assess the individual- and population-level dependence of resource use on body-size and prey-size selection. The predicted size-density scaling for all models matched closely to the observed scaling, and the simplest model was sufficient to predict the pattern. Variation around the mean size-density scaling relationship may be generated by variation in prey productivity and area of capture, but residuals are relatively insensitive to variation in prey size selection. After controlling for body size, many consumer-resource interaction parameters were correlated, and a positive correlation between residual prey size selection and conversion efficiency neutralizes the apparent fitness advantage of taking large prey. Our results indicate that widespread community-level patterns can be explained with simple population models that apply consistently across a range of sizes. They also indicate that the parameter space governing the dynamics and the steady states in these systems is structured such that some parts of the parameter space are unlikely to represent real systems. Finally, predator-prey size ratios represent a kind of conundrum, because they are widely observed but apparently have little influence on population size and fitness, at least at this level of organization. PMID:22803630

  15. Kinetic theory of turbulence modeling: smallness parameter, scaling and microscopic derivation of Smagorinsky model

    NASA Astrophysics Data System (ADS)

    Ansumali, Santosh; Karlin, Iliya V.; Succi, Sauro

    2004-07-01

    A mean-field approach (filtering out subgrid scales) is applied to the Boltzmann equation in order to derive a subgrid turbulence model based on kinetic theory. It is demonstrated that the only Smagorinsky type model which survives in the hydrodynamic limit on the viscosity time scale is the so-called tensor-diffusivity model. Scaling of the filter-width with Reynolds number and Knudsen number is established. This sets the first rigorous step in deriving turbulence models from kinetic theory.

  16. 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.

  17. 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.

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

    SciTech Connect

    Ohya, Satoshi

    2014-12-15

    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. - Highlights: • Supersymmetric quantum mechanics is an ideal playground for studying geometric phase. • We determine the parameter space of supersymmetric point-like interactions. • Berry’s connection is given by a Wu–Yang-like magnetic monopole in SU(2) Yang–Mills.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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.

  4. Parameter estimation in stochastic chemical kinetic models using derivative free optimization and bootstrapping

    PubMed Central

    Srivastava, Rishi; Rawlings, James B.

    2014-01-01

    Recent years have seen increasing popularity of stochastic chemical kinetic models due to their ability to explain and model several critical biological phenomena. Several developments in high resolution fluorescence microscopy have enabled researchers to obtain protein and mRNA data on the single cell level. The availability of these data along with the knowledge that the system is governed by a stochastic chemical kinetic model leads to the problem of parameter estimation. This paper develops a new method of parameter estimation for stochastic chemical kinetic models. There are three components of the new method. First, we propose a new expression for likelihood of the experimental data. Second, we use sample path optimization along with UOBYQA-Fit, a variant of of Powells unconstrained optimization by quadratic approximation, for optimization. Third, we use a variant of Efrons percentile bootstrapping method to estimate the confidence regions for the parameter estimates. We apply the parameter estimation method in an RNA dynamics model of E. coli. We test the parameter estimates obtained and the confidence regions in this model. The testing of the parameter estimation method demonstrates the efficiency, reliability, and accuracy of the new method. PMID:24920866

  5. 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.

  6. 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.

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

    PubMed Central

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

    2015-01-01

    Opportunistic fungal pathogens can cause bloodstream infection and severe sepsis upon entering the blood stream of the host. The early immune response in human blood comprises the elimination of pathogens by antimicrobial peptides and innate immune cells, such as neutrophils or monocytes. Mathematical modeling is a predictive method to examine these complex processes and to quantify the dynamics of pathogen-host interactions. Since model parameters are often not directly accessible from experiment, their estimation is required by calibrating model predictions with experimental data. Depending on the complexity of the mathematical model, parameter estimation can be associated with excessively high computational costs in terms of run time and memory. We apply a strategy for reliable parameter estimation where different modeling approaches with increasing complexity are used that build on one another. This bottom-up modeling approach is applied to an experimental human whole-blood infection assay for Candida albicans. Aiming for the quantification of the relative impact of different routes of the immune response against this human-pathogenic fungus, we start from a non-spatial state-based model (SBM), because this level of model complexity allows estimating a priori unknown transition rates between various system states by the global optimization method simulated annealing. Building on the non-spatial SBM, an agent-based model (ABM) is implemented that incorporates the migration of interacting cells in three-dimensional space. The ABM takes advantage of estimated parameters from the non-spatial SBM, leading to a decreased dimensionality of the parameter space. This space can be scanned using a local optimization approach, i.e., least-squares error estimation based on an adaptive regular grid search, to predict cell migration parameters that are not accessible in experiment. In the future, spatio-temporal simulations of whole-blood samples may enable timely stratification of sepsis patients by distinguishing hyper-inflammatory from paralytic phases in immune dysregulation. PMID:26150807

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed Central

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

    2014-01-01

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

  10. 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...

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

    PubMed

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

    2016-01-26

    The identification of potential drug-target interaction pairs is very important, which is useful not only for providing greater understanding of protein function, but also for enhancing drug research, especially for drug function repositioning. Recently, numerous machine learning-based algorithms (e.g. kernel-based, matrix factorization-based and network-based inference methods) have been developed for predicting drug-target interactions. All these methods implicitly utilize the assumption that similar drugs tend to target similar proteins and yield better results for predicting interactions between drugs and target proteins. To further improve the accuracy of prediction, a new method of network-based label propagation with mutual interaction information derived from heterogeneous networks, namely LPMIHN, is proposed to infer the potential drug-target interactions. LPMIHN separately performs label propagation on drug and target similarity networks, but the initial label information of the target (or drug) network comes from the drug (or target) label network and the known drug-target interaction bipartite network. The independent label propagation on each similarity network explores the cluster structure in its network, and the label information from the other network is used to capture mutual interactions (bicluster structures) between the nodes in each pair of the similarity networks. As compared to other recent state-of-the-art methods on the four popular benchmark datasets of binary drug-target interactions and two quantitative kinase bioactivity datasets, LPMIHN achieves the best results in terms of AUC and AUPR. In addition, many of the promising drug-target pairs predicted from LPMIHN are also confirmed on the latest publicly available drug-target databases such as ChEMBL, KEGG, SuperTarget and Drugbank. These results demonstrate the effectiveness of our LPMIHN method, indicating that LPMIHN has a great potential for predicting drug-target interactions. PMID:26675534

  12. Interactions of acylated methylglucoside derivatives with CO2: simulation and calculations.

    PubMed

    Chang, H H; Cao, R X; Yang, C C; Wei, W L; Pang, X Y; Qiao, Y

    2016-01-01

    Carbohydrates have drawn considerable interest from researchers recently due to their affinity for CO2. However, most of the research in this field has focused on peracetylated derivatives. Compared with acetylated carbohydrates, which have already been studied in depth, methyl D-glucopyranoside derivatives are more stable and could have additional applications. Thus, in the present work, ab initio calculations were performed to elucidate the characteristics of the interactions of methylglucoside derivatives with CO2, and to investigate how the binding energy (ΔE) is affected by isomerization or the introduction of various acyl groups. Four methyl D-glucopyranosides (each with two anomers) bearing acetyl, propionyl, butyryl, and isobutyryl moieties, respectively, were designed as substrates, and the 1:1 complexes of a CO2 molecule with each of these sugar substrates were modeled. The results indicate that ΔE is mainly influenced by interaction distance and the number of negatively charged donors or interacting pairs in the complex; the structure of the acyl group present in the substrate is a secondary influence. Except in the case of methyl 2-O-acetyl-D-glucopyranose, the ΔE values of the α- and β-anomers of each methylglucoside were found to be almost the same. Therefore, we would expect the CO2 affinities of the four derivatives studied here to be as strong as or even stronger than that of peracetylated D-glucopyranose. Graphical Abstract The binding energy between methyl D-glucopyranoside derivatives with various substituted acyl groups and CO2 are evaluated by ab initio calculations. The strong interaction between these methyl dglucopyranoside derivatives and CO2 showed the potential of their application for CO2 capture. PMID:26781667

  13. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

    Kleinjung, Jens; Scott, Walter R P; Allison, Jane R; van Gunsteren, Wilfred F; Fraternali, Franca

    2012-07-10

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

  16. 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

  17. 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 highlands (0.47×0.16). Since c controls the fraction of backward/forward scattering in H-G2, lower c for the maria indicates more forward scattering relative to the highlands. This trend is opposite to what was expected because darker particles are usually more backscattering. However, the lower albedo of the maria is due to the higher abundance of ilmenite, which is an opaque mineral that scatters all of the light by specular reflection from the its surface. If their surface facets are relatively smooth the ilmenite particles will be forward scattering. Other factors (e.g. grain shape, grain size, porosity, maturity) besides the mineralogy might also be affecting c. The angular-width of SHOE (hs) typically shows lower values (0.047×0.02) for the maria relative to the highlands (0.074×0.025). An increase in hs for the maria theoretically suggests lower porosity or a narrower grain size distribution [1], but the link between actual materials and hs is not well constrained. Further experiments using both laboratory and spacecraft observations will help to unravel the photometric properties of the surface materials of the Moon. [1] Hapke, B.: Cambridge Univ. Press, 2012. [2] Sato, H. et al.: 42nd LPSC, abstract #1974, 2011. [3] Scholten, F. et al.: JGR, 117, E00H17, 2012. [4] Hapke, B.: Icarus, 221(2), p1079-1083, 2012.

  18. 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.

  19. 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

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

    NASA Astrophysics Data System (ADS)

    Steyaert, Louis T.; Knox, Robert 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.

  1. User's manual for DWNWND: an interactive Gaussian plume atmospheric transport model with eight dispersion parameter options

    SciTech Connect

    Fields, D.E.; Miller, C.W.

    1980-05-01

    The most commonly used approach for estimating the atmospheric concentration and deposition of material downwind from its point of release is the Gaussian plume atmospheric dispersion model. Two of the critical parameters in this model are sigma/sub y/ and sigma/sub z/, the horizontal and vertical dispersion parameters, respectively. A number of different sets of values for sigma/sub y/ and sigma/sub z/ have been determined empirically for different release heights and meteorological and terrain conditions. The computer code DWNWND, described in this report, is an interactive implementation of the Gaussian plume model. This code allows the user to specify any one of eight different sets of the empirically determined dispersion paramters. Using the selected dispersion paramters, ground-level normalized exposure estimates are made at any specified downwind distance. Computed values may be corrected for plume depletion due to deposition and for plume settling due to gravitational fall. With this interactive code, the user chooses values for ten parameters which define the source, the dispersion and deposition process, and the sampling point. DWNWND is written in FORTRAN for execution on a PDP-10 computer, requiring less than one second of central processor unit time for each simulation.

  2. Whirling and stability of flywheel systems, part I: Derivation of combined and lumped parameter models

    NASA Astrophysics Data System (ADS)

    Ramanujam, G.; Bert, C. W.

    1983-06-01

    The objective of this paper is to provide a theoretical foundation to predict many aspects of dynamic behavior of flywheel systems when spin-tested with a quill shaft support and driven by an air turbine. Theoretical analyses for the following are presented: (1) determination of natural frequencies (or for brevity critical speeds of various orders), (2) Routh-type stability analysis to determine the stability limits (i.e., the speed range within which small perturbations attenuate rather than cause catastrophic failure), and (3) forced whirling analysis to estimate the response of major components of the system to flywheel mass eccentricity and initial tilt. For the first and third kinds of analyses, two different mathematical models of the generic system are investigated. One is a seven-degree-of-freedom lumped parameter analysis, while the other is a combined distributed and lumped parameter analysis.

  3. 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 9010 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 ? between the propagation direction and the plan of the sky). We find that the radial velocities and the ?-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.

  4. Vaccinia virus p37 interacts with host proteins associated with LE-derived transport vesicle biogenesis

    PubMed Central

    Chen, Yali; Honeychurch, Kady M; Yang, Guang; Byrd, Chelsea M; Harver, Chris; Hruby, Dennis E; Jordan, Robert

    2009-01-01

    Background Proteins associated with the late endosome (LE) appear to play a central role in the envelopment of a number of taxonomically diverse viruses. How viral proteins interact with LE-associated proteins to facilitate envelopment is not well understood. LE-derived transport vesicles form through the interaction of Rab9 GTPase with cargo proteins, and TIP47, a Rab9-specific effector protein. Vaccinia virus (VV) induces a wrapping complex derived from intracellular host membranes to envelope intracellular mature virus particles producing egress-competent forms of virus. Results We show that VV p37 protein associates with TIP47-, Rab9-, and CI-MPR-containing membranes. Mutation of a di-aromatic motif in p37 blocks association with TIP47 and inhibits plaque formation. ST-246, a specific inhibitor of p37 function, inhibits these interactions and also blocks wrapped virus particle formation. Vaccinia virus expressing p37 variants with reduced ST-246 susceptibility associates with Rab9 and co-localizes with CI-MPR in the presence and absence of compound. Conclusion These results suggest that p37 localizes to the LE and interacts with proteins associated with LE-derived transport vesicle biogenesis to facilitate assembly of extracellular forms of virus. PMID:19400954

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. The interaction of folic acid derivatives in the methylation of homocysteine

    PubMed Central

    Guest, J. R.; Woods, D. D.

    1965-01-01

    1. The cobalamin-independent synthesis of methionine from serine and homocysteine by ultrasonic extracts of E. coli with tetrahydropteroyltriglutamate as cofactor was inhibited competitively by tetrahydropteroylmonoglutamate and derivatives which were readily converted into this compound. 2. The potency of these inhibitors was directly related to their ability to function as cofactors or substrates in the alternative, cobalamin- dependent mechanism for homocysteine methylation. 3. The cobalamin-dependent and -independent mechanisms of homocysteine methylation were both inhibited by reduced derivatives of aminopterin in a similar manner. 4. It was tentatively concluded that the inhibition was due to a competitive interaction between the folates for N5N10-methylenetetrahydrofolate reductase. PMID:16749156

  10. 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 parameter for soil organic matter.

  11. Intercomparisons of GOES-derived cloud parameters and surface observations over San Nicolas Island

    NASA Technical Reports Server (NTRS)

    Minnis, Patrick; Fairall, C. W.; Young, David F.

    1990-01-01

    The spatial sampling limitations of surface measurement systems necessitate the use of satellite data for the investigation of large-scale cloud processes. Understanding the information contained in the satellite-observed radiances, however, requires a connection between the remotely sensed cloud properties and those more directly observed within the troposphere. Surface measurements taken during the First ISCCP Regional Experiment (FIRE) Marine Stratocumulus Intensive Field Observations (IFO) are compared here to cloud properties determined from Geostationary Operational Environmental Satellite (GOES) data in order to determine how well the island measurements represent larger areas and to verify some of the satellite-measured parameters.

  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 frame reference. Restrictions: Low Earth orbits, altitudes between 150 and 2000 km. Running time: Approximately two seconds to parameterize a full orbit with 1000 points.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  16. 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

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

    PubMed

    Rowan-Robinson, M

    1993-06-01

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

  18. TID Parameters over the Antarctic Peninsula as Derived from TEC Measurements.

    NASA Astrophysics Data System (ADS)

    Paznukhov, V.; Galushko, V.; Groves, K. M.; Sopin, A.; Yampolski, Y.

    2014-12-01

    Results of TID analysis from multi-site TEC observations over the Antarctic Peninsula for the period from 2009 to 2012 are presented. Diurnal dependences of the occurrence frequency, and motion velocity and direction probability density distributions are determined for middle-scale traveling ionospheric disturbances (MSTIDs). TID parameters are calculated using dynamic approach to the problem of ionospheric disturbance diagnostics which has been extended to allow for an arbitrary waveform of TEC perturbations. We have also developed a dedicated algorithm to determine the presence of TID disturbances in the TEC records which is based on the correlation analysis. Statistical treatment of the obtained results shows that during daytime the TIDs propagate predominantly in the northern and northeastern directions. In the evening and nocturnal hours the northwestern direction is prevailing, with the characteristic TID velocities range from 10 to 250 m/s. The most probable TID velocities are tens of meters per second, while the mean values are equal to about 100 - 130 m/s. During the daytime the velocities of the ionospheric disturbances are even higher. The work also presents variations of the TID parameters with seasons and geomagnetic conditions and the role of the solar terminator as a possible source of the disturbances is discussed.

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

    PubMed Central

    Rowan-Robinson, M

    1993-01-01

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

  20. Prevalence of Keratoconus and Subclinical Keratoconus in Subjects with Astigmatism Using Pentacam Derived Parameters

    PubMed Central

    Serdarogullari, Huseyin; Tetikoglu, Mehmet; Karahan, Hatice; Altin, Feyza; Elcioglu, Mustafa

    2013-01-01

    Purpose To determine the prevalence of keratoconus (KCN) and subclinical KCN among subjects with two or more diopters (D) of astigmatism, and to compare Pentacam parameters among these subjects. Methods One hundred and twenty eight eyes of 64 subjects with astigmatism ≥2D were included in the study. All subjects underwent a complete ophthalmic examination which included refraction, visual acuity measurement, slit lamp biomicroscopy, retinoscopy, fundus examination, conventional corneal topography and elevation-based topography with Pentacam. The diagnosis of KCN and subclinical KCN was made by observing clinical findings and topographic features; and confirmed by corneal thickness and elevation maps of Pentacam. Several parameters acquired from Pentacam were analyzed employing the Mann-Whitney U Test. Results Mean age of the study population was 29.9±9.8 (range 15-45) years which included 39 (60.9%) female and 25 (39.1%) male subjects. Maximum corneal power, index of vertical asymmetry, keratoconus index and elevation values were significantly higher and pachymetry was significantly thinner in eyes with clinical or subclinical KCN than normal astigmatic eyes (P< 0.05). Conclusion The current study showed that subjects with 2D or more of astigmatism who present to outpatient clinics should undergo corneal topography screening for early diagnosis of KCN even if visual acuity is not affected. Pentacam may provide more accurate information about anterior and posterior corneal anatomy especially in suspect eyes. PMID:24349664

  1. Snow Parameters Derived from Microwave Measurements During the BOREAS Winter Field Campaign

    NASA Technical Reports Server (NTRS)

    Chang, A. T. C.; Foster, J. L.; Hall, D. K.; Goodison, B. E.; Walker, A. E.; Metcalfe, J. R.; Harby, A.

    1997-01-01

    Passive microwave data have been used to infer the snow-covered area and snow water equivalent (SWE) over forested areas, but the accuracy of these retrieved snow parameters cannot be easily validated for heterogeneous vegetated regions. The Boreal Ecosystem-Atmosphere Study Winter Field Campaign provided the opportunity to study the effect of boreal forests on snow parameter retrieval in detail. Microwave radiometers (18, 37, and 92 GHz) were flown on board the Canadian National Aeronautical Establishment's Twin Otter. Flight lines covered both the southern study area near Prince Albert and the northern study area near Thompson, Canada. During the 1994 winter campaign, extensive ground-based snow cover information, including depth, density, and grain size, was collected along most of the flight lines, jointly by U.S. and Canadian investigators. Satellite data collected by the special sensor microwave imager are also used for comparison. Preliminary results reconfirmed the relationship between microwave brightness temperature and SWE. However, the effect of forest cover observed by the aircraft sensors is different from that of the satellite observations. This is probably due to the difference in footprint averaging. There were also several flight lines flown over Candle Lake and Waskesiu Lake to assess lake ice signatures. Preliminary results show the thickness of the lake ice may be inferred from the airborne microwave observations. The microwave signature relationship between lake ice and snow matches the results from radiative transfer calculations.

  2. Snow parameters derived from microwave measurements during the BOREAS winter field campaign

    NASA Astrophysics Data System (ADS)

    Chang, A. T. C.; Foster, J. L.; Hall, D. K.; Goodison, B. E.; Walker, A. E.; Metcalfe, J. R.; Harby, A.

    1997-12-01

    Passive microwave data have been used to infer the snow-covered area and snow water equivalent (SWE) over forested areas, but the accuracy of these retrieved snow parameters cannot be easily validated for heterogeneous vegetated regions. The Boreal Ecosystem-Atmosphere Study Winter Field Campaign provided the opportunity to study the effect of boreal forests on snow parameter retrieval in detail. Microwave radiometers (18, 37, and 92 GHz) were flown on board the Canadian National Aeronautical Establishment's Twin Otter. Flight lines covered both the southern study area near Prince Albert and the northern study area near Thompson, Canada. During the 1994 winter campaign, extensive ground-based snow cover information, including depth, density, and grain size, was collected along most of the flight lines, jointly by U.S. and Canadian investigators. Satellite data collected by the special sensor microwave imager are also used for comparison. Preliminary results reconfirmed the relationship between microwave brightness temperature and SWE. However, the effect of forest cover observed by the aircraft sensors is different from that of the satellite observations. This is probably due to the difference in footprint averaging. There were also several flight lines flown over Candle Lake and Waskesiu Lake to assess lake ice signatures. Preliminary results show the thickness of the lake ice may be inferred from the airborne microwave observations. The microwave signature relationship between lake ice and snow matches the results from radiative transfer calculations.

  3. 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

  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. 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-pregnant females and during pregnancy. This is the first of such comprehensive study to establish reference values among adult Nigerians and difference observed underscore the need to establish reference values for different populations. PMID:24832127

  6. 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.

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

    SciTech Connect

    Pederson, Mark R.

    2015-02-14

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Improved snow interception modeling using canopy parameters derived from airborne LiDAR data

    NASA Astrophysics Data System (ADS)

    Moeser, D.; Stähli, M.; Jonas, T.

    2015-07-01

    Forest snow interception can account for large snow storage differences between open and forested areas. The effect of interception can also lead to significant variations in sublimation, with estimates varying from 5 to 60% of total snowfall. Most current interception models utilize canopy closure and LAI to partition interception from snowfall and calculate interception efficiency as an exponential decrease of interception efficiency with increasing precipitation. However, as demonstrated, these models can show specific deficiencies within heterogeneous canopy. Seven field areas were equipped with 1932 surveyed points within various canopy density regimes in three elevation bands surrounding Davos, Switzerland. Snow interception measurements were taken from 2012 to 2014 (˜9000 samples) and compared with measurements at two open sites. The measured data indicated the presence of snow bridging from a demonstrated increase in interception efficiency as precipitation increased until a maximum was reached. As precipitation increased beyond this maximum, the data then exhibited a decrease in interception efficiency. Standard and novel canopy parameters were developed using aerial LiDAR data. These included estimates of LAI, canopy closure, distance to canopy, gap fraction, and various tree size parameters. These canopy metrics and the underlying efficiency distribution were then integrated to formulate a conceptual model based upon the snow interception measurements. This model gave a ˜27% increase in the r2 (from 0.39 to 0.66) and a ˜40% reduction in RMSE (from 5.19 to 3.39) for both calibration and validation data sets when compared to previous models at the point scale. When upscaled to larger grid sizes, the model demonstrated further increases in performance.

  13. 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.

  14. 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.

  15. Interaction of Salmonella typhi strains with cultured human monocyte-derived macrophages.

    PubMed Central

    Sizemore, D R; Elsinghorst, E A; Eck, L C; Branstrom, A A; Hoover, D L; Warren, R L; Rubin, F A

    1997-01-01

    Human monocyte-derived macrophages (MDM) provided this laboratory with a tool to develop a primary-cell assay for evaluating the relative virulence of newly constructed Salmonella typhi carrier strains. In this study, the interaction with and survival within MDM were compared for delta aroA143-attenuated strains, wild-type virulent strains, and the current oral-vaccine strain, Ty21a. PMID:8975929

  16. 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. Importantly, the changes in water-SOM interactions induced by the presence of organic compounds may demonstrate the cooperative behavior: (1) several water molecules may be involved in an enhanced hydration of SOM, (2) at the presence of an organic sorbate, interactions of water molecules with SOM enhance the uptake of the following water molecules. The proposed cooperative water-SOM interactions may result from a perturbation of the SOM matrix due to a sorption of organic and water molecules where a partial disrupting of molecular contacts in SOM makes easier the following SOM-water interactions thus promoting the enhanced SOM hydration.

  17. Electronic polarizability and interaction parameter of gadolinium tungsten borate glasses with high WO3 content

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Glasses with the compositions of 25Gd2O3-xWO3-(75-x)B2O3 with x=25-65 were prepared by using a conventional melt quenching method, and their electronic polarizabilities, optical basicities Λ(no), and interaction parameters A(no) 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 WO3 contents. The optical basicity of the glasses increases monotonously with the substitution of WO3 for B2O3, and contrary the interaction parameter decreases monotonously with increasing WO3 content. A good linear correlation was observed between Λ(no) and A(no) and between the glass transition temperature and A(no). It was proposed that Gd2O3 oxide belongs to the category of basic oxide with a value of A(no)=0.044 Å-3 as similar to WO3. The relationship between the glass formation and electronic polarizability in the glasses was discussed, and it was proposed that the glasses with high WO3 and Gd2O3 contents would be a floppy network system consisting of mainly basic oxides.

  18. Interaction between chitosan and uranyl ions. Part 1. Role of physicochemical parameters.

    PubMed

    Piron, E; Domard, A

    1997-12-01

    This work is devoted to the comprehension of the sorption mechanism of uranyl ions on chitosan particle dispersions. The uranyl concentration measurements were obtained by inductively coupled plasma atomic emission spectrometry (ICP-AES) and we considered the role of various physicochemical parameters (pH; nature and concentration of added salts; degree of acetylation, DA). The use of appropriate calculation software allowed us to determine the chemical nature of uranyl species in solution in relation to these different parameters. The optimal pH of fixation has been found to be within 6.5-7.5 and can be related to the necessity of having both deprotonated amino groups and no carbonate ions, which are a strong complexant of uranyl ions, thus inhibiting their interaction with chitosan. The decrease of metal uptake with an increase of DA and the lack of influence of ionic strength, confirm the results obtained with pH and allowed us to suppose the formation of a complex with chitosan amino groups rather than interactions of an electrostatic nature. PMID:9493056

  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. 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 soil.In both cases both the 2-m and surface skin UHIs showed positive values at night and negative values (an urban cool island, UCI) during the day. The larger nighttime 2-m UHI was on the dry day (0.8° vs 0.6°C), while the larger daytime 2-m UCI was on the moist soil day (0.3° vs 0.5°C). Note that the surface differences were almost always greater than the 2-m differences.These day-night differences imply a rural thermal inertia lower than its urban values on both days, which is in conflict with the observations on the wet uniform soil moisture day. On the uniform thermal inertia day (wet day), both the UHI and UCI amplitudes should be less than on the other day, but this is not the case. A possible explanation for both of these conflicts is the improper influence of the urban plume on this day on lowering the thermal inertia and moisture availability values used in the replacement urban simulation.

  1. Simple interpretation of nuclear orientation for Coulomb barrier distributions derived from a realistic effective interaction

    SciTech Connect

    Ismail, M.; Seif, W. M.

    2010-03-15

    A simple straightforward method has been presented to predict the dependence of barrier distributions at arbitrary orientations on different deformations. The proposed interpretation is developed independently of the complicated numerical calculations. It is related to the change of half-density radius of the deformed nucleus, in the direction of the separation vector. The microscopic calculations of Coulomb barrier are carried out by using a realistic density dependent nucleon-nucleon (NN) interaction, BDM3Y, for the interaction between spherical, {sup 48}Ca, and deformed, {sup 244}Pu, nuclei, as an example. To do so, the double-folding model for the interaction of spherical-deformed nuclei is put in a suitable computational form for the calculation of the potential at several separation distances and orientation angles using the density dependent NN force without consuming computational time. We found that the orientation distributions of the Coulomb barrier parameters show similar patterns to those of the interacting deformed nucleus radius. It is found that the orientation distribution of the Coulomb barrier radius follows the same variation of the deformed nucleus radius while the barrier height distribution follows it inversely. This correlation (anticorrelation) allows a simple evaluation of the orientation barrier distribution which would be very helpful to estimate when the barrier parameters will increase or decrease and at which orientations they will be independent of the deformation. This also allows us to estimate the compact and elongated configurations of the interacting nuclei which lead to hot and cold fusion, respectively.

  2. Simple interpretation of nuclear orientation for Coulomb barrier distributions derived from a realistic effective interaction

    NASA Astrophysics Data System (ADS)

    Ismail, M.; Seif, W. M.

    2010-03-01

    A simple straightforward method has been presented to predict the dependence of barrier distributions at arbitrary orientations on different deformations. The proposed interpretation is developed independently of the complicated numerical calculations. It is related to the change of half-density radius of the deformed nucleus, in the direction of the separation vector. The microscopic calculations of Coulomb barrier are carried out by using a realistic density dependent nucleon-nucleon (NN) interaction, BDM3Y, for the interaction between spherical, Ca48, and deformed, Pu244, nuclei, as an example. To do so, the double-folding model for the interaction of spherical-deformed nuclei is put in a suitable computational form for the calculation of the potential at several separation distances and orientation angles using the density dependent NN force without consuming computational time. We found that the orientation distributions of the Coulomb barrier parameters show similar patterns to those of the interacting deformed nucleus radius. It is found that the orientation distribution of the Coulomb barrier radius follows the same variation of the deformed nucleus radius while the barrier height distribution follows it inversely. This correlation (anticorrelation) allows a simple evaluation of the orientation barrier distribution which would be very helpful to estimate when the barrier parameters will increase or decrease and at which orientations they will be independent of the deformation. This also allows us to estimate the compact and elongated configurations of the interacting nuclei which lead to hot and cold fusion, respectively.

  3. 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 drop, by using the numerical simulator EROS, which is a versatile particle-based numerical method. We first assess the role of each parameter on the form and dynamics of canyon incision. The best-fitting inversion gives values of m, n and Ld of 1.5, 1 and less than 1 km, with reasonable confidence. The exponents are consistent with those obtained from the analysis of topography in tectonically active areas. To our knowledge, it is the first time that Ld is estimated.

  4. 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

  5. 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 is thermodynamically favorable under a broad range of conditions. This includes low temperatures and absence of microbial catalysators. Our approach has potential for use in other applications that involve exploration of relationships in geochemical simulation model data.

  6. 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

  7. Precision and accuracy of the orbital parameters derived from 2D & 1D space observations of visual or astrometric binaries

    NASA Astrophysics Data System (ADS)

    Pourbaix, D.

    2002-04-01

    Recent investigations (e.g. Han et al. \\cite{Han-2001:a}) have shown that fitting the Hipparcos observations with an orbital model when the astrometric wobble caused by the companion is below the noise level can have rather unexpected consequences. With new astrometric missions coming out within the next ten years, it is worth investigating the orbit reconstruction capabilities of such instruments at low signal-to-noise ratio. This is especially important because some of them will have no input catalogue, thus meaning that all the orbital parameters will have to be derived from scratch. The puzzling case of almost parabolic orbits is also investigated.

  8. Theoretical studies of weak interactions of formamide with methanol and its derivates

    NASA Astrophysics Data System (ADS)

    Zheng, Xiao-Wen; Wang, Lu; Han, Shu-Min; Cui, Xiang-Yang; Du, Chong-Yang; Liu, Tao

    2015-08-01

    Theoretical calculations have been performed for the complexes of formamide (FA) with methanol and its derivates (MAX, X = F, Cl, Br, NO2, H, OH, CH3, and NH2) to study their structures and properties. Substituent effects on the hydrogen bond (H-bond) strength and cooperative effect by using water and its derivatives (HOZ, Z = H, NH2, and Br) as weak interaction probe were also explored. The calculation results show that electron-donating groups strengthen the weak interaction between formamide with methanol whereas electron-withdrawing groups weaken it. The cooperativity is present for the N-HïO H-bond in MAX-FA-HOZ and the cooperative effect increases in a series HONH2, HOH, and HOBr. In addition, we investigated the interaction between FA with hypohalous acids HOY (Y = F, Cl, and Br). It was found that the weak interaction between FA and HOY became stronger with the increase of the size of halogen atom. The nature of the halogen atom has negligible impact on the strength of the H-bond in MAX-FA (X = F, Cl, and Br), whereas it has an obvious influence on the strength of the H-bond in HOY-FA (Y = F, Cl, and Br).

  9. 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.

  10. 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.

  11. 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

  12. 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.

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

    PubMed

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

    2016-03-01

    Exercise echocardiography is an underutilized tool in pediatrics with current applications including detecting segmental wall abnormalities, assessing the utility of global ventricular function, and measuring pulmonary hemodynamics. No prior study has applied speckle-tracking echocardiography (STE) during exercise echocardiography in children. The aim of this study was to determine the feasibility of measuring speckle-tracking-derived peak systolic velocities, global longitudinal and circumferential strain, and global strain rates at various phases of exercise. Ninety-seven healthy children underwent cardiopulmonary exercise testing using supine cycle ergometry. The exercise stress test consisted of baseline pulmonary function testing, monitoring of blood pressure and heart rate responses, electrocardiographic recordings, and oxygen saturations while subjects pedaled against a ramp protocol based on body weight. Echocardiographic measurements and specifically speckle-tracking analysis were performed during exercise at baseline, at a heart rate of 160 beats per minute and at 10 min after exercise. Peak systolic velocity, peak systolic strain, and peak systolic strain rate at these three phases were compared in the subjects in which all measurements were accurately obtained. We were able to complete peak velocity, strain, and strain rate measurements in all three exercise phases for 36 out of the 97 subjects tested. There was no significant difference between the feasibility of measuring circumferential versus longitudinal strain (p = 0.25, B-corrected = 0.75). In the 36 subjects studied, the magnitude of circumferential strain values decreased from -18.3 ± 4.8 to -13.7 ± 4.0 % from baseline to HR 160 (p < 0.0001, B-corrected < 0.0001), before returning to -19.6 ± 4.4 % at recovery (p = 0.19 when compared to baseline). Longitudinal strain did not vary significantly from baseline to HR 160 (from -17.7 ± 4.4 to -16.6 ± 4.4 %, p = 0.16); likewise the average recovery strain was no different from those values (-18.4 ± 3.6 %; p = 0.34). Peak circumferential and longitudinal strain rates increased from baseline to HR 160, but neither decreased to baseline levels after 10 min of recovery, which correlated with heart rate variations with exercise. We studied the effects of frame rate on deformation measurements and we observed no difference between measurements taken at lower (<60 frames per second, fps) and higher (≥60 fps) frame rates. This study shows that it is technically difficult to retrospectively measure peak velocities, strain, and strain rate in exercising pediatric subjects with STE. The majority of subjects that were excluded from the study had inadequate echocardiographic images when tachycardic from increased respiratory effort and body movements near peak exercise. Improvements in technique and higher image frame rates could make application of STE to pediatric cardiopulmonary testing more successful in the future. PMID:26671508

  14. 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.

  15. 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.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  18. 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

  19. 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.

  20. 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.

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

    PubMed Central

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

    2015-01-01

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

  2. Soil erosion modelled with USLE and PESERA using QuickBird derived vegetation parameters in an alpine catchment

    NASA Astrophysics Data System (ADS)

    Meusburger, K.; Konz, N.; Schaub, M.; Alewell, C.

    2010-06-01

    The focus of soil erosion research in the Alps has been in two categories: (i) on-site measurements, which are rather small scale point measurements on selected plots often constrained to irrigation experiments or (ii) off-site quantification of sediment delivery at the outlet of the catchment. Results of both categories pointed towards the importance of an intact vegetation cover to prevent soil loss. With the recent availability of high-resolution satellites such as IKONOS and QuickBird options for detecting and monitoring vegetation parameters in heterogeneous terrain have increased. The aim of this study is to evaluate the usefulness of QuickBird derived vegetation parameters in soil erosion models for alpine sites by comparison to Cesium-137 (Cs-137) derived soil erosion estimates. The study site (67 km 2) is located in the Central Swiss Alps (Urseren Valley) and is characterised by scarce forest cover and strong anthropogenic influences due to grassland farming for centuries. A fractional vegetation cover (FVC) map for grassland and detailed land-cover maps are available from linear spectral unmixing and supervised classification of QuickBird imagery. The maps were introduced to the Pan-European Soil Erosion Risk Assessment (PESERA) model as well as to the Universal Soil Loss Equation (USLE). Regarding the latter model, the FVC was indirectly incorporated by adapting the C factor. Both models show an increase in absolute soil erosion values when FVC is considered. In contrast to USLE and the Cs-137 soil erosion rates, PESERA estimates are low. For the USLE model also the spatial patterns improved and showed "hotspots" of high erosion of up to 16 t ha -1 a -1. In conclusion field measurements of Cs-137 confirmed the improvement of soil erosion estimates using the satellite-derived vegetation data.

  3. 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 information for monitoring HIFU treatment. PMID:23878517

  4. 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 useful information for monitoring HIFU treatment.

  5. 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 information for monitoring HIFU treatment. PMID:23878517

  6. 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.

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

    PubMed

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

    2015-11-01

    In this work the novel cationic surfactant derived from lysine (S)-5-acetamido-6-(dodecylamino)-N,N,N-trimethyl-6-oxohexan-1-ammonium chloride, LYCl, was prepared and the physicochemical characterization of its aqueous solutions was carried out. The binding of LYCl to bovine serum albumin, BSA, and to double stranded calf thymus DNA, ctDNA, was investigated using several techniques. Results show that LYCl binding to BSA is followed by a decrease in the α-helix content caused by the unfolding of the protein. LYCl association to ctDNA mainly occurs through groove binding and electrostatic interactions. These interactions cause morphological changes in the polynucleotide from an elongated coil structure to a more compact globular structure, resulting in the compaction of ctDNA. Addition of β-cyclodextrin, β-CD, to the BSA-LYCl and ctDNA-LYCl complexes is followed by the refolding of BSA and the decompaction of ctDNA. This can be explained by the ability of β-CD to hinder BSA-LYCl and ctDNA-LYCl interactions due to the stronger and more specific β-CD-LYCl hydrophobic interactions. The stoichiometry of the β-CD:LYCl inclusion complex and its formation equilibrium constant were determined in this work. The reported procedure using β-CD is an efficient way to refold proteins and to decompact DNA, after the morphological changes caused in the biomolecules by their interaction with cationic surfactants. PMID:26263220

  8. Hirshfeld Surface Investigation of Structure-Directing Interactions within Dipicolinic Acid Derivatives

    PubMed Central

    2015-01-01

    Six compounds based on dipicolinic acid esters have been synthesized and Hirshfeld surfaces used to investigate the structure-directing effects of functional groups in controlling their solid-state behavior. Compounds 14 are 4-bromo dipicolinic acid esters substituted with methyl, ethyl, propyl, and benzyl groups, respectively. The main structure-directing motif within 13 is a pairwise OH interaction involving two carbonyl oxygen atoms and two aromatic H atoms. The introduction of bulky benzyl groups in 4 forces a significant change in the position of this interaction. Compounds 2 and 4 were used in Suzuki coupling reactions to prepare extended analogues 5 and 6, respectively, and their solid-state behavior was also studied using Hirshfeld surfaces. Extension of these dipicolinic acid esters results in the complete loss of the pairwise OH interaction in 5, where the dominant structure-directing motifs are ?-based interactions. However, the pairwise OH interaction reappears for the more flexible 6, demonstrating control of the solid-state structure of these dipicolinic acid derivatives through the choice of functional groups. PMID:25866487

  9. DNA-Binding Interaction Studies of Microwave Assisted Synthesized Sulfonamide Substituted 8-Hydroxyquinoline Derivatives

    PubMed Central

    Dixit, Ritu B.; Patel, Tarosh S.; Vanparia, Satish F.; Kunjadiya, Anju P.; Keharia, Harish R.; Dixit, Bharat C.

    2011-01-01

    Sulfonamide substituted 8-hydroxyquinoline derivatives were prepared using a microwave synthesizer. The interaction of sulfonamide substituted 8-hydroxyquinoline derivatives and their transition metal complexes with Plasmid (pUC 19) DNA and Calf Thymus DNA were investigated by UV spectroscopic studies and gel electrophoresis measurements. The interaction between ligand/metal complexes and DNA was carried out by increasing the concentration of DNA from 0 to 12 μl in UV spectroscopic study, while the concentration of DNA in gel electrophoresis remained constant at 10 μl. These studies supported the fact that, the complex binds to DNA by intercalation via ligand into the base pairs of DNA. The relative binding efficacy of the complexes to DNA was much higher than the binding efficacy of ligands, especially the complex of Cu-AHQMBSH had the highest binding ability to DNA. The mobility of the bands decreased as the concentration of the complex was increased, indicating that there was increase in the interaction between the metal ion and DNA. Complexes of AHQMBSH were excellent for DNA binding as compared to HQMABS. PMID:21773067

  10. Interactions of lactoferricin-derived peptides with LPS and antimicrobial activity.

    PubMed

    Farnaud, Sebastien; Spiller, Claire; Moriarty, Laura C; Patel, Alpesh; Gant, Vanya; Odell, Edward W; Evans, Robert W

    2004-04-15

    Synthetic peptides derived from human and bovine lactoferricin, as well as tritrpticin sequences, were assayed for antimicrobial activity against wild-type Escherichia coli and LPS mutant strains. Antimicrobial activity was only obtained with peptides derived from the bovine lactoferricin sequence and peptides corresponding to chimeras of human and bovine sequences. None of the peptides corresponding to different regions of native human lactoferricin showed any antimicrobial activity. The results underline the importance of the content of tryptophan and arginine residues, and the relative location of these residues for antimicrobial activity. Results obtained for the same assays performed with LPS mutants suggest that lipid A is not the main binding site for lactoferricin which interacts first with the negative charges present in the inner core. Computer modelling of the most active peptides led to a model in which positively charged residues of the cationic peptide interact with negative charges carried by the LPS to disorganise the structure of the outer membrane and facilitate the approach of tryptophan residues to the lipid A in order to promote hydrophobic interactions. PMID:15063486

  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. Comparative studies of different concretes on the basis of some photon interaction parameters.

    PubMed

    Kaur, Updesh; Sharma, J K; Singh, Parjit S; Singh, Tejbir

    2012-01-01

    Different photon interaction parameters viz. linear attenuation coefficient, mass attenuation coefficient, penetration depth, equivalent atomic number, exposure buildup factor have been computed for seven different concretes (ordinary, hematite-serpentine, ilmenite-limonite, basalt-magnetite, ilmenite, steel-scrap and steel magnetite) in the energy region of 0.015-15.0MeV. The computed parameters were studied as a function of incident photon energy, chemical composition and penetration depth of the selected concretes. It has been observed that among the selected concretes, steel magnetite offers maximum value for linear attenuation coefficient, mass attenuation coefficient, equivalent atomic number and least values in terms of penetration depth equivalent to mean free path and exposure buildup factors. Hence, it is concluded that it offers better shielding among the selected concretes. It is expected that in case of any nuclear accident, the presented buildup factor data may be helpful in estimating the effective dose given to people living in buildings constructed from one of the selected concretes. PMID:21820906

  13. 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.

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

    PubMed

    Belozerov, A S; Anisimov, V I

    2014-09-17

    We study the influence of Coulomb interaction parameters on electronic structure and magnetic properties of paramagnetic bcc Fe by means of the local density approximation plus dynamical mean-field theory approach. We consider the local Coulomb interaction in the density-density form as well as in the form with spin rotational invariance approximated by averaging over all directions of the quantization axis. Our results indicate that the magnetic properties of bcc Fe are mainly affected by the Hund's rule coupling J rather than by the Hubbard U. By employing the constrained density functional theory approach in the basis of Wannier functions of spd character, we obtain U = 4 eV and J = 0.9 eV. In spite of the widespread belief that U = 4 eV is too large for bcc Fe, our calculations with the obtained values of U and J result in a satisfactory agreement with the experiment. The correlation effects caused by U are found to be weak even for large U = 6 eV. The agreement between the calculated and experimental Curie temperatures is further improved if J is reduced to 0.8 eV. However, with the decrease of J, the effective local magnetic moment moves further away from the experimental value. PMID:25156797

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

    PubMed

    Warner, Daniel A; Shine, Richard

    2011-01-22

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

  16. 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

  17. Compost mixture influence of interactive physical parameters on microbial kinetics and substrate fractionation.

    PubMed

    Mohajer, Ardavan; Tremier, Anne; Barrington, Suzelle; Teglia, Cecile

    2010-01-01

    Composting is a feasible biological treatment for the recycling of wastewater sludge as a soil amendment. The process can be optimized by selecting an initial compost recipe with physical properties that enhance microbial activity. The present study measured the microbial O(2) uptake rate (OUR) in 16 sludge and wood residue mixtures to estimate the kinetics parameters of maximum growth rate mu(m) and rate of organic matter hydrolysis K(h), as well as the initial biodegradable organic matter fractions present. The starting mixtures consisted of a wide range of moisture content (MC), waste to bulking agent (BA) ratio (W/BA ratio) and BA particle size, which were placed in a laboratory respirometry apparatus to measure their OUR over 4 weeks. A microbial model based on the activated sludge process was used to calculate the kinetic parameters and was found to adequately reproduced OUR curves over time, except for the lag phase and peak OUR, which was not represented and generally over-estimated, respectively. The maximum growth rate mu(m), was found to have a quadratic relationship with MC and a negative association with BA particle size. As a result, increasing MC up to 50% and using a smaller BA particle size of 8-12 mm was seen to maximize mu(m). The rate of hydrolysis K(h) was found to have a linear association with both MC and BA particle size. The model also estimated the initial readily biodegradable organic matter fraction, MB(0), and the slower biodegradable matter requiring hydrolysis, MH(0). The sum of MB(0) and MH(0) was associated with MC, W/BA ratio and the interaction between these two parameters, suggesting that O(2) availability was a key factor in determining the value of these two fractions. The study reinforced the idea that optimization of the physical characteristics of a compost mixture requires a holistic approach. PMID:20395122

  18. 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...

  19. Intermolecular interactions in solutions of some amino-nitro-benzene derivatives, studied by spectral means

    NASA Astrophysics Data System (ADS)

    Dorohoi, Dana-Ortansa; Airinei, Anton; Dimitriu, Mihaela

    2009-07-01

    The spectral shifts in the visible electronic absorption spectra of three amino-nitro-benzene derivatives in different solvents were correlated with the macroscopic parameters (refractive index and electric permittivity) of the solvents. The wavenumbers in the maximum of the visible charge transfer absorption band of o-nitro-aniline, 4-amino-3-nitrophenol and 3-amino-4-nitrophenol depend linearly on the Baur-Nicol function of electric permittivity. This dependence allows to estimate the electric polarizability in the electronic excited states if the electric polarizability in the ground state of the spectrally active molecule is determined by other procedures, such as by quanto-mechanical calculations.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. About intermolecular interactions in binary and ternary solutions of some azo-benzene derivatives

    NASA Astrophysics Data System (ADS)

    Ivan, Liliana Mihaela; Closca, Valentina; Burlea, Marin; Rusu, Elena; Airinei, Anton; Dorohoi, Dana Ortansa

    2015-02-01

    The nature and strength of the intermolecular interactions in the solutions of three azo-benzene derivatives (ADi, i = 1, 2, 3) were established by solvatochromic effects in solvents with different electric permittivities, refractive indices and Kamlet-Taft constants. A quantum mechanical analysis corroborated with spectral data offered information about the excited state dipole moments and polarizabilities of the studied compounds. The separation of the supply of universal and specific interactions to the total spectral shift was made based on the regression coefficients from the equations describing the solvatochromic effect. Supplementary information about the composition of the first solvation shell and the energy in the solute-solvent molecular pairs were obtained analyzing the ternary solutions of ADi, i = 1, 2, 3 compounds in solvent mixture Methanol (M) + n-Hexane (H).

  6. 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

  7. 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.

  8. Unconditionally stable indole-derived glass blends having very high photorefractive gain: the role of intermolecular interactions.

    PubMed

    Angelone, Rocco; Ciardelli, Francesco; Colligiani, Arturo; Greco, Francesco; Masi, Paolo; Romano, Annalisa; Ruggeri, Giacomo; Stehlé, Jean-Louis

    2008-12-20

    The photorefractivity of an indole derivative and of its polymer blends has been studied at room temperature. The indole derivative 3-[2-(4-nitrophenyl)ethenyl]-1-(2-ethylhexyl)-2-methylindole (NPEMI-E) is a typical low-molecular-weight glass-forming molecule having peculiar nonlinear optics characteristics. It is unconditionally soluble in the photoconductive poly-(N-vinyl-2,3-dimethylindole) so that all the possible blends can be studied for a weight percent (wt. %) content of NPEMI-E ranging from zero to 100. A very high and sharp maximum of the photorefractive optical gain Gamma(2) approximately 2000 cm(-1) was obtained for a NPEMI-E wt. % content of about 90. On the basis of recently published theoretical calculations, we have made the hypothesis that the rapid change of Gamma(2) can also be ascribed to a correspondingly quick variation of the molecular electro-optic parameters of the dissolved chromophore for some well distinguished values of its concentration in the polymer matrix. Differential scanning calorimetry measurements were made and the results carefully analyzed with the aim of obtaining information on the intermolecular interactions. These last measurements also allowed rationalizing the unconditionally stable glass appearance of the obtained blends. Measurements of spectroscopic ellipsometry were also made on blends with different NPEMI-E content. PMID:19104520

  9. 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

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

    NASA Astrophysics Data System (ADS)

    Ban, Masashi

    2016-02-01

    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.

  11. 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.

  12. Garlic allyl derivatives interact with membrane lipids to modify the membrane fluidity.

    PubMed

    Tsuchiya, Hironori; Nagayama, Motohiko

    2008-09-01

    As a novel approach to the mode of medicinal action of garlic, its constituents were comparatively studied with respect to their interactions with membrane lipids to modify the membrane fluidity. Allyl derivatives rigidified tumor cell and platelet model membranes consisting of unsaturated phospholipids and cholesterol at 20-500 muM with the potency being diallyl trisulfide (DATS) > diallyl disulfide (DADS) by preferentially acting on the hydrocarbon cores of lipid bilayers. They were also effective in rigidifying candida cell model membranes prepared with ergosterol and phospholipids at 100-500 microM with the potency being DADS > DATS > diallyl sulfide (DAS), but not bacteria cell model membranes without ergosterol. Alliin, a precursor of these DASs, was not active on any membranes at 500 microM. Both relative intensity and selectivity in membrane effects correlated with those in antiproliferative, antiplatelet and antimicrobial effects. In cell culture experiments, membrane-active DASs inhibited the growth of tumor cells cultured for 24 and 48 h at 20-500 muM to show the potency being DATS > DADS, together with rigidifying cell membranes by acting on their deeper regions more intensively. However, membrane-inactive allyl derivatives were not growth-inhibitory on tumor cells. The membrane lipid interactions of DASs appear to be one of possible mechanisms underlying different effects of garlic. PMID:18506599

  13. 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.

  14. 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

  15. Photoisomerization of cyanine derivatives in 1-butyl-3-methylimidazolium hexafluorophosphate and aqueous glycerol: Influence of specific interactions

    SciTech Connect

    Mali, K. S.; Dutt, G. B.; Mukherjee, T.

    2008-03-28

    Photoisomerization of two cyanine derivatives, 3,3{sup '}-diethyloxadicarbocyanine iodide (DODCI) and merocyanine 540 (MC 540), has been investigated in an ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate and aqueous glycerol (93 wt % glycerol +7 wt % water) by measuring fluorescence lifetimes and quantum yields. The aim of this work is to understand how the rates of photoisomerization of DODCI and MC 540 are influenced by specific solute-solvent interactions besides the viscosity of the medium. For DODCI, it has been observed that the nonradiative rate constants, which represent the rates of photoisomerization, are almost identical in the ionic liquid and aqueous glycerol at given temperature, indicating that viscosity is the sole parameter that governs the rate of photoisomerization. In contrast, the photoisomerization rate constants of MC 540 have been found to be a factor of 2 higher in aqueous glycerol compared to the ionic liquid. The observed behavior is due to the zwitterionic character of MC 540, a consequence of which, the twisted state gets stabilized by the solute-solvent hydrogen bonding interactions in aqueous glycerol, thus lowering the barrier for isomerization.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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

  1. A study of photon interaction parameters in some commonly used solvents.

    PubMed

    Singh, Tejbir; Kaur, Paramjeet; Singh, Parjit S

    2007-03-01

    Various parameters of dosimetric interest such as mass attenuation coefficients, effective atomic numbers and electron densities of some commonly used solvents such as acetonitrile (C(4)H(3)N), butanol (C(4)H(9)OH), chlorobenzene (C(6)H(5)Cl), diethylether (C(4)H(10)O), ethanol (C(2)H(5)OH), methanol (CH(3)OH), propanol (C(3)H(7)OH) and water (H(2)O) were computed in the wide energy range of 10 keV-100 GeV. A comparative study of two different methods used to compute effective atomic numbers has been done. It is observed that in the intermediate energy region (0.1-5 MeV), the mass attenuation coefficient values becomes almost the same for all the solvents, and the effective atomic number and electron density show almost constant values, whereas significant variation is observed in both lower (10-100 keV) and higher (5 MeV-100 GeV) energy regions for all the solvents, which may be due to the dominance of different partial interaction processes in different energy regions. PMID:17341806

  2. 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.

  3. 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.

  4. 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

  5. Salmonella‐infected crypt‐derived intestinal organoid culture system for host–bacterial interactions

    PubMed Central

    Zhang, Yong‐Guo; Wu, Shaoping; Xia, Yinglin; Sun, Jun

    2014-01-01

    Abstract The in vitro analysis of bacterial–epithelial interactions in the intestine has been hampered by a lack of suitable intestinal epithelium culture systems. Here, we report a new experimental model using an organoid culture system to study pathophysiology of bacterial–epithelial interactions post Salmonella infection. Using crypt‐derived mouse intestinal organoids, we were able to visualize the invasiveness of Salmonella and the morphologic changes of the organoids. Importantly, we reported bacteria‐induced disruption of epithelial tight junctions in the infected organoids. In addition, we showed the inflammatory responses through activation of the NF‐κB pathway in the organoids. Moreover, our western blot, PCR, and immunofluorescence data demonstrated that stem cell markers (Lgr5 and Bmi1) were significantly decreased by Salmonella infection (determined using GFP‐labeled Lgr5 organoids). For the first time, we created a model system that recapitulated a number of observations from in vivo studies of the Salmonella‐infected intestine, including bacterial invasion, altered tight junctions, inflammatory responses, and decreased stem cells. We have demonstrated that the Salmonella‐infected organoid culture system is a new experimental model suitable for studying host–bacterial interactions. PMID:25214524

  6. Study of the interaction of antiplasmodial strychnine derivatives with the glycine receptor.

    PubMed

    Philippe, Geneviève; Nguyen, Laurent; Angenot, Luc; Frédérich, Michel; Moonen, Gustave; Tits, Monique; Rigo, Jean-Michel

    2006-01-13

    Strychnos icaja Baill. (Loganiaceae) is a liana found in Central Africa known to be an arrow and ordeal poison but also used by traditional medicine to treat malaria. Recently, many dimeric or trimeric indolomonoterpenic alkaloids with antiplasmodial properties have been isolated from its rootbark. Since these alkaloids are derivatives of strychnine, it was important, in view of their potential use as antimalarial drugs, to assess their possible convulsant strychnine-like properties. In that regard, their interaction with the strychnine-sensitive glycine receptor was investigated by whole-cell patch-clamp recordings on glycine-gated currents in mouse spinal cord neurons in culture and by [(3)H]strychnine competition assays on membranes from adult rat spinal cord. These experiments were carried out on sungucine (leading compound of the chemical class) and on the antiplasmodial strychnogucine B (dimeric) and strychnohexamine (trimeric). In comparison with strychnine, all compounds interact with a very poor efficacy and only at concentrations >1 microM with both [(3)H]strychnine binding and glycine-gated currents. Furthermore, the effects of strychnine and protostrychnine, a monomeric alkaloid (without antiplasmodial activity) also isolated from S. icaja and differing from strychnine only by a cycle opening, were compared in the same way. The weak interaction of protostrychnine confirms the importance of the G cycle ring structure in strychnine for its binding to the glycine receptor and its antagonist properties. PMID:16375888

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

    PubMed Central

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

    1997-01-01

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

  8. 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 2.6 suggest the presence of small ice particles at temperatures below 230 K. the parameterization of visible reflectance in terms of cloud optical depth and clear sky reflectance shows promise as a simplified method for interpreting visible satellite data reflected from cirrus clouds. Large uncertainties in the optical parameters due to cloud reflectance anisotropy and shading were found by analyzing data for various solar zenith angles and for simultaneous advanced very high resolution radiometer (AVHRR) data. Inhomogeneities in the cloud fields result in uneven cloud shading that apparently causes the occurrence of anomalously dark, cloud pixels in the GOES data. These shading effects complicate the interpretation of the satellite data. The results highlight the need for additional study or cirrus cloud scattering processes and remote sensing techniques.

  9. 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 particles at temperatures below 230 K. The parameterization of visible reflectance in terms of cloud optical depth and clear-sky reflectance shows promise as a simplified method for interpreting visible satellite data reflected from cirrus clouds. Large uncertainties in the optical parameters due to cloud reflectance anisotropy and shading were found by analyzing data for various solar zenith angles and for simultaneous AVHRR data. Inhomogeneities in the cloud fields result in uneven cloud shading that apparently causes the occurrence of anomalously dark, cloudy pixels in the GOES data. These shading effects complicate the interpretation of the satellite data. The results highlight the need for additional study of cirrus cloud scattering processes and remote sensing techniques.

  10. 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 90W 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 with vegetation indices of NDVI and EVI derived from MODIS data were used. Higher CO2 mixing ratios anti-correlated with the vegetation indices derived from MODIS data were observed. This is attributable to the photosynthetic uptake of CO2 by plants and convective mixing of the atmosphere. Details of satellite data characteristics related with the in-situ CO2 measurements will be presented.

  11. New natural shapes of non-Gaussianity from high-derivative interactions and their optimal limits from WMAP 9-year data

    NASA Astrophysics Data System (ADS)

    Behbahani, Siavosh R.; Mirbabayi, Mehrdad; Senatore, Leonardo; Smith, Kendrick M.

    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 fNLorth in WMAP9.

  12. Concerted mitigation of O···H and C(π)···H interactions prospects sixfold gain in optical nonlinearity of ionic stilbazolium derivatives.

    PubMed

    Cole, Jacqueline M; Lin, Tze-Chia; Edwards, Alison J; Piltz, Ross O; Depotter, Griet; Clays, Koen; Lee, Seung-Chul; Kwon, O-Pil

    2015-03-01

    DAST (4-dimethylamino-N-methyl-4-stilbazolium tosylate) is the most commercially successful organic nonlinear optical (NLO) material for frequency-doubling, integrated optics, and THz wave applications. Its success is predicated on its high optical nonlinearity with concurrent sufficient thermal stability. Many chemical derivatives of DAST have therefore been developed to optimize their properties; yet, to date, none have surpassed the overall superiority of DAST for NLO photonic applications. This is perhaps because DAST is an ionic salt wherein its NLO-active cation is influenced by multiple types of subtle intermolecular forces that are hard to quantify, thus, making difficult the molecular engineering of better functioning DAST derivatives. Here, we establish a model parameter, ηinter, that isolates the influence of intermolecular interactions on second-order optical nonlinearity in DAST and its derivatives, using second-harmonic generation (SHG) as a qualifier; by systematically mapping intercorrelations of all possible pairs of intermolecular interactions to ηinter, we uncover a relationship between concerted intermolecular interactions and SHG output. This correlation reveals that a sixfold gain in the intrinsic second-order NLO performance of DAST is possible, by eliminating the identified interactions. This prediction offers the first opportunity to systematically design next-generation DAST-based photonic device nanotechnology to realize such a prospect. PMID:25654641

  13. 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

  14. Dye-tissue interactions: mechanisms, quantification and bonding parameters for dyes used in biological staining.

    PubMed

    Dapson, R W

    2005-01-01

    Staining of tissues by dyes is accomplished through various types of bonds, some of which have been poorly defined in traditional biological literature. Here, basic principles of bonding are reviewed to establish uniform terminology and definitions consistent with the field of chemistry. The concept of charge - its presence or absence, magnitude, extent of delocalization and potential for being displaced by outside forces - underlies all bonding phenomena. These same attributes influence solubility and resistance to extraction during dehydration of tissue sections. Covalent bonds involve shared electrons; they are very strong and essentially irreversible under conditions encountered during staining. Polar covalent bonds within dye molecules generate partial atomic charges that create the potential for hydrogen bonding. This is measured by the hydrogen bonding parameter (h), the number of groups bearing charges within the ranges -0.15 to -0.50 eV or +0.15 to +0.30 eV. The potential for ionic bonding is indicated by net charge (Z), while the strength of such bonds is a function of charge site geometry on both bonding partners. Charge delocalization owing to conjugation, electron influencing groups, and resonance creates soft charge sites in which the ionic charge is spread over a large volume. Poorly delocalized charges or point charges are hard (small in volume). Firm bonds result from hard-hard or soft-soft pairs. Hard-soft combinations are weak, readily displaced in competitive interactions, and disrupted by solvents. Coordinate bonds with certain metals are involved with mordant staining and metal chelation dyes. Three different van der Waals attractions comprise the remainder of bonding types, all involving dipoles: Keesom (dipole-dipole) forces, Debye (dipole-induced dipole) forces and London (induced dipole-induced dipole) forces. Potentials for engaging in any of these is quantified by measures of polarity (dipole moment, d), polarizability (crudely with pi atoms describing the size of the conjugated system, or more directly with alpha), hydrophobicity (with the octanol-water partition coefficient, log P or the more convenient Hydrophobic Index, HI), and the number of halogen atoms (X). By using molecular modeling software, quantitative measures of bonding potential (bonding parameters) have been determined for over 400 dyes. PMID:16195171

  15. 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

  16. Including gauge-group parameters into the theory of interactions: an alternative mass-generating mechanism for gauge fields

    SciTech Connect

    Aldaya, V.; Lopez-Ruiz, F. F.; Sanchez-Sastre, E.; Calixto, M.

    2006-11-03

    We reformulate the gauge theory of interactions by introducing the gauge group parameters into the model. The dynamics of the new 'Goldstone-like' bosons is accomplished through a non-linear {sigma}-model Lagrangian. They are minimally coupled according to a proper prescription which provides mass terms to the intermediate vector bosons without spoiling gauge invariance. The present formalism is explicitly applied to the Standard Model of electroweak interactions.

  17. 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.

  18. Insights into the Interactions between Maleimide Derivates and GSK3? 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 (GSK3?) using docking experiments. We found that the orientations that these compounds adopt inside GSK3? 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 structureactivity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3? inhibitory activities for the studied compounds. We found a model to explain the structureactivity 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

  19. Insights into the interactions between maleimide derivates and GSK3? 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 (GSK3?) using docking experiments. We found that the orientations that these compounds adopt inside GSK3? 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 GSK3? 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

  20. Structural determinants for the membrane interaction of novel bioactive undecapeptides derived from gaegurin 5.

    PubMed

    Won, Hyung-Sik; Seo, Min-Duk; Jung, Seo-Jeong; Lee, Sang-Jae; Kang, Su-Jin; Son, Woo-Sung; Kim, Hyun-Jung; Park, Tae-Kyu; Park, Sung-Jean; Lee, Bong-Jin

    2006-08-10

    Gaegurin 5 is a 24-residue, membrane-active antimicrobial peptide isolated from the skin of an Asian frog, Rana rugosa. We recently reported the antimicrobial activities of two novel undecapeptides derived from an inactive N-terminal fragment (residues 1-11) of gaegurin 5 (Won, et al. J. Biol. Chem. 2004, 279, 14784-14791). In the present work, the anticancer activities of the two antimicrobial undecapeptide analogues were additionally identified. The relationships between their structural properties and biological activities were assessed by characterizing the fundamental structural determinant for the basic membrane interaction. The circular dichroism and nuclear magnetic resonance results revealed that in a membrane-mimetic environment, the active peptides adopt a more stabilized helical conformation than that of the inactive fragment, and this conformation conferred an overall amphipathicity to the active peptides. Therefore, the most decisive factor responsible for the activity and selectivity could be the intramolecular amphipathic cooperativity, rather than the amphipathicity itself. Especially, the tryptophan residue of the active peptides seems to play a crucial role at the critical amphipathic interface that promotes and balances the amphipathic cooperativity by stabilizing both the hydrophilic and hydrophobic interactions with the membrane. Altogether, the present results suggest that the two novel undecapeptides are worthy of therapeutic development as new antibiotic and anticancer agents and provide structural information about their action mechanism. PMID:16884301

  1. 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.

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

    PubMed

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

    2016-02-01

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

  3. 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

  4. 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.

  5. Peroxynitrite scavenging activity of indole derivatives: interaction of indoles with peroxynitrite.

    PubMed

    Soung, Do Yu; Choi, Hye Rhi; Kim, Ji Young; No, Jae Kyung; Lee, Jee Hyun; Kim, Min Sun; Rhee, Sook Hee; Park, Jin Seng; Kim, Myung Jung; Yang, Ryung; Chung, Hae Young

    2004-01-01

    One of the products of nitrogen-derived free radicals, peroxynitrite (ONOO(-)), is formed by the reaction of superoxide anion (O(2)(*-)) with nitric oxide (NO). ONOO(-) can cause damage to proteins and DNA through nitration. In particular, proteins and their constituent amino acids have been proven to be extremely sensitive to ONOO(-). However, the lack of specific endogenous defense enzymes to protect against ONOO(-) has prompted many researchers to search for endogenous scavengers. We previously found 5-hydroxytryptamine (HT), which is an indole derivative (ID), to be an efficient ONOO(-) scavenger. In the present study, the interaction of several other indoles was further investigated: tryptophan (TRP), 5-hydroxyL-tryptophan (HLT), HT, N-acetyl-5-hydroxytryptamine (AHT), 5-methoxyindole-3-acetate (MIA), 5-methoxytryptamine (MT), and melatonin. The ONOO(-) scavenging activity of ID was assayed by measuring the formation of oxidized dihydrorhodamine-123 (DHR-123). The scavenging efficacy was expressed as the IC(50), denoting the concentration of each indole required to cause 50% inhibition of DHR-123 formation. In a separate in vitro study, the protective effect of IDs against ONOO(-)-induced nitration of bovine serum albumin was investigated. Nitration was quantified using an immunoassay with a monoclonal anti-nitrotyrosine antibody, and a horseradish peroxidase-conjugated anti-mouse secondary antibody from sheep. The results revealed that the inhibitory activities of indoles were as follows: HLT, IC(50) = 0.73 microM; HT, IC(50) = 1.03 microM; and AHT, IC(50) = 0.98 microM), showing relatively strong activities against ONOO(-). Interestingly, TRP, MIA, MT, and melatonin were less effective. Regarding the protection of albumin by IDs, the data showed that the formation of ONOO(-) was inhibited in a dose-dependent manner. Further probing of the mode of the interaction of indoles revealed that the hydroxyl groups in IDs are required for the enhanced scavenging action. It was concluded that several indole derivatives with hydroxyl groups are effective scavengers against ONOO(-), and that the scavenging efficacy depends on the presence of hydroxyl groups located within the indole ring structure. PMID:15117558

  6. Peroxynitrite scavenging activity of indole derivatives: interaction of indoles with peroxynitrite.

    TOXLINE Toxicology Bibliographic Information

    Soung DY; Choi HR; Kim JY; No JK; Lee JH; Kim MS; Rhee SH; Park JS; Kim MJ; Yang R; Chung HY

    2004-01-01

    One of the products of nitrogen-derived free radicals, peroxynitrite (ONOO(-)), is formed by the reaction of superoxide anion (O(2)(*-)) with nitric oxide (NO). ONOO(-) can cause damage to proteins and DNA through nitration. In particular, proteins and their constituent amino acids have been proven to be extremely sensitive to ONOO(-). However, the lack of specific endogenous defense enzymes to protect against ONOO(-) has prompted many researchers to search for endogenous scavengers. We previously found 5-hydroxytryptamine (HT), which is an indole derivative (ID), to be an efficient ONOO(-) scavenger. In the present study, the interaction of several other indoles was further investigated: tryptophan (TRP), 5-hydroxyL-tryptophan (HLT), HT, N-acetyl-5-hydroxytryptamine (AHT), 5-methoxyindole-3-acetate (MIA), 5-methoxytryptamine (MT), and melatonin. The ONOO(-) scavenging activity of ID was assayed by measuring the formation of oxidized dihydrorhodamine-123 (DHR-123). The scavenging efficacy was expressed as the IC(50), denoting the concentration of each indole required to cause 50% inhibition of DHR-123 formation. In a separate in vitro study, the protective effect of IDs against ONOO(-)-induced nitration of bovine serum albumin was investigated. Nitration was quantified using an immunoassay with a monoclonal anti-nitrotyrosine antibody, and a horseradish peroxidase-conjugated anti-mouse secondary antibody from sheep. The results revealed that the inhibitory activities of indoles were as follows: HLT, IC(50) = 0.73 microM; HT, IC(50) = 1.03 microM; and AHT, IC(50) = 0.98 microM), showing relatively strong activities against ONOO(-). Interestingly, TRP, MIA, MT, and melatonin were less effective. Regarding the protection of albumin by IDs, the data showed that the formation of ONOO(-) was inhibited in a dose-dependent manner. Further probing of the mode of the interaction of indoles revealed that the hydroxyl groups in IDs are required for the enhanced scavenging action. It was concluded that several indole derivatives with hydroxyl groups are effective scavengers against ONOO(-), and that the scavenging efficacy depends on the presence of hydroxyl groups located within the indole ring structure.

  7. 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

  8. 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.

  9. End-to-end distance distribution in fluorescent derivatives of bradykinin in interaction with lipid vesicles.

    PubMed

    Montaldi, L R; Berardi, M; Souza, E S; Juliano, L; Ito, A S

    2012-07-01

    Cellular membranes have relevant roles in processes related to proteases like human kallikreins and cathepsins. As enzyme and substrate may interact with cell membranes and associated co-factors, it is important to take into account the behavior of peptide substrates in the lipid environment. In this paper we report an study based on energy transfer in two bradykinin derived peptides labeled with the donor-acceptor pair Abz/Eddnp (ortho-aminobenzoic acid/N-[2,4-dinitrophenyl]-ethylenediamine). Time-resolved fluorescence experiments were performed in phosphate buffer and in the presence of large unilamelar vesicles of phospholipids, and of micelles of sodium dodecyl sulphate (SDS). The decay kinetics were analyzed using the program CONTIN to obtain end-to-end distance distribution functions f(r). Despite of the large difference in the number of residues the end-to-end distance of the longer peptide (9 amino acid residues) is only 20 % larger than the values obtained for the shorter peptide (5 amino acid residues). The proline residue, in position 4 of the bradykinin sequence promotes a turn in the longer peptide chain, shortening its end-to-end distance. The surfactant SDS has a strong disorganizing effect, substantially broadening the distance distributions, while temperature increase has mild effects in the flexibility of the chains, causing small increase in the distribution width. The interaction with phospholipid vesicles stabilizes more compact conformations, decreasing end-to-end distances in the peptides. Anisotropy experiments showed that rotational diffusion was not severely affected by the interaction with the vesicles, suggesting a location for the peptides in the surface region of the bilayer, a result consistent with small effect of lipid phase transition on the peptides conformations. PMID:22488046

  10. Computation, validation and sensitivity of the DTM-derived geomorphic parameters: the case of Stream-Length Gradient Index

    NASA Astrophysics Data System (ADS)

    Della Seta, M.; Galve, J. P.; Piacentini, D.; Troiani, F.

    2012-04-01

    Quantitative geomorphic analysis from DTMs has become a common procedure for creating and analysing geo-thematic maps. Nevertheless, it is often neglected that the accuracy of interpretations generally depends on the accuracy of the DTMs itself (i.e., both the ground resolution and interpolation method). In the case of the DTM-derived quantitative geomorphic indices different open-questions are still the object of a suggestive debate. One of the crucial questions is the objective identification/characterization of processes and landforms responsible for anomalous values of the parameter analysed; particularly, in those cases where either the same process can result in different anomalies or the same anomalous value can be related to different processes/landforms. In this frame, our work is aimed at providing a new geostatistical methodology to validate the computation goodness of the geomorphic indices from DTMs and to interpret the anomalous values in their spatial distribution. We applied the proposed methodology to the computation and spatial analysis of the DTM-derived Stream-Length Gradient Index (SL Index). Since the SL Index is a proxy of the Stream-Power per Unit Length and is proportional to the total stream-power available at a particular channel reach, it is very sensitive to changes in river gradient and represents a practical tool to highlight perturbations along the longitudinal profiles. In addition to the known relationship between rock resistance and SL Index, the latter may be used to detect the surface effects of fault activity through anomalously high index values on a specific rock type. Recently, some researches outlined that in small river basins extreme values of the SL Index seem to reflect the topographic fingerprint of slope failures directly reaching the stream channels. In this work we created a statistical, well-constrained SL Index map within the Upper Tena river valley, which occupies approximately 47 km2 in the mountainous sector of the central Spanish Pyrenees. The procedure proposed here is aimed at distinguishing objectively the averaged response of the SL Index values to lithology, fault displacements and slope failures. As for statistical interpolation of DTM-derived SL Index values, we proceeded in two steps: 1) computation of the experimental variogram and its best-related theoretic fit that took also into account anisotropies of the river patterns; this latter was used in the second interpolation procedure; 2) statistical validation of different interpolators (i.e., O-Kriging, U-Kriging, IDW, NeN, TLI) basing on the leave-one-out cross-validation. Finally, once obtained the SL Index map, we applied a map filtering using the representative "range-values" (RV) for all processes in order to distinguish the different topographic fingerprints of lithology, fault displacements and slope failures. Encouraging results suggest the goodness of the proposed methodology that validates at the same time both the computation and the spatial analysis of a DTM-derived quantitative geomorphic index. Moreover, we have confirmed the sensitivity of the SL Index, calculated from DTMs with different spatial resolution, to detect slope failures within mountainous small river basins.

  11. 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

  12. Derivation of force field parameters for SnO2-H2O surface systems from plane-wave density functional theory calculations.

    PubMed

    Bandura, A V; Sofo, J O; Kubicki, J D

    2006-04-27

    Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well. PMID:16623524

  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 in blacks. PMID:26739395

  14. Halogen-bond and hydrogen-bond interactions between three benzene derivatives and dimethyl sulphoxide.

    PubMed

    Zheng, Yan-Zhen; Wang, Nan-Nan; Zhou, Yu; Yu, Zhi-Wu

    2014-04-21

    Halogen-bonds, like hydrogen-bonds, are a kind of noncovalent interaction and play an important role in diverse fields including chemistry, biology and crystal engineering. In this work, a comparative study was carried out to examine the halogen/hydrogen-bonding interactions between three fluoro-benzene derivatives and dimethyl sulphoxide (DMSO). A number of conclusions were obtained by using attenuated total reflection infrared spectroscopy (ATR-IR), nuclear magnetic resonance (NMR) and ab initio calculations. Electrostatic surface potential, geometry, energy, vibrational frequency, intensity and the natural population analysis (NPA) of the monomers and complexes are studied at the MP2 level of theory with the aug-cc-pVDZ basis set. First, the interaction strength decreases in the order C6F5H-DMSO ∼ ClC6F4H-DMSO > C6F5Cl-DMSO, implying that the hydrogen-bond is stronger than the halogen-bond in the systems and, when interacting with ClC6F4H, DMSO favors the formation of a hydrogen-bond rather than a halogen-bond. Second, attractive energy dependences on 1/r(3.3) and 1/r(3.1) were established for the hydrogen-bond and halogen-bond, respectively. Third, upon the formation of a hydrogen-bond and halogen-bond, there is charge transfer from DMSO to the hydrogen-bond and halogen-bond donor. The back-group CH3 was found to contribute positively to the stabilization of the complexes. Fourth, an isosbestic point was detected in the ν(C-Cl) absorption band in the C6F5Cl-DMSO-d6 system, indicating that there exist only two dominating forms of C6F5Cl in binary mixtures; the non-complexed and halogen-bond-complexed forms. The presence of stable complexes in C6F5H-DMSO and ClC6F4H-DMSO systems are evidenced by the appearance of new peaks with fixed positions. PMID:24595314

  15. 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 mechanism type, with thrust events showing an exponent of 2.0, consistent with L-model scaling, and strike-slip events an exponent of 1.6. These results do not favor self-similarity, however some authors have suggested that both self-similarity and quasi-L model scaling could be maintained if earthquake slip in the largest events penetrates beneath the brittle-ductile transition (Shaw and Wesnousky, 2008). Systematic comparisons of the depths of the base of the slipping zone from large earthquakes, compared with seismic evidence such as the depths of microseismicity and/or aftershocks in the epicentral areas may be one way of evaluating this hypothesis in future.

  16. Influence of physico-chemical parameters of some barbituric acid derivatives on their retention on an amide embedded RP silica column.

    PubMed

    Jakab, Annamaria; Prodan, Miklos; Forgács, Esther

    2002-03-01

    Retention parameters of 45 different barbituric acid derivatives were determined on an amide embedded RP silica column (Discovery RP-AmideC16) using non-buffered water-acetonitrile eluent systems. Linear correlation were calculated between the logarithm of the capacity factor and the acetonitrile concentration in the eluent. To determine the retention behavior of barbituric acid derivatives, stepwise regression analysis (SRA) and principal component analysis (PCA) followed by two-dimensional nonlinear and modified nonlinear mapping was used. It can be concluded, the retention of barbituric acid derivatives are governed mainly by the steric parameters of the substituents. Principal component analysis indicated that the barbituric acid derivatives have mixed retention on this amide embedded RP silica column in water-acetonitrile eluent. PMID:11836055

  17. 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

  18. Asymmetry parameters in the lower troposphere derived from aircraft measurements of aerosol scattering coefficients over tropical India

    NASA Astrophysics Data System (ADS)

    Ramachandran, S.; Rajesh, T. A.

    2008-08-01

    Aerosol scattering coefficients (total βsca and backscatter βbacksca) are measured on board an aircraft using an integrating nephelometer at 450, 550, and 700 nm in the 0 to 3000-m region over four locations in India in an air campaign held during March-May 2006. βsca is a factor of two higher in the east (Bhubaneshwar, Chennai) than in the west (Trivandrum, Goa). βsca is about 5-10 × 10-5 m-1 over Bhubaneshwar and Chennai. βbacksca is about an order of magnitude lower than βsca. Seven-day air back trajectory analysis indicate that air masses originating from arid/semiraid regions, continents, and marine regions are found to influence the aerosol characteristics, in addition to local urban sources. No elevated aerosol layers are seen during the campaign. b, the aerosol backscatter fraction, is greater than 0.13 in the lower troposphere. The columnar mean Ångström exponent (α) is >1.75. Asymmetry parameter g profiles are derived for the first time over India in the lower troposphere, using the relation between b and g. 550-nm g corresponding to 30% RH is in the 0.3-0.6 range over India. Higher b, higher α, and lower g values over these locations suggest the dominance of submicron aerosols during the campaign. Scattering aerosols corrected to 30% RH in the 0 to 3000-m altitude region contribute about 20-35% to MODIS aerosol optical depths (AODs). The variation in the contribution of scattering aerosols to AODs highlights the spatial and vertical differences in aerosol properties.

  19. 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 percentage of rain water travelling through the quickflow reservoir). End users can then eliminate parameter combinations with unrealistic outcomes based on expert knowledge using interactive parallel plots. In these plots, for instance, ranges can be selected for each signature and only model runs which yield signature values in these ranges are highlighted. The resulting selection of realistic parameter sets can be used for ensemble simulations. C.C. Brauer, A.J. Teuling, P.J.J.F. Torfs, R. Uijlenhoet (2014a): The Wageningen Lowland Runoff Simulator (WALRUS): a lumped rainfall-runoff model for catchments with shallow groundwater, Geoscientific Model Development, 7, 2313-2332, www.geosci-model-dev.net/7/2313/2014/gmd-7-2313-2014.pdf C.C. Brauer, P.J.J.F. Torfs, A.J. Teuling, R. Uijlenhoet (2014b): The Wageningen Lowland Runoff Simulator (WALRUS): application to the Hupsel Brook catchment and Cabauw polder, Hydrology and Earth System Sciences, 18, 4007-4028, www.hydrol-earth-syst-sci.net/18/4007/2014/hess-18-4007-2014.pdf

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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 monotonously with increasing WO{sub 3} content. • Interaction parameter decreases monotonously with increasing WO{sub 3} content. • Glasses with high WO{sub 3}contents is regarded as a floppy network system.

  5. Entropy and superfluid critical parameters of a strongly interacting Fermi gas

    NASA Astrophysics Data System (ADS)

    Luo, Le

    Strongly interacting Fermi gases provide a paradigm for studying strong interactions in nature. Strong interactions play a central role in the physics of a wide range of exotic systems, including high temperature superconductors, neutron stars, quark-gluon plasmas, and even a particular class of black holes. In an ultracold degenerate 6Li Fermi gas, interactions between the atoms in the two lowest hyperfine states can be widely tuned by a magnetic-field-dependent collisional resonance. At the resonance, the strongly interacting Fermi gas has an infinite s-wave scattering length and a negligible potential range, which ensures that the behavior of the gas is independent of the microscopic details of the interparticle interactions. In this limit, a strongly interacting Fermi gas is known as the unitary Fermi gas. The unitary Fermi gas emerges as one of the most fascinating problems in current many-body physics. It not only exhibits universal thermodynamic properties in common with a variety of strongly interacting systems, but also shows ideal hydrodynamic behavior. In this dissertation, I present the first model-independent thermodynamic study of a strongly interacting degenerate Fermi gas. The measurements determine the entropy and energy. The entropy versus energy data has been adopted by several theoretical groups as a benchmark to test current strong-coupling many-body theories, which reveals universal thermodynamics in unitary Fermi gases. My measurements show a transition in the energy-entropy behavior at Sc/kB = 2.2 +/- 0.1 corresponding to the energy Ec/EF = 0.83 +/- 0.02, where Sc and Ec are the critical entropy and energy per particle respectively, k B is Boltzmann constant, and EF is the Fermi energy of a trapped gas. This behavior change of entropy is interpreted as a thermodynamic signature of a superfluid transition in a strongly interacting Fermi gas. By parametrization of energy-entropy data, the temperature is extracted by T = ∂E/∂S, where E and S are the energy and entropy of a strongly interacting Fermi gas. I find that the critical temperature is about T/TF = 0.21 +/- 0.01, which agrees extremely well with very recent theoretical predictions. I also present an investigation of viscosity from the hydrodynamics of a strongly interacting Fermi gas. First, the study of the hydrodynamic expansion of a rotating strongly interacting Fermi gas reveals nearly prefect irrotational flow arising in both the superfluid and the normal fluid regime. Second, by modeling the damping data of the breathing mode, I present an estimation of the upper bound of viscosity in a strongly interacting Fermi gas. Using the entropy data, this study provides the first experimental estimate of the ratio of the viscosity eta to the entropy density s in strongly interacting Fermi systems. Recently the lower bound of eta/s is conjectured by using a string theory method, which shows eta/ s ≥ h/(4pikB). Our experimental estimate indicates that this quantity in strongly interacting Fermi gases approaches the lower bound limit. Finally, I describe the technical details of building a new all-optical cooling and trapping apparatus in our lab for the purpose of the above research as well as our studies on optimizing the evaporative cooling of a unitary Fermi gas in an optical trap.

  6. Effect of hydrophobic interactions on volume and thermal expansivity as derived from micelle formation.

    PubMed

    Nazari, Mozhgan; Fan, Helen Y; Heerklotz, Heiko

    2012-10-01

    Volumetric parameters have long been used to elucidate the phenomena governing the stability of protein structures, ligand binding, or transitions in macromolecular or colloidal systems. In spite of much success, many problems remain controversial. For example, hydrophobic groups have been discussed to condense adjacent water to a volume lower than that of bulk water, causing a negative contribution to the volume change of unfolding. However, expansivity data were interpreted in terms of a structure-making effect that expands the water interacting with the solute. We have studied volume and expansivity effects of transfer of alkyl chains into micelles by pressure perturbation calorimetry and isothermal titration calorimetry. For a series of alkyl maltosides and glucosides, the methylene group contribution to expansivity was obtained as 5 uL/(mol K) in a micelle (mimicking bulk hydrocarbon) but 27 uL/(mol K) in water (20 °C). The latter value is virtually independent of temperature and similar to that obtained from hydrophobic amino acids. Methylene contributions of micellization are about -60 J/(mol K) to heat capacity and 2.7 mL/mol to volume. Our data oppose the widely accepted assumption that water-exposed hydrophobic groups yield a negative contribution to expansivity at low temperature that would imply a structure-making, water-expanding effect. PMID:22950856

  7. 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...

  8. General two-order-parameter Ginzburg-Landau model with quadratic and quartic interactions.

    PubMed

    Ivanov, I P

    2009-02-01

    The Ginzburg-Landau model with two-order parameters appears in many condensed-matter problems. However, even for scalar order parameters, the most general U(1)-symmetric Landau potential with all quadratic and quartic terms contains 13 independent coefficients and cannot be minimized with straightforward algebra. Here, we develop a geometric approach that circumvents this computational difficulty and allows one to study properties of the model without knowing the exact position of the minimum. In particular, we find the number of minima of the potential, classify explicit symmetries possible in this model, establish conditions when and how these symmetries are spontaneously broken, and explicitly describe the phase diagram. PMID:19391715

  9. 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.

  10. Hydrogen-bonded complexes resulting from the interaction of alkylated barbituric acid and 2,6-diamidopyridine derivatives

    NASA Astrophysics Data System (ADS)

    Sideratou, Z.; Tsiourvas, D.; Paleos, C. M.; Peppas, E.; Anastassopoulou, J.; Theophanides, T.

    1999-06-01

    In the present study a hydrophilic or a lipophilic alkylated barbituric acid derivative was allowed to interact in the melt and in solution with a complementary series of alkylated diamidopyridine derivatives, both hydrophilic or lipophilic. The interaction between the molecules was mainly studied by FT-IR spectroscopy. Phase transitions of reaction mixtures were studied with polarized optical microscopy and differential scanning calorimetry. It was found that the molecular recognition of the interacting components is only effective between the molecularly compatible ones. Specifically, employing Methods I and II, (see text) the short chain derivatives form 1 : 1 complexes whereas the long-chain derivatives are only partially complexed. Derivatives of dissimilar lipophilicity do not form complexes employing the same methods. However, comparing the two methods, complexation is more effective employing Method II. The induction of molecular recognition in the presence of an apolar solvent is enhanced in solution, Method III. The equilibrium which was established in solution is shifted to different directions during the evaporation step (Method II), leading either to the formation of complexes or to self-association.

  11. 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.

  12. 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

  13. Characteristic parameters of superconductor-coolant interaction including high Tc current density limits

    NASA Technical Reports Server (NTRS)

    Frederking, T. H. K.

    1989-01-01

    In the area of basic mechanisms of helium heat transfer and related influence on super-conducting magnet stability, thermal boundary conditions are important constraints. Characteristic lengths are considered along with other parameters of the superconducting composite-coolant system. Based on helium temperature range developments, limiting critical current densities are assessed at low fields for high transition temperature superconductors.

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

    NASA Astrophysics Data System (ADS)

    Brito, Paula; Antunes, Fernando

    2014-10-01

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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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 to mineral surface area. Catalysis was found to be saturable, suggesting the presence of discrete catalytic sites on the mineral surface. These and other results will be presented and discussed. References Bernal, J. D. (1951) The Physical Basis of Life (Routledge, London). Cleaves, H.J., Aubrey, A.D., Bada, J.L. (2009) An evaluation of the critical parameters for abiotic peptide synthesis in submarine hydrothermal systems. Origins of Life Evol Biosph. 39:109-26. Kauffman, S.A. (1971) Cellular homeostasis, epigenesis and replication in randomly aggregated macromolecular systems. Cybernetics and Systems: An International Journal 1: 71 - 96. Lambert, J. (2008) Adsorption and polymerization of amino acids on mineral surfaces: A review. Origins of Life Evol. Biosph. 38: 211-42. Miller, S.L. and Orgel, L.E. (1974) The Origins of Life on the Earth, Prentice Hall (Englewood Cliffs, NJ) Yao, Y., Ghosh, I., Zutshi, R., Chmielewski, J. (1998) Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature 396, 447 - 450.

  1. Account of the Gravitational Interaction in an Estimate of the Parameters of Pinch Plasmoids

    NASA Astrophysics Data System (ADS)

    Bogdanovich, B. Yu.; Nesterovich, A. V.; Sukhanova, L. A.; Khlestkov, Yu. A.

    2015-02-01

    Exact solutions of the Einstein-Maxwell equations in GTR for centrosymmetric dust and a free electromagnetic field are applied to a description of pinch plasmoids formed in experiments on the collapse of a charge-neutralized high-voltage discharge in a medium in which superhigh energy densities are reached, where an account of the curvature of spacetime becomes important. The given solutions are also used to estimate the parameters of cosmological objects - maximons, whose electric charge is equal to the "gravitational charge." These objects are identified with the throat - the extremal static hypersurface of the inner space of the plasmoid and maximon observed from the Reissner-Nordstrm vacuum.

  2. Study of parameters important to soil-structure interaction in seismic analyses of nuclear power plants

    SciTech Connect

    Nelson, T.A.

    1983-12-01

    The development of state-of-the-art techniques for analyzing the effects of soil-structure interaction (SSI) on structures during earthquakes is outlined. Emphasis is placed on methods to account for energy dissipation as a result of both wave propagation away from the structure's foundation and hysteretic soil response. Solution techniques are grouped into two major types: substructure methods, which break the problem into a series of steps; and direct methods, which analyze the soil-structure model in one step. In addition to theoretical and historical development of SSI methodology, case studies are presented illustrating the application of these solution techniques. 94 references.

  3. 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

  4. Measurement of the phonon contribution to quasiparticle lifetime and of the mass enhancement parameter lambda from the sp-derived surface state on copper(111) and gold(111) by angle-resolved photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    McDougall, Brendan Anthony

    2000-10-01

    This thesis reports studies of the phonon contribution to hole lifetime at a metal surface by angle-resolved photoemission (ARP). The hole lifetime is determined by the electron-phonon, electron-electron, and electron-impurity interactions. Each interaction is described and the contribution of each interaction to hole lifetime is calculated. At high temperature (T) and at low energies of the hole, the T dependence of inverse hole lifetime is dominated by the electron-phonon interaction and is (2pilambdakbT)/h where 2pih is Planck's constant and kb is Boltzman's constant. lambda is a dimensionless measure of the strength of the electron-phonon interaction. From the temperature dependence of hole lifetime, the mass enhancement parameter lambda is extracted. All previous determinations of the mass enhancement parameter are for the bulk (lambdab). This thesis describes how to measure a mass enhancement parameter at the surface (lambdas) using ARP. lambda depends on the electronic density of states (DOS), an average of a square phonon angular frequency, and an average of a squared electron-phonon matrix element. Bulk and surface differences between these quantities are expected to make lambdas different from lambda b. This thesis reports lambdas = 0.15 +/- 0.01 at Cu(111), while lambdab = 0.15 +/- 0.03. This thesis reports preliminary measurement of lambdas = 0.34 +/- 0.04 at Au (111), while lambdab = 0.17 +/- 0.05. Recent theoretical work indicates the difference between lambdas and lambda b of Au(111) is not readily attributable to bulk and surface differences in the electron DOS. The quasiparticle picture of photoemission is verified to be a valid interpretation of ARP spectra from the sp-derived surface states of Cu(111) and Au(111). The predicted and observed lineshapes are Lorentzian. The linewidths are consistent with linewidth being determined by inverse hole lifetime.

  5. 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

  6. Diagnostic value of combined parameters derived from ambulatory electrocardiography for detecting coronary artery disease in non-active chest pain patients

    PubMed Central

    Jiang, Yue; Tian, Jun-Ping; Wang, Hong; Chen, Bu-Xing; Du, Feng-He

    2014-01-01

    Background and Objective: The diagnostic value of ST-segment deviation detected by ambulatory electrocardiography (AECG) is controversial in identifying coronary artery disease (CAD) referred for coronary angiography (CAG). Recently, many parameters which evaluate CAD can be derived from AECG. Therefore, we aimed to investigate the diagnostic value of AECG in screening CAD referred for CAG when several parameters were combined. Methods: We studied the 104 chest pain inpatients. All patients received the CAG and AECG. A lumen diameter reduction of ≥ 50% was considered CAD according to CAG. The parameters derived from AECG included ST-segment deviation, apnea hypopnea index (AHI), QT interval dispersion (QTd) and heart rate variability (HRV). The diagnostic value of AECG in screening CAD was evaluated. Results: Of the 104 patients, 57 (54.8%) had CAD according to CAG. The sensitivity of ST-segment deviation in screening CAD was 64.9%; the specificity was 89.4%; and the Kappa value was 0.528. The sensitivity of at least three combined parameters including ST-segment deviation, AHI, QTd and HRV was 89.5%; the specificity was 87.2%; and the Kappa value was 0.767. Conclusion: AECG is very useful in screening CAD referred for CAG, especially while several parameters including ST-segment deviation, AHI, HRV and QTd are combined. PMID:25674134

  7. Nature of noncovalent carbon-bonding interactions derived from experimental charge-density analysis.

    PubMed

    Escudero-Adán, Eduardo C; Bauzá, Antonio; Frontera, Antonio; Ballester, Pablo

    2015-08-24

    In an effort to better understand the nature of noncovalent carbon-bonding interactions, we undertook accurate high-resolution X-ray diffraction analysis of single crystals of 1,1,2,2-tetracyanocyclopropane. We selected this compound to study the fundamental characteristics of carbon-bonding interactions, because it provides accessible σ holes. The study required extremely accurate experimental diffraction data, because the interaction of interest is weak. The electron-density distribution around the carbon nuclei, as shown by the experimental maps of the electrophilic bowl defined by a (CN)2 CC(CN)2 unit, was assigned as the origin of the interaction. This fact was also evidenced by plotting the Δ(2) ρ(r) distribution. Taken together, the obtained results clearly indicate that noncovalent carbon bonding can be explained as an interaction between confronted oppositely polarized regions. The interaction is, thus electrophilic-nucleophilic (electrostatic) in nature and unambiguously considered as attractive. PMID:26098702

  8. Temporal reproducibility of diastolic filling parameters derived from Doppler left ventricular inflow time velocity curves. Studies in normal subjects.

    PubMed

    Golia, G; Zanolla, L; Prioli, M A; Scazzina, L; Marino, P; Zardini, P

    1989-05-01

    Doppler left ventricular inflow time-velocity curves have been extensively used to evaluate left ventricular filling. The reproducibility of the technique, however, has been rarely assessed, its temporal variability being, presently, unknown. In order to define the temporal reproducibility of Doppler parameters of left ventricular filling, 10 normal subjects were studied at 3 different times (baseline, after 24 hours, and after 1 week). No parameter changed significantly during 1 week follow-up. When variability, however, was expressed as percent changes relative to baseline, values ranging from 5.7% to 25% were found, the largest variability being associated with acceleration-deceleration parameters (p less than 0.001). In conclusion temporal variability of parameters obtained from Doppler diastolic mitral time-velocity curves is acceptable in homogeneous groups of subjects. When the technique, however, is used for serial evaluation of ventricular filling in a single patient, the specific temporal variability of the parameter considered must be taken into account before any variation can be ascribed to real hemodynamic changes. PMID:2758444

  9. 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:25071540

  10. 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 are the most useful for addressing remedial needs of actinide-contaminated aquifers.

  11. Disentangling fluxes of energy and matter in plasma-surface interactions: Effect of process parameters

    NASA Astrophysics Data System (ADS)

    Wolter, M.; Levchenko, I.; Kersten, H.; Kumar, S.; Ostrikov, K.

    2010-09-01

    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+H2, and Ar+H2+CH4 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.

  12. Identifying the Cognitive Needs of Visitors and Content Selection Parameters for Designing the Interactive Kiosk Software for Museums

    NASA Astrophysics Data System (ADS)

    Katre, Dinesh; Sarnaik, Mandar

    This research presents the findings of contextual interviews, visitor survey and behavioural study that were carried out in Indian museums. It originates from the hypothesis that the museum exhibits are unable to express their relevance, historical significance and related knowledge to satisfy the curiosity of visitors. Our objective is to identify the cognitive needs of museum visitors and the content selection parameters for designing the interactive kiosk software, which is expected to be set up in every thematic gallery of the museum. The kiosk software is intended to offer higher level of engaging and learnable experience to the museum visitors. The research involved participation of 100+ visitors in Indian museums. The access restrictions and constraints of museums cause cognitive deprivation of visitors and compromise the quality of experience. Therefore, the interactivity, animations and multimedia capabilities of kiosk software must be focused on overcoming these limitations.

  13. 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.

  14. 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.

  15. 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, ...

  16. 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.

  17. Establishing dependences between different lipophilic parameters of new potentially biologically active N-substituted-2-phenylacetamide derivatives by applying multivariate methods.

    PubMed

    Vastag, Gyngyi; Apostolov, Suzana; Matijevi?, Borko; Petrovi?, Slobodan

    2015-02-01

    Lipophilicity, a very important parameter in the potential biological activities of molecules, was investigated for newly synthesized N-substituted-2-phenylacetamide derivatives. The determination was carried out in two ways: first experimentally, by applying thin-layer chromatography (TLC) on reversed-phase TLC (RPTLC) RP18F254s in the presence of one protic (methanol) and one aprotic solvent (acetonitrile) and then mathematically, by using different software packages. The intercept of the linear dependence between volume fractions of the organic solvent and the retention parameters obtained by TLC is known as the retention chromatographic constant, R(M)(0), while the slope represents the m value. In order to establish the dependences between the partition coefficient, log P as the standard measure of lipophilicity and the alternative lipophilic parameters obtained experimentally by TLC, R(M)(0) and m values, linear regression analysis and multivariate methods, cluster analysis (CA) and principal component analysis (PCA), were used. All applied methods gave approximately similar results. Although there is a linear dependence between the two chromatographic parameters, the retention constant, R(M)(0), and the m values, only R(M)(0) shows suitable similarity with the standard measure of lipophilicity of the investigated N-substituted-2-phenylacetamide derivatives at the given conditions. The existence of this resemblance proves that the chromatographic retention constant, R(M)(0), obtained by RPTLC could be successfully used for the description of lipophilicity of investigated compounds. On the other hand, the results confirmed that the applied linear regression analysis and the multivariate analysis (CA and PCA) have the ability to compare lipophilic parameters of the investigated phenylacetamide derivatives obtained in different ways. PMID:24981978

  18. An Interactive Tool for Analysis and Optimization of Texture Parameters in Photorealistic Virtual 3d Models

    NASA Astrophysics Data System (ADS)

    Sima, A. A.; Buckley, S. J.; Viola, I.

    2012-07-01

    Texture mapping is a common method for combining surface geometry with image data, with the resulting photorealistic 3D models being suitable not only for visualization purposes but also for interpretation and spatiameasurement, in many application fields, such as cultural heritage and the earth sciences. When acquiring images for creation of photorealistic models, it is usual to collect more data than is finally necessary for the texturing process. Images may be collected from multiple locations, sometimes with different cameras or lens configurations and large amounts of overlap may exist. Consequently, much redundancy may be present, requiring sorting to choose the most suitable images to texture the model triangles. This paper presents a framework for visualization and analysis of the geometric relations between triangles of the terrain model and covering image sets. The application provides decision support for selection of an image subset optimized for 3D model texturing purposes, for non-specialists. It aims to improve the communication of geometrical dependencies between model triangles and the available digital images, through the use of static and interactive information visualization methods. The tool was used for computer-aided selection of image subsets optimized for texturing of 3D geological outcrop models. The resulting textured models were of high quality and with a minimum of missing texture, and the time spent in time-consuming reprocessing was reduced. Anecdotal evidence indicated that an increased user confidence in the final textured model quality and completeness makes the framework highly beneficial.

  19. Quantification of interaction and topological parameters of polyisoprene star polymers under good solvent conditions

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    Mass fractal scaling, reflected in the mass fractal dimension df, is independently impacted by topology, reflected in the connectivity dimension c , and by tortuosity, reflected in the minimum dimension dmin. The mass fractal dimension is related to these other dimensions by df=c dmin . Branched fractal structures have a higher mass fractal dimension compared to linear structures due to a higher c , and extended structures have a lower dimension compared to convoluted self-avoiding and Gaussian walks due to a lower dmin. It is found, in this work, that macromolecules in thermodynamic equilibrium display a fixed mass fractal dimension df under good solvent conditions, regardless of chain topology. These equilibrium structures accommodate changes in chain topology such as branching c by a decrease in chain tortuosity dmin. Symmetric star polymers are used to understand the structure of complex macromolecular topologies. A recently published hybrid Unified scattering function accounts for interarm correlations in symmetric star polymers along with polymer-solvent interaction for chains of arbitrary scaling dimension. Dilute solutions of linear, three-arm and six-arm polyisoprene stars are studied under good solvent conditions in deuterated p -xylene. Reduced chain tortuosity can be viewed as steric straightening of the arms. Steric effects for star topologies are quantified, and it is found that steric straightening of arms is more significant for lower-molecular-weight arms. The observation of constant df is explained through a modification of Flory-Krigbaum theory for branched polymers.

  20. Specimen specific parameter identification of ovine lumbar intervertebral discs: On the influence of fibre-matrix and fibre-fibre shear interactions.

    PubMed

    Reutlinger, Christoph; Bürki, Alexander; Brandejsky, Vaclav; Ebert, Lars; Büchler, Philippe

    2014-02-01

    Numerical models of the intervertebral disc, which address mechanical questions commonly make use of the difference in water content between annulus and nucleus, and thus fluid and solid parts are separated. Despite this simplification, models remain complex due to the anisotropy and nonlinearity of the annulus and regional variations of the collagen fibre density. Additionally, it has been shown that cross-links make a large contribution to the stiffness of the annulus. Because of this complex composite structure, it is difficult to reproduce several sets of experimental data with one single set of material parameters. This study addresses the question to which extent the ultrastructure of the intervertebral disc should be modelled so that its moment-angle behaviour can be adequately described. Therefore, a hyperelastic constitutive law, based on continuum mechanical principles was derived, which does not only consider the anisotropy from the collagen fibres, but also interactions among the fibres and between the fibres and the ground substance. Eight ovine lumbar intervertebral discs were tested on a custom made spinal loading simulator in flexion/extension, lateral bending and axial rotation. Specimen-specific geometrical models were generated using CT images and T2 maps to distinguish between annulus fibrosus and nucleus pulposus. For the identification of the material parameters the annulus fibrosus was described with two scenarios: with and without fibre-matrix and fibre-fibre interactions. Both scenarios showed a similar behaviour on a load displacement level. Comparing model predictions to the experimental data, the mean RMS of all specimens and all load cases was 0.54±0.15° without the interaction and 0.54±0.19° when the fibre-matrix and fibre-fibre interactions were included. However, due to the increased stiffness when cross-links effects were included, this scenario showed more physiological stress-strain relations in uniaxial and biaxial stress states. Thus, the present study suggests that fibre-matrix and fibre-fibre interactions should be considered in the constitutive law when the model addresses questions concerning the stress field of the annulus fibrosus. PMID:24361932

  1. 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

  2. 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

  3. 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.

  4. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters.

    PubMed

    Wang, Jinan; Shao, Qiang; Cossins, Benjamin P; Shi, Jiye; Chen, Kaixian; Zhu, Weiliang

    2016-01-01

    The calculation of protein-ligand binding free energy (ΔG) is of great importance for virtual screening and drug design. Molecular dynamics (MD) simulation has been an attractive tool to investigate this scientific problem. However, the reliability of such approach is affected by many factors including electrostatic interaction calculation. Here, we present a practical protocol using quantum mechanics/molecular mechanics (QM/MM) calculations to generate polarizable QM protein charge (QMPC). The calculated QMPC of some atoms in binding pockets was obviously different from that calculated by AMBER ff03, which might significantly affect the calculated ΔG. To evaluate the effect, the MD simulations and MM/GBSA calculation with QMPC for 10 protein-ligand complexes, and the simulation results were then compared to those with the AMBER ff03 force field and experimental results. The correlation coefficient between the calculated ΔΔG using MM/GBSA under QMPC and the experimental data is .92, while that with AMBER ff03 force field is .47 for the complexes formed by streptavidin or its mutants and biotin. Moreover, the calculated ΔΔG with QMPC for the complexes formed by ERβ and five ligands is positively related to experimental result with correlation coefficient of .61, while that with AMBER ff03 charge is negatively related to experimental data with correlation coefficient of .42. The detailed analysis shows that the electrostatic polarization introduced by QMPC affects the electrostatic contribution to the binding affinity and thus, leads to better correlation with experimental data. Therefore, this approach should be useful to virtual screening and drug design. PMID:25761118

  5. 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

  6. 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.

  7. 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.

  8. High Throughput Layer-by-Layer Films for Extracting Film Forming Parameters and Modulating Film Interactions with Cells.

    PubMed

    Jaklenec, Ana; Anselmo, Aaron C; Hong, Jinkee; Vegas, Arturo J; Kozminsky, Molly; Langer, Robert; Hammond, Paula T; Anderson, Daniel G

    2016-01-27

    A high-throughput approach which automates the synthesis of polyelectrolyte-based layer-by-layer films (HT-LbL) to facilitate rapid film generation, systematic film characterization, and rational investigations into their interactions with cells is described. Key parameters, such as polyelectrolyte adsorption time and polyelectrolyte deposition pH, were used to modulate LbL film growth to create LbL films of distinct thicknesses using the widely utilized polyelectrolytes poly(allylamine hydrochloride) (PAH) and poly(acrylic acid) (PAA). We highlight how HT-LbL can be used to rapidly characterize film-forming parameters and robustly create linearly growing films of various molecular architectures. Film thickness and growth rates of HT-LbL films were shown to increase as a function of adsorption time. Subsequently, we investigated the role that polyelectrolyte solution pH (ranging from 2.5 to 9) has in forming molecularly distinct films of weak polyelectrolytes and report the effect this has on modulating cell attachment and spreading. Films synthesized at PAA-pH of 5.5 and PAH-pH 2.5-5.5 exhibited the highest cellular attachment. These results indicate that HT-LbL is a robust method that can shift the paradigm regarding the use of LbL in biomedical applications as it provides a rapid method to synthesize, characterize, and screen the interactions between molecularly distinct LbL films and cells. PMID:26713554

  9. 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

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

    NASA Astrophysics Data System (ADS)

    Hanni, Matti; Lantto, Perttu; Iliaš, Miroslav; Jensen, Hans Jørgen Aagaard; Vaara, Juha

    2007-10-01

    Relativistic effects on the Xe129 nuclear magnetic resonance shielding and Xe131 nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe2 system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift δ, the anisotropy of the shielding tensor Δσ, and the NQC constant along the internuclear axis χ ‖ 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 Møller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for δ and Δσ by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for δ and Δσ in Xe2. 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 χ ‖, 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 Xe129 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 previously published state of the art theoretical potential energy curve for Xe2, are in excellent agreement with the experiment for the first time.

  11. Problems in the Derivations of the Renormalization Group Equation for the Low Momentum Nucleon Interactions

    NASA Astrophysics Data System (ADS)

    Harada, K.

    2008-10-01

    We carefully examine one of the derivations of the renormalization group equation (RGE) for the so-called V_{low k} potential, given by Bogner et al. [nucl-th/0111042]. The derivation, based on the completeness relation of the model space, must be modified if there are bound states. It is however shown that the RGE is unchanged if the bound state wavefunctions in the reduced theory are required to have the same low-momentum components as those in the original theory. Several aspects of the V_{low k} approach are also discussed.

  12. Breather interactions, higher-order rogue waves and nonlinear tunneling for a derivative nonlinear Schrödinger equation in inhomogeneous nonlinear optics and plasmas

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Li, Min; Qi, Feng-Hua; Geng, Chao

    2015-05-01

    Under investigation in this paper is a variable-coefficient derivative nonlinear Schrödinger (vc-DNLS) equation governing the femtosecond pulses in the inhomogeneous optical fibers or nonlinear Alfvén waves in the inhomogeneous plasmas. Higher-order breather and rogue wave solutions of the vc-DNLS equation are obtained via the variable-coefficient modified Darboux transformation. Two types of the breather interactions (the head-on and overtaking collisions) are exhibited with different spectral parameters. By suitably choosing the inhomogeneous functions, the parabolic breather, periodic breather, breather amplification and breather evolution are demonstrated. Furthermore, the characteristics of the higher-order fundamental rogue wave, periodic rogue wave and composite rogue wave are graphically discussed. Additionally, the nonlinear tunneling of the higher-order breathers and rogue waves are studied.

  13. 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.

  14. Double porosity in fluid-saturated elastic media: deriving effective parameters by hierarchical homogenization of static problem

    NASA Astrophysics Data System (ADS)

    Rohan, Eduard; Naili, Salah; Lemaire, Thibault

    2015-09-01

    We propose a model of complex poroelastic media with periodic or locally periodic structures observed at microscopic and mesoscopic scales. Using a two-level homogenization procedure, we derive a model coherent with the Biot continuum, describing effective properties of such a hierarchically structured poroelastic medium. The effective material coefficients can be computed using characteristic responses of the micro- and mesostructures which are solutions of local problems imposed in representative volume elements describing the poroelastic medium at the two levels of heterogeneity. In the paper, we discus various combinations of the interface between the micro- and mesoscopic porosities, influence of the fluid compressibility, or solid incompressibility. Gradient of porosity is accounted for when dealing with locally periodic structures. Derived formulae for computing the poroelastic material coefficients characterize not only the steady-state responses with static fluid, but are relevant also for quasistatic problems. The model is applicable in geology, or in tissue biomechanics, in particular for modeling canalicular-lacunar porosity of bone which can be characterized at several levels.

  15. Pharmacodynamic interaction of fenugreek, insulin and glimepiride on sero-biochemical parameters in diabetic Sprague-Dawley rats

    PubMed Central

    Haritha, C.; Reddy, A. Gopala; Reddy, Y. Ramana; Anilkumar, B.

    2015-01-01

    Aim: This study was undertaken to assess the pharmacodynamic interaction of fenugreek, insulin and glimepiride on sero-biochemical parameters in streptozotocin-induced diabetic rats. Materials and Methods: A total of 56 male Sprague-Dawley rats, randomly divided into seven Groups. Group 1: Non-diabetic control; Group 2: Streptozotocin induced diabetic control; Groups 3, 4 and 5 were treated with insulin, glimepiride and fenugreek seed powder, respectively; Groups 6 and 7: Insulin + fenugreek seed powder treatment and glimepiride + fenugreek seed powder treatment respectively, in diabetic rats. Body weights, blood glucose, lipids total cholesterol (TC), high-density lipoprotein (HDL), low-density lipoprotein (LDL), triglycerides (TG) and proteins (total protein, albumin, globulin, A/G ratios) were studied at different time intervals. Rats were sacrified at the end of 8 weeks, pancreas and aorta collected for histopathological study. Results: The results of Group 2 showed significantly (p<0.05) higher concentration of glucose, TC, TG, LDL, globulin, A/G ratios and significantly (p<0.05) lower concentration of albumin, total protein, HDL and body weights when compared to Group 1 at the end of 4th and 8th weeks intervals with marked alteration in histopathology of pancreas and aorta. All the treatment Groups 3-7 showed significantly (p<0.05) improvement in the all the parameters and the Groups 6 and 7 showed highest decrease in the concentration blood glucose, TC, TG, LDL and increase in the albumin, total protein and body weights during 6th and 8th week, respectively. Conclusion: The treatment with fenugreek, insulin and glimepiride countered the alteration in the sero biochemical parameters in diabetic rats, and their combination was found a positive interaction in improving the sero biochemical status of diabetic rats. PMID:27047152

  16. 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 help generate the optimal system inputs and enhance the model's applicability.

  17. 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)...

  18. 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

  19. 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.

    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.

  20. 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 of satellite and aerial thermal images available at different spatial resolutions and related to varying epochs helped to highlight variables which seem more appropriate to define the relationships between the LST and the urban features at different scales of analysis. This derived relationship far from linearity and more complex rules are needed to explain the mutual dependency between the parameters. A multivariate statistical analysis was therefore used to adequately represent both the mutual relationships among the explanatory variables and between the explanatory variables and the LST.

  1. Synthesis of fluorinated maltose derivatives for monitoring protein interaction by (19)F NMR.

    PubMed

    Braitsch, Michaela; Kählig, Hanspeter; Kontaxis, Georg; Fischer, Michael; Kawada, Toshinari; Konrat, Robert; Schmid, Walther

    2012-01-01

    A novel reporter system, which is applicable to the (19)F NMR investigation of protein interactions, is presented. This approach uses 2-F-labeled maltose as a spy ligand to indirectly probe protein-ligand or protein-protein interactions of proteins fused or tagged to the maltose-binding protein (MBP). The key feature is the simultaneous NMR observation of both (19)F NMR signals of gluco/manno-type-2-F-maltose-isomers; one isomer (α-gluco-type) binds to MBP and senses the protein interaction, and the nonbinding isomers (β-gluco- and/or α/β-manno-type) are utilized as internal references. Moreover, this reporter system was used for relative affinity studies of fluorinated and nonfluorinated carbohydrates to the maltose-binding protein, which were found to be in perfect agreement with published X-ray data. The results of the NMR competition experiments together with the established correlation between (19)F chemical shift data and molecular interaction patterns, suggest valuable applications for studies of protein-ligand interaction interfaces. PMID:22509216

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

    SciTech Connect

    Marina, Olga A.; Pederson, Larry R.; Coyle, Christopher A.; Edwards, Danny J.; Chou, Y. S.; Cramer, Carolyn N.

    2010-05-28

    Chromium-containing iron-based alloys Crofer22 APU and SS 441 and nickel-based alloy Inconel600, all commonly used in a solid oxide fuel cell (SOFC) stack as interconnect materials, heat exchanger and gas feeding pipes, were exposed at 700-850oC to a synthetic coal gas containing ?2 ppm phosphine, arsine, sulfur and antimony. Samples were characterized by SEM/EDS and XRD to monitor the secondary phase formation. Exposure of ferritic stainless steels to P led to the formation of surface Cr-Mn-P-O and Fe-P-O compounds and increased temperatures accelerated the rate of interactions. Fewer interactions were observed after exposures to As and Sb. No sulfur containing compounds were found. Nickel-based alloy exhibited much stronger interactions with As and P in comparison with ferritic steels and the arsenic interactions were particularly strong. The difference between the iron- and nickel-based alloys is explained by the different chemistry and morphology of the scales grown on the alloy surfaces in coal gas. While P and As interactions with the metallic parts in the SOFC are likely to mitigate the nickel/zirconia anode poisoning, the other degradation mechanisms should be taken into consideration to avoid potential stack failures. Manganese spinels were found to be effective as phosphorus getters and could be used in coal gas cleanup.

  3. Critical look at the role of the bare parameters in the renormalization of ϕ-derivable approximations

    NASA Astrophysics Data System (ADS)

    Reinosa, Urko; Szép, Zsolt

    2012-02-01

    We revisit the renormalization of Φ-derivable approximations from a slightly different point of view than the one which is usually followed in previous works. We pay particular attention to the question of the existence of a solution to the self-consistent equation that defines the two-point function in the Cornwall-Jackiw-Tomboulis formalism and to the fact that some of the ultraviolet divergences which appear if one formally expands the solution in powers of the bare coupling do not always appear as divergences at the level of the solution itself. We discuss these issues using a particular truncation of the Φ functional, namely, the simplest truncation which brings nontrivial momentum and field dependence to the two-point function.

  4. 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

  5. OPACOS: OVRO POST-AGB CO (1-0) EMISSION SURVEY. I. DATA AND DERIVED NEBULAR PARAMETERS

    SciTech Connect

    Sanchez Contreras, C.; Sahai, R.

    2012-11-15

    We have performed interferometric observations of the {sup 12}CO (J = 1-0) emission in a sample of 27 objects spanning different evolutionary stages from the late asymptotic giant branch (late-AGB), through the post-AGB (pAGB) phase, and to the planetary nebula (PN) stage, but dominated by pAGB objects and young PNs ({>=}81%). In this paper (the first in a series) we present our maps and main nebular properties derived for the whole sample. Observations were performed with the Caltech Millimeter Array at the Owens Valley Radio Observatory. The angular resolution obtained in our survey ranges between 2.''3 and 10.''7. The {sup 13}CO and C{sup 18}O (J = 1-0) transitions as well as the 2.6 mm continuum emission have also been observed in several objects. The detection statistics in the {sup 12}CO, {sup 13}CO, C{sup 18}O transitions and 2.6 mm continuum are 89%, 83%, 0%, and 37%, respectively. We report first detections of {sup 12}CO (J = 1-0) emission in 13 targets and confirm emission from several previous marginal detections. The molecular envelope probed by {sup 12}CO (J = 1-0) emission is extended for 18 (out of 24) sources; envelope asymmetries and/or velocity gradients are found in most extended objects. Our data have been used to derive accurate target coordinates and systemic velocities and to characterize the envelope size, morphology, and kinematics. We also provide an estimate of the total molecular mass and the fraction of it contained in fast flows, lower limits to the linear momentum and to the isotopic {sup 12}C/{sup 13}C ratio, as well as the AGB mass-loss rate and timescale for sources with extended CO emission.

  6. Derivative expansion for the boundary interaction terms in the Casimir effect: Generalized {delta} potentials

    SciTech Connect

    Fosco, C. D.; Lombardo, F. C.; Mazzitelli, F. D.

    2009-10-15

    We calculate the Casimir energy for scalar fields in interaction with finite-width mirrors, described by nonlocal interaction terms. These terms, which include quantum effects due to the matter fields inside the mirrors, are approximated by means of a local expansion procedure. As a result of this expansion, an effective theory for the vacuum field emerges, which can be written in terms of generalized {delta} potentials. We compute explicitly the Casimir energy for these potentials and show that, for some particular cases, it is possible to reinterpret them as imposing imperfect Dirichlet boundary conditions.

  7. Temporally restricted substrate interactions direct fate and specification of neural precursors derived from embryonic stem cells

    PubMed Central

    Goetz, A. Katrin; Scheffler, Bjorn; Chen, Huan-Xin; Wang, Shanshan; Suslov, Oleg; Xiang, Hui; Brüstle, Oliver; Roper, Steve N.; Steindler, Dennis A.

    2006-01-01

    It was, until now, not entirely clear how the nervous system attains its cellular phenotypic diversity and wired complexity during development. Here we describe how environmental interactions alone can modify the development of neurogenic precursor cells. Upon evaluating distinct growth-permissive substrates in an embryonic stem cell–neurogenesis assay, we found that laminin, fibronectin, and gelatin instruct neural fate and alter the functional specification of neurons when applied at distinct stages of development. Changes in phenotypic, electrophysiological, and molecular characteristics could resemble cellular events and interactions in the early embryonic brain and may explain why these extracellular matrix components transiently demarcate certain developing brain structures. PMID:16832065

  8. Global variations in gravity-derived oceanic crustal thickness: Implications on oceanic crustal accretion and hotspot-lithosphere interactions

    NASA Astrophysics Data System (ADS)

    Lin, J.; Zhu, J.

    2012-12-01

    We present a new global model of oceanic crustal thickness based on inversion of global oceanic gravity anomaly with constrains from seismic crustal thickness profiles. We first removed from the observed marine free-air gravity anomaly all gravitational effects that can be estimated and removed using independent constraints, including the effects of seafloor topography, marine sediment thickness, and the age-dependent thermal structure of the oceanic lithosphere. We then calculated models of gravity-derived crustal thickness through inversion of the residual mantle Bouguer anomaly using best-fitting gravity-modeling parameters obtained from comparison with seismically determined crustal thickness profiles. Modeling results show that about 5% of the global crustal volume (or 9% of the global oceanic surface area) is associated with model crustal thickness <5.2 km (designated as "thin" crust), while 56% of the crustal volume (or 65% of the surface area) is associated with crustal thickness of 5.2-8.6 km thick (designated as "normal" crust). The remaining 39% of the crustal volume (or 26% of the surface area) is associated with crustal thickness >8.6 km and is interpreted to have been affected by excess magmatism. The percentage of oceanic crustal volume that is associated with thick crustal thickness (>8.6 km) varies greatly among tectonic plates: Pacific (33%), Africa (50%), Antarctic (33%), Australia (30%), South America (34%), Nazca (23%), North America (47%), India (74%), Eurasia (68%), Cocos (20%), Philippine (26%), Scotia (41%), Caribbean (89%), Arabian (82%), and Juan de Fuca (21%). We also found that distribution of thickened oceanic crust (>8.6 km) seems to depend on spreading rate and lithospheric age: (1) On ocean basins younger than 5 Ma, regions of thickened crust are predominantly associated with slow and ultraslow spreading ridges. The relatively strong lithospheric plate at slow and ultraslow ridges might facilitate the loading of large magmatic emplacements on the plate. (2) In contrast, crustal thickness near fast and intermediately fast spreading ridges typically does not exceed 7-8 km. The relatively weak lithosphere at fast and intermediately fast ridges might make it harder for excess magmatism to accrete. We further speculate that the relatively wide partial melting zones in the upper mantle beneath the fast and intermediately fast ridges might act as "buffer" zones, thus diluting the melt anomalies from the underlying hotspots or regions of mantle heterogeneities. (3) As the crustal age increases and the lithospheric plate thickens, regions of thickened crust start to develop on ocean basins that were originally created at fast and intermediately fast ridges. The integrated crustal volume for fast and intermediately fast ocean crust appears to reach peak values for certain geological periods, such as 40-50 Ma and 70-80 Ma. The newly constructed global models of gravity-derived crustal thickness, combining with geochemical and other constraints, can be used to investigate the processes of oceanic crustal accretion and hotspot-lithosphere interactions.

  9. tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins

    PubMed Central

    Shigematsu, Megumi; Kirino, Yohei

    2015-01-01

    The advent of next-generation sequencing technologies has not only accelerated findings on various novel non-coding RNA (ncRNA) species but also led to the revision of the biological significance and versatility of fundamental RNA species with canonical function, such as transfer RNAs (tRNAs). Although tRNAs are best known as adapter components of translational machinery, recent studies suggest that tRNAs are not always end products but can further serve as a source for short ncRNAs. In many organisms, various tRNA-derived ncRNA species are produced from mature tRNAs or their precursor transcripts as functional molecules involved in various biological processes beyond translation. In this review, we focus on the tRNA-derived ncRNAs associated with Argonaute proteins and summarize recent studies on their conceivable biogenesis factors and on their emerging roles in gene expression regulation as regulatory RNAs. PMID:26401098

  10. Derivation of Structure Parameters of Temperature and Humidity in the Convective Boundary Layer from Large-Eddy Simulations and Implications for the Interpretation of Scintillometer Observations

    NASA Astrophysics Data System (ADS)

    Maronga, Björn; Moene, Arnold F.; van Dinther, Daniëlle; Raasch, Siegfried; Bosveld, Fred C.; Gioli, Beniamino

    2013-07-01

    We derive the turbulent structure parameters of temperature CT^2 and humidity C_q^2 from high-resolution large-eddy simulations (LES) of a homogeneously-heated convective boundary layer. Boundary conditions and model forcing were derived from measurements at Cabauw in The Netherlands. Three different methods to obtain the structure-parameters from LES are investigated. The shape of the vertical structure-parameter profiles from all three methods compare well with former experimental and LES results. Depending on the method, deviations in the magnitude up to a factor of two are found and traced back to the effects of discretization and numerical dissipation of the advection scheme. Furthermore, we validate the LES data with airborne and large-aperture scintillometer (LAS) measurements at Cabauw. Virtual path measurements are used to study the variability of CT^2 in the mixed layer and surface layer and its implications for airborne and LAS measurements. A high variability of CT^2 along a given horizontal path in the LES data is associated with plumes (high values) and downdrafts (low values). The path average of CT^2 varies rapidly in time due to the limited path length. The LES results suggest that measured path averages require sufficient temporal averaging and an adequate ratio of path length to height above the ground for the LAS in order to approach the domain average of CT^2.

  11. High-throughput multi-parameter profiling of electrophysiological drug effects in human embryonic stem cell derived cardiomyocytes using multi-electrode arrays.

    PubMed

    Clements, Mike; Thomas, Nick

    2014-08-01

    Human stem cell derived cardiomyocytes (hESC-CM) provide a potential model for development of improved assays for pre-clinical predictive drug safety screening. We have used multi-electrode array (MEA) analysis of hESC-CM to generate multi-parameter data to profile drug impact on cardiomyocyte electrophysiology using a panel of 21 compounds active against key cardiac ion channels. Our study is the first to apply multi-parameter phenotypic profiling and clustering techniques commonly used for high-content imaging and microarray data to the analysis of electrophysiology data obtained by MEA analysis. Our data show good correlations with previous studies in stem cell derived cardiomyocytes and demonstrate improved specificity in compound risk assignment over convention single-parametric approaches. These analyses indicate great potential for multi-parameter MEA data acquired from hESC-CM to enable drug electrophysiological liabilities to be assessed in pre-clinical cardiotoxicity assays, facilitating informed decision making and liability management at the optimum point in drug development. PMID:24812011

  12. High-throughput multi-parameter profiling of electrophysiological drug effects in human embryonic stem cell derived cardiomyocytes using multi-electrode arrays.

    TOXLINE Toxicology Bibliographic Information

    Clements M; Thomas N

    2014-08-01

    Human stem cell derived cardiomyocytes (hESC-CM) provide a potential model for development of improved assays for pre-clinical predictive drug safety screening. We have used multi-electrode array (MEA) analysis of hESC-CM to generate multi-parameter data to profile drug impact on cardiomyocyte electrophysiology using a panel of 21 compounds active against key cardiac ion channels. Our study is the first to apply multi-parameter phenotypic profiling and clustering techniques commonly used for high-content imaging and microarray data to the analysis of electrophysiology data obtained by MEA analysis. Our data show good correlations with previous studies in stem cell derived cardiomyocytes and demonstrate improved specificity in compound risk assignment over convention single-parametric approaches. These analyses indicate great potential for multi-parameter MEA data acquired from hESC-CM to enable drug electrophysiological liabilities to be assessed in pre-clinical cardiotoxicity assays, facilitating informed decision making and liability management at the optimum point in drug development.

  13. Interactions of marine-derived γ-pyrone natural products with phospholipid membranes.

    PubMed

    Powell, Kimberley J; Sharma, Pallavi; Richens, Joanna L; Davis, Benjamin M; Moses, John E; O'Shea, Paul

    2012-11-14

    The sacoglossan mollusc-derived metabolite, tridachiahydropyrone (3), and its proposed biosynthetic precursors (1 and 2) form part of a complex chemical defence system against predators and harmful UV light. Here, we provide supporting biophysical evidence that the metabolites become selectively localised at cell membranes and outline a binding scheme that accommodates the observed data. The possibility that localised lipid domains within the membrane have an effect on the localisation is also addressed. PMID:23032190

  14. 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.

  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. 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

  17. 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.

  18. 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.

  19. 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; Alvarez, Joseph M.; Young, David F.; Sassen, Kenneth; 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 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. Variability of Air-Sea Interactions over the Indian Ocean Derived from Satellite Observations.

    NASA Astrophysics Data System (ADS)

    Gautier, Catherine; Peterson, Peter; Jones, Charles

    1998-08-01

    Novel ways of monitoring the large-scale variability of the southwest monsoon in the Indian Ocean are presented using multispectral satellite datasets. The fields of sea surface temperature (SST), surface latent heat flux (LHF), net surface solar radiation (SW), precipitation (P), and SW LHF over the Indian Ocean are analyzed to characterize the seasonal and interannual variability with special emphasis on the period 1988-90. It is shown that satellite data are able to make a significant contribution to the multiplatform strategy necessary to describe the large-scale spatial and temporal variability of air-sea interactions associated with the Indian Ocean Monsoon. The satellite data analyzed here has shown for the first time characteristics of the interannual variability of air-sea interactions over the entire Indian Ocean. Using monthly means of SST, LHF, SW, P, and the difference SW LHF, the main features of the seasonal and interannual variability of air-sea interactions over the Indian Ocean are characterized. It is shown that the southwest monsoon strongly affects these interactions, inducing dramatic exchanges of heat between air and sea and large temporal variations of these exchanges over relatively small timescale (with regards to typical oceanic timescales). The analyses indicate an overall good agreement between satellite and in situ (ship) estimates, except in the southern Indian Ocean, where ship sampling is minimal, the disagreement can be large. In the latitudinal band of 10N-15S, differences in climatological in situ estimates of surface sensible heat flux and net longwave radiation has a larger influence on the net surface heat flux than the difference between satellite and in situ estimates of SW and LHF.

  6. Novel surface-based methodologies for investigating GH11 xylanase-lignin derivative interactions.

    PubMed

    Zeder-Lutz, G; Renau-Ferrer, S; Agui-Bghin, V; Rakotoarivonina, H; Chabbert, B; Altschuh, D; Rmond, 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

  7. Myeloid-Derived Suppressor Cells as an Immune Parameter in Patients with Concurrent Sunitinib and Stereotactic Body Radiotherapy

    PubMed Central

    Gildener-Leapman, Neil; Eisenstein, Samuel; Coakley, Brian A.; Ozao, Junko; Mandeli, John; Divino, Celia; Schwartz, Myron; Sung, Max; Ferris, Robert; Kao, Johnny; Wang, Lu-Hai; Pan, Ping-Ying; Ko, Eric C.; Chen, Shu-Hsia

    2016-01-01

    Purpose The clinical effects of sunitinib on human myeloid-derived suppressor cell (MDSC) subsets and correlation of the T-cell–mediated immune responses and clinical outcomes in patients with oligometastases treated by stereotactic body radiotherapy (SBRT) have been evaluated. Experimental Design The numbers of granulocytic and monocytic MDSC subsets, effector T cells, and regulatory T cells in the peripheral blood were evaluated pre- and post-sunitinib treatment and concurrent with SBRT. Correlations between MDSC, Treg, and T-cell responses and clinical outcomes were analyzed. Results Patients with oligometastases of various cancer types had elevated granulocytic MDSC and certain subsets of monocytic MDSC population. Sunitinib treatment resulted in a significant reduction in monocytic MDSC, phosphorylated STAT3, and arginase levels in monocytic MDSC (CD33+CD14+CD16+), and an increase in T-cell proliferative activity in cancer patients. Interestingly, the effects of sunitinib on reducing the accumulation and immune-suppressive function of MDSC were significantly correlated with Treg reduction, in responders but not in nonresponding patients. SBRT synergized the therapeutic effects of sunitinib, especially as related to decreased numbers of monocytic MDSC, Treg, and B cells, and augmented Tbet expression in primary CD4 and CD8 T cells. These effects were not observed in patients receiving radiation therapy alone. Most interestingly, the responders, defined by sunitinib-mediated reduction in CD33+CD11b+ myeloid cell populations, tend to exhibit improved progression-free survival and cause-specific survival. Conclusions Sunitinib treatment increased the efficacy of SBRT in patients with oligometastases by reversing MDSC and Treg-mediated immune suppression and may enhance cancer immune therapy to prevent tumor recurrence post-SBRT. PMID:25922428

  8. Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics.

    PubMed

    Carmody, Rachel N; Turnbaugh, Peter J

    2014-10-01

    Our associated microbial communities play a critical role in human health and predisposition to disease, but the degree to which they also shape therapeutic interventions is not well understood. Here, we integrate results from classic and current studies of the direct and indirect impacts of the gut microbiome on the metabolism of therapeutic drugs and diet-derived bioactive compounds. We pay particular attention to microbial influences on host responses to xenobiotics, adding to the growing consensus that treatment outcomes reflect our intimate partnership with the microbial world, and providing an initial framework from which to consider a more comprehensive view of pharmacology and nutrition. PMID:25105361

  9. 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

  10. 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.

  11. GENOME-WIDE GENETIC INTERACTION ANALYSIS OF GLAUCOMA USING EXPERT KNOWLEDGE DERIVED FROM HUMAN PHENOTYPE NETWORKS

    PubMed Central

    HU, TING; DARABOS, CHRISTIAN; CRICCO, MARIA E.; KONG, EMILY; MOORE, JASON H.

    2014-01-01

    The large volume of GWAS data poses great computational challenges for analyzing genetic interactions associated with common human diseases. We propose a computational framework for characterizing epistatic interactions among large sets of genetic attributes in GWAS data. We build the human phenotype network (HPN) and focus around a disease of interest. In this study, we use the GLAUGEN glaucoma GWAS dataset and apply the HPN as a biological knowledge-based filter to prioritize genetic variants. Then, we use the statistical epistasis network (SEN) to identify a significant connected network of pairwise epistatic interactions among the prioritized SNPs. These clearly highlight the complex genetic basis of glaucoma. Furthermore, we identify key SNPs by quantifying structural network characteristics. Through functional annotation of these key SNPs using Biofilter, a software accessing multiple publicly available human genetic data sources, we find supporting biomedical evidences linking glaucoma to an array of genetic diseases, proving our concept. We conclude by suggesting hypotheses for a better understanding of the disease. PMID:25592582

  12. 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".

  13. 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

  14. Social anxiety, acute social stress, and reward parameters interact to predict risky decision-making among adolescents.

    PubMed

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

    2015-01-01

    Risk-taking behavior increases during adolescence, leading to potentially disastrous consequences. Social anxiety emerges in adolescence and may compound risk-taking propensity, particularly during stress and when reward potential is high. However, the manner in which social anxiety, stress, and reward parameters interact to impact adolescent risk-taking is unclear. To clarify this question, a community sample of 35 adolescents (15-18yo), characterized as having high or low social anxiety, participated in a study over two separate days, during each of which they were exposed to either a social stress or a control condition, while performing a risky decision-making task. The task manipulated, orthogonally, reward magnitude and probability across trials. Three findings emerged. First, reward magnitude had a greater impact on the rate of risky decisions in high social anxiety (HSA) than low social anxiety (LSA) adolescents. Second, reaction times (RTs) were similar during the social stress and the control conditions for the HSA group, whereas the LSA group's RTs differed between conditions. Third, HSA adolescents showed the longest RTs on the most negative trials. These findings suggest that risk-taking in adolescents is modulated by context and reward parameters differentially as a function of social anxiety. PMID:25465884

  15. 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.

  16. 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

  17. 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

  18. 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

  19. Re-Processing of ERS-1/-2 SAR data for derivation of glaciological parameters on the Antarctic Peninsula

    NASA Astrophysics Data System (ADS)

    Friedl, Peter; Höppner, Kathrin; Braun, Matthias; Lorenz, Rainer; Diedrich, Erhard

    2015-04-01

    Climate Change, it`s polar amplification and impacts are subject of current research in various thematic and methodological fields. In this context different spaceborne remote sensing techniques play an important role for data acquisition and measurement of different geophysical variables. A recently founded Junior Researchers Group at the German Aerospace Center (DLR) is studying changing processes in cryosphere and atmosphere above the Antarctic Peninsula. It is the aim of the group to make use of long-term remote sensing data sets of the land and ice surface and the atmosphere in order to characterize changes in this sensitive region. One aspect focuses on the application of synthetic aperture radar (SAR) data for glaciological investigations on the Antarctic Peninsula. The data had been acquired by the European Remote Sensing (ERS-1 and ERS-2) satellites and received at DLR's Antarctic station GARS O'Higgins. Even though recent glaciological investigations often make use of modern polar-orbiting single-pass SAR-systems like e.g. TanDEM-X, only ERS-1 (1991 - 2000) and its follow-up mission ERS-2 (1995 - 2011) provided a 20 years' time series of continuous measurements, which offers great potential for long-term studies. Interferometric synthetic radar (InSAR) and differential interferometric synthetic radar (DInSAR) methods as well as the intensity tracking technique are applied to create value-added glaciological SAR-products, such as glacier velocity maps, coherence maps, interferograms and differential interferograms with the aim to make them accessible to interested scientific end-users. These products are suitable for glaciological applications, e.g. determinations of glacier extend, and grounding line position, glacier and ice-stream velocities and glacier mass balance calculations with the flux-gate approach. We represent results of case studies from three test sites located at different latitudes and presenting different climatic and glaciological conditions in order to do first parameter adjustments for the processing. The subsequent aim of the entire project is to re-process the entire 20 years' ERS SAR archive for the Antarctic Peninsula.

  20. Lateral interaction energy derived from Frumkin isotherm for c(2 x 2) Br/Ag(100)

    SciTech Connect

    Wang, J.X.; Ocko, B.M.; Wandlowski, T.

    1997-10-01

    The structure of the bromide adlayer on Ag(100) and the adsorption isotherm have been determined by using in situ surface x-ray scattering techniques and chronocoulometry. Bromide adsorbed on Ag(100) forms a fourfold-hollow-site lattice gas and the adsorption saturates at 1/2 monolayer in a c(2 x 2) structure. The Frumkin isotherm has been employed to fit the experimentally obtained isotherm. Using the experimentally determined electrosorption valency, the lateral interaction energy of 220 meV/atom at full coverage is obtained.

  1. 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.

  2. 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

  3. 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

  4. Hedgehog-mediated paracrine interaction between hepatic stellate cells and marrow-derived mesenchymal stem cells

    SciTech Connect

    Lin Nan Tang Zhaofeng; Deng Meihai; Zhong Yuesi; Lin Jizong; Yang Xuhui; Xiang Peng; Xu Ruiyun

    2008-07-18

    During liver injury, bone marrow-derived mesenchymal stem cells (MSCs) can migrate and differentiate into hepatocytes. Hepatic stellate cell (SC) activation is a pivotal event in the development of liver fibrosis. Therefore, we hypothesized that SCs may play an important role in regulating MSC proliferation and differentiation through the paracrine signaling pathway. We demonstrate that MSCs and SCs both express hedgehog (Hh) pathway components, including its ligands, receptors, and target genes. Transwell co-cultures of SCs and MSCs showed that the SCs produced sonic hedgehog (Shh), which enhanced the proliferation and differentiation of MSCs. These findings demonstrate that SCs indirectly modulate the activity of MSCs in vitro via the Hh pathway, and provide a plausible explanation for the mechanisms of transplanted MSCs in the treatment of liver fibrosis.

  5. 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

  6. Interaction between Cu2+ ions and cholic acid derivatives followed by polarography.

    PubMed

    Feroci, G; Fazio, G; Fini, A; Zuman, P

    1995-01-01

    Interaction of bile salts with Cu2+ ions in unbuffered systems containing 0.15 M NaNO3 was followed by measuring polarographic limiting currents and half-wave potentials. Whereas taurocholate forms neither soluble complexes nor compounds of limited solubility, cholate, glycocholate, and dehydrocholate from both soluble complexes and slightly soluble salts of copper(II) with small aggregates of bile salts. The stability of soluble complexes is comparable for cholates, dehydrocholates, acetates, and acetylglycinates, but smaller for glycocholates. The solubility of the copper(II) salts with small aggregates decreases in the sequence: glycocholate > cholate > dehydrocholate. It is proposed that these salts are formed by interaction of a copper(II) ion with two carboxylic groups located on the small aggregate in a sufficiently small distance. In the presence of excess cholate the precipitated copper(II) salts are dissolved. It is assumed that at high bile salt concentrations, where precipitates are not observed, larger aggregates are formed that have free carboxylate groups, which increase their solubility in aqueous solutions. For glycocholate, within the accessible concentration range and within the time-frame used (24 h for the establishment of the equilibrium), the formation of such larger aggregates was not observed, even when its "cmc" is comparable with that of cholate. The absence of formation of larger aggregates for dehydrocholate parallels its tendency not to form "micelles". PMID:7714733

  7. Semi-Empirical Effective Interactions for Inelastic Scattering Derived from the Reid Potential

    NASA Astrophysics Data System (ADS)

    Fiase, J. O.; Sharma, L. K.; Winkoun, D. P.; Hosaka, A.

    2001-09-01

    An effective local interaction suitable for inelastic scattering is constructed from the Reid soft - core potential. We proceed in two stages: We first calculated a set of relative two - body matrix elements in a variational approach using the Reid soft-core potential folded with two-body correlation functions. In the second stage we constructed a potential for inelastic scattering by fitting the matrix elements to a sum of Yukawa central, tensor and spin-orbit terms to the set of relative two - body matrix elements obtained in the first stage by a least squares fitting procedure. The ranges of the new potential were selected to ensure the OPEP tails in the relevant channels as well as the short - range part of the interaction. It is found that the results of our variational techniques are very similar to the G - matrix calculations of Bertsch and co - workers in the singlet - even, triplet - even, tensor - even and spin-orbit odd channels thus putting our calculations of two - body matrix elements of nuclear forces in these channels on a sound footing. However, there exist major differences in the singlet - odd, triplet - odd, tensor - odd and spin - orbit even channels which casts some doubt on our understanding of nuclear forces in these channels.

  8. DNA interaction and cytotoxicity studies of new ruthenium(II) cyclopentadienyl derivative complexes containing heteroaromatic ligands.

    PubMed

    Moreno, Virtudes; Font-Bardia, Mercè; Calvet, Teresa; Lorenzo, Julia; Avilés, Francesc X; Garcia, M Helena; Morais, Tânia S; Valente, Andreia; Robalo, M Paula

    2011-02-01

    Four ruthenium(II) complexes with the formula [Ru(η(5)-C(5)H(5))(PP)L][CF(3)SO(3)], being (PP = two triphenylphosphine molecules), L = 1-benzylimidazole, ; (PP = two triphenylphosphine molecules), L = 2,2'bipyridine, ; (PP = two triphenylphosphine molecules), L = 4-Methylpyridine, ; (PP = 1,2-bis(diphenylphosphine)ethane), L = 4-Methylpyridine, , were prepared, in view to evaluate their potentialities as antitumor agents. The compounds were completely characterized by NMR spectroscopy and their crystal and molecular structures were determined by X-ray diffraction. Electrochemical studies were carried out giving for all the compounds quasi-reversible processes. The images obtained by atomic force microscopy (AFM) suggest interaction with pBR322 plasmid DNA. Measurements of the viscosity of solutions of free DNA and DNA incubated with different concentrations of the compounds confirmed this interaction. The cytotoxicity of compounds 1234 was much higher than that of cisplatin against human leukemia cancer cells (HL-60 cells). IC(50) values for all the compounds are in the range of submicromolar amounts. Apoptotic death percentage was also studied resulting similar than that of cisplatin. PMID:21194624

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

    NASA Astrophysics Data System (ADS)

    Fei, Xuening; Yu, Miaozhuo; Zhang, Baolian; Cao, Lingyun; Yu, Lu; Jia, Guozhi; Zhou, Jianguo

    2016-01-01

    The LCC-CdTe quantum dots (QDs) hybrid was fabricated by mixing the N-lauryl-N, O-carboxymethyl chitosan (LCC) micelle with water-soluble CdTe QDs in an aqueous solution via hydrophobic forces and the electronic attraction. The structures of LCC and LCC-CdTe QDs hybrid were determined by differential scanning calorimetry (DSC), Fourier transform infrared (FT-IR) spectroscopy and transmission electron microscopy (TEM). The results showed that the lauryl and carboxymethyl were successfully grafted to chitosan oligosaccharide (CSO), and a number of CdTe QDs were encapsulated by LCC micelle to form a core/shell structure. The tested results of the fluorescent characteristics of LCC, CdTe QDs and LCC-CdTe QDs hybrid showed that there were some obvious fluorescent interactions between LCC and CdTe QDs. Meanwhile, with the change in LCC space structure, the fluorescent interactions between LCC and QDs showed different fluorescent characteristics. The QDs fluorescent (FL) intensity increased first and then decreased to almost quenching, while LCC FL intensity decreased continually.

  10. 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 markedly lower additive concentration compared to conventional osmolyte protecting agents. They do not modify IgG permanently, which is an asset for applications in therapeutic protein formulations since the in vivo efficacy of the protein should not be affected. PMID:25019321

  11. Exploring the Molecular Interactions of 7,8-Dihydroxyflavone and Its Derivatives with TrkB and VEGFR2 Proteins

    PubMed Central

    Chitranshi, Nitin; Gupta, Vivek; Kumar, Sanjay; Graham, Stuart L.

    2015-01-01

    7,8-Dihydroxyflavone (7,8-DHF) is a TrkB receptor agonist, and treatment with this flavonoid derivative brings about an enhanced TrkB phosphorylation and promotes downstream cellular signalling. Flavonoids are also known to exert an inhibitory effect on the vascular endothelial growth factor receptor (VEGFR) family of tyrosine kinase receptors. VEGFR2 is one of the important receptors involved in the regulation of vasculogenesis and angiogenesis and has also been implicated to exhibit various neuroprotective roles. Its upregulation and uncontrolled activity is associated with a range of pathological conditions such as age-related macular degeneration and various proliferative disorders. In this study, we investigated molecular interactions of 7,8-DHF and its derivatives with both the TrkB receptor as well as VEGFR2. Using a combination of molecular docking and computational mapping tools involving molecular dynamics approaches we have elucidated additional residues and binding energies involved in 7,8-DHF interactions with the TrkB Ig2 domain and VEGFR2. Our investigations have revealed for the first time that 7,8-DHF has dual biochemical action and its treatment may have divergent effects on the TrkB via its extracellular Ig2 domain and on the VEGFR2 receptor through the intracellular kinase domain. Contrary to its agonistic effects on the TrkB receptor, 7,8-DHF was found to downregulate VEGFR2 phosphorylation both in 661W photoreceptor cells and in retinal tissue. PMID:26404256

  12. Exploring the Molecular Interactions of 7,8-Dihydroxyflavone and Its Derivatives with TrkB and VEGFR2 Proteins.

    PubMed

    Chitranshi, Nitin; Gupta, Vivek; Kumar, Sanjay; Graham, Stuart L

    2015-01-01

    7,8-dihydroxyflavone (7,8-DHF) is a TrkB receptor agonist, and treatment with this flavonoid derivative brings about an enhanced TrkB phosphorylation and promotes downstream cellular signalling. Flavonoids are also known to exert an inhibitory effect on the vascular endothelial growth factor receptor (VEGFR) family of tyrosine kinase receptors. VEGFR2 is one of the important receptors involved in the regulation of vasculogenesis and angiogenesis and has also been implicated to exhibit various neuroprotective roles. Its upregulation and uncontrolled activity is associated with a range of pathological conditions such as age-related macular degeneration and various proliferative disorders. In this study, we investigated molecular interactions of 7,8-DHF and its derivatives with both the TrkB receptor as well as VEGFR2. Using a combination of molecular docking and computational mapping tools involving molecular dynamics approaches we have elucidated additional residues and binding energies involved in 7,8-DHF interactions with the TrkB Ig2 domain and VEGFR2. Our investigations have revealed for the first time that 7,8-DHF has dual biochemical action and its treatment may have divergent effects on the TrkB via its extracellular Ig2 domain and on the VEGFR2 receptor through the intracellular kinase domain. Contrary to its agonistic effects on the TrkB receptor, 7,8-DHF was found to downregulate VEGFR2 phosphorylation both in 661W photoreceptor cells and in retinal tissue. PMID:26404256

  13. Association of the parameters derived from the relation between RR intervals and left ventricle performance with a history of heart failure in patients with atrial fibrillation.

    PubMed

    Lee, Wang Soo; Lee, Kwang Je; Kim, Chee Jeong

    2009-10-01

    Parameters derived from the relation between RR intervals and left ventricular (LV) performance in atrial fibrillation (AF) have been useful to evaluate systolic LV function. This study investigated the association of these parameters with a history of heart failure. Echocardiography was performed in 107 patients with AF. LV outflow peak ejection velocity (Vpe) was adjusted for the effect of pre-preceding RR interval (RR-2) using the logarithmic equation between RR-2 and Vpe. The logarithmic equation between adjusted Vpe and preceding RR interval (RR-1) was calculated in the co-ordinates with RR-1 from 0.6 to 1 second. From this equation, the ratio of slope to Vpe at RR-1 = 1 second (slope/Vpe-1) was obtained. When patients were divided into 2 groups according to a history of heart failure, old age, high slope/Vpe-1, mitral regurgitation, and left atrial enlargement independently predicted the occurrence of heart failure. Fractional shortening was not different between the 2 groups. In patients with normal LV size and without significant regurgitation (n = 69), old age and high slope/Vpe-1 independently predicted the occurrence of heart failure. Areas under the receiver operating characteristics curve of slope/Vpe-1 for identifying heart failure were 0.72 (p <0.000) and 0.74 (p <0.001) in all patients and in patients with normal LV size, respectively. In conclusion, the new parameter, slope/Vpe-1, was one of the most useful predictors for the occurrence of heart failure in AF and was superior to the classic hemodynamic parameters. This parameter might be determined not only by systolic function but also by diastolic function of the left ventricle. PMID:19766764

  14. 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.

  15. 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

  16. Interaction of nickel-based SOFC anodes with trace contaminants from coal-derived synthesis gas

    NASA Astrophysics Data System (ADS)

    Hackett, Gregory Allen

    New and efficient methods of producing electrical energy from natural resources have become an important topic for researchers. Integrated gasification and fuel cell (IGFC) systems offer a fuel-flexible, high-efficiency method of energy generation. Specifically, in coal gasification processes, coal can be changed into a high-quality gaseous fuel suitable for feeding solid oxide fuel cells (SOFCs). However, trace species found in coal synthesis gas (syngas) may have a deleterious effect on the performance of nickel-based SOFC anodes. Generally, the cost of removing these species down to parts per million (ppm) levels is high. The purpose of this research is to determine the highest amount of contaminant that results in a low rate (˜1% per 1000 h) of cell performance degradation, allowing the SOFC to produce usable power for 40,000 hours. The cell performance degradation rate was determined for benzene, naphthalene, and mercury-doped syngas based on species concentration. Experimental data are fitted with degradation models to predict cell lifetime behavior. From these results, the minimum coal syngas cleanup required for these trace materials is determined. It is found that for a final cell voltage of 0.6 V, naphthalene and benzene must be cleaned to 360 ppm and less than 150 ppm, respectively. No additional cleaning is required for mercury beyond established environmental standards. Additionally, a detailed attack and recovery mechanism is proposed for the hydrocarbon species and their interaction with the fuel cell. This mechanism is proposed by considering the type of degradation models predicted and how carbon would interact with the Ni-YSZ anode to justify those models. The mechanism postulates that carbon is diffusing into the nickel structure, creating a metal solution. Once the nickel is saturated, the carbon begins to deposit on the nickel surface, reducing the electrode active area. The formation of metal solutions and the deposition of carbon results in reduced cell productivity.

  17. Peptide labeling with photoactivatable trifunctional cadaverine derivative and identification of interacting partners by biotin transfer.

    PubMed

    App, Christine; Knop, Jana; Huff, Thomas; Seebahn, Angela; Becker, Cord-Michael; Iavarone, Federica; Castagnola, Massimo; Hannappel, Ewald

    2014-07-01

    A new photoactivatable trifunctional cross-linker, cBED (cadaverine-2-[6-(biotinamido)-2-(p-azidobenzamido) hexanoamido]ethyl-1,3'-dithiopropionate), was synthesized by chemical conversion of sulfo-SBED (sulfosuccinimidyl-2-[6-(biotinamido)-2-(p-azidobenzamido) hexanoamido]ethyl-1,3'-dithiopropionate) with cadaverine. This cross-linker was purified by reversed-phase high-performance liquid chromatography (RP-HPLC) and characterized using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis. cBED is based on sulfo-SBED that has a photoactivatable azido group, a cleavable disulfide bond for label transfer methods, and a biotin moiety for highly sensitive biotin/avidin detection. By ultraviolet (UV) light, the azido group is converted to a reactive nitrene, transforming transient bindings of interacting structures to covalent bonds. In contrast to the sulfo-N-hydroxysuccinimide (sulfo-NHS) moiety of sulfo-SBED, which attaches quite unspecifically to amino groups, cBED includes a cadaverine moiety that can be attached by transglutaminase more specifically to certain glutamine residues. For instance, thymosin β4 can be labeled with cBED using tissue transglutaminase. By high-resolution HPLC/ESI-MS (electrospray ionization-mass spectrometry) and tandem MS (MS/MS) of the trypsin digest, it was established that glutamine residues at positions 23 and 36 were labeled, whereas Q39 showed no reactivity. The covalent binding of cBED to thymosin β4 did not influence its G-actin sequestering activity, and the complex could be used to identify new interaction partners. Therefore, cBED can be used to better understand the multifunctional role of thymosin β4 as well as of other proteins and peptides. PMID:24732115

  18. 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

  19. Genetic evidence that brain-derived neurotrophic factor mediates competitive interactions between individual cortical neurons

    PubMed Central

    English, Christopher N.; Vigers, Alison J.; Jones, Kevin R.

    2012-01-01

    Brain-derived neurotrophic factor (BDNF) is a secreted protein important for development and function of neocortical circuitry. Although it is well established that BDNF contributes to the sculpting of dendrite structure and modulation of synapse strength, the range and directionality of BDNF signaling underlying these functions are incompletely understood. To gain insights into the role of BDNF at the level of individual neurons, we tested the cell-autonomous requirements for Bdnf in visual cortical layer 2/3 neurons. We found that the number of functional Bdnf alleles a neuron carries relative to the prevailing genotype determines its density of dendritic spines, the structures at which most excitatory synapses are made. This requirement for Bdnf exists both during postnatal development and in adulthood, suggesting that the amount of BDNF a neuron is capable of producing determines its success in ongoing competition in the environment of the neocortex. Our results suggest that BDNF may perform a long-sought function for a secreted growth factor in mediating the competitive events that shape individual neurons and their circuits. PMID:23129644

  20. 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

  1. 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

  2. Robustness of quantitative compressive sensing MRI: The effect of random undersampling patterns on derived parameters for DCE- and DSC-MRI

    PubMed Central

    Smith, David. S.; Li, Xia; Gambrell, James V.; Arlinghaus, Lori R.; Quarles, C. Chad; Yankeelov, Thomas E.; Welch, E. Brian

    2012-01-01

    Compressive sensing (CS) in Cartesian magnetic resonance imaging (MRI) involves random partial Fourier acquisitions. The random nature of these acquisitions can lead to variance in reconstruction errors. In quantitative MRI, variance in the reconstructed images translates to an uncertainty in the derived quantitative maps. We show that for a spatially regularized 2×-accelerated human breast CS DCE-MRI acquisition with a 1922 matrix size, the coefficients of variation (CoVs) in voxel-level parameters due to the random acquisition are 1.1%, 0.96%, and 1.5% for the tissue parameters Ktrans, ve, and vp, with an average error in the mean of −2.5%, −2.0%, and −3.7%, respectively. Only 5% of the acquisition schemes had a systematic underestimation larger than than 4.2%, 3.7%, and 6.1%, respectively. For a 2×-accelerated rat brain CS DSC-MRI study with a 642 matrix size, the CoVs due to the random acquisition were 19%, 9.5%, and 15% for the cerebral blood flow and blood volume and mean transit time, respectively, and the average errors in the tumor mean were 9.2%, 0.49%, and −7.0%, respectively. Across 11 000 different CS reconstructions, we saw no outliers in the distribution of parameters, suggesting that, despite the random undersampling schemes, CS accelerated quantitative MRI may have a predictable level of performance. PMID:22010146

  3. Model based inversion for deriving maps of histological parameters characteristic of cancer from ex-vivo multispectral images of the colon.

    PubMed

    Claridge, Ela; Hidović-Rowe, Džena

    2014-04-01

    A model-based inversion method was used to obtain quantitative estimates of histological parameters from multispectral images of the colon and to examine their potential for discriminating between normal and pathological tissues. Pixel-wise estimates of the mucosal blood volume fraction, density of the scattering particles and thickness were derived using a two-stage method. In the first (forward) stage reflectance spectra corresponding to given instances of the parameter values were computed using Monte Carlo simulation of photon propagation through a multi-layered tissue. In the second (inversion) stage the parameter values were obtained via optimization using an iterated conditional modes algorithm based on Discrete Markov Random Fields. The method was validated on computer generated data contaminated with noise giving a mean normalized root mean square deviation (NRMSD) of 2.04. Validation on ex vivo images demonstrated that parametric maps show gross correspondence with histological features of mucosa characteristic of cancerous, precancerous and noncancerous colon lesions. The key signs of abnormality were shown to be the increase in the blood volume fraction and decrease in the density of scattering particles. PMID:24239991

  4. HIV-1 Interacts with Human Endogenous Retrovirus K (HML-2) Envelopes Derived from Human Primary Lymphocytes

    PubMed Central

    Brinzevich, Daria; Young, George R.; Sebra, Robert; Ayllon, Juan; Maio, Susan M.; Deikus, Gintaras; Chen, Benjamin K.; Fernandez-Sesma, Ana; Simon, Viviana

    2014-01-01

    ABSTRACT Human endogenous retroviruses (HERVs) are viruses that have colonized the germ line and spread through vertical passage. Only the more recently acquired HERVs, such as the HERV-K (HML-2) group, maintain coding open reading frames. Expression of HERV-Ks has been linked to different pathological conditions, including HIV infection, but our knowledge on which specific HERV-Ks are expressed in primary lymphocytes currently is very limited. To identify the most expressed HERV-Ks in an unbiased manner, we analyzed their expression patterns in peripheral blood lymphocytes using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing. We observe that three HERV-Ks (KII, K102, and K18) constitute over 90% of the total HERV-K expression in primary human lymphocytes of five different donors. We also show experimentally that two of these HERV-K env sequences (K18 and K102) retain their ability to produce full-length and posttranslationally processed envelope proteins in cell culture. We show that HERV-K18 Env can be incorporated into HIV-1 but not simian immunodeficiency virus (SIV) particles. Moreover, HERV-K18 Env incorporation into HIV-1 virions is dependent on HIV-1 matrix. Taken together, we generated high-resolution HERV-K expression profiles specific for activated human lymphocytes. We found that one of the most abundantly expressed HERV-K envelopes not only makes a full-length protein but also specifically interacts with HIV-1. Our findings raise the possibility that these endogenous retroviral Env proteins could directly influence HIV-1 replication. IMPORTANCE Here, we report the HERV-K expression profile of primary lymphocytes from 5 different healthy donors. We used a novel deep-sequencing technology (PacBio SMRT) that produces the long reads necessary to discriminate the complexity of HERV-K expression. We find that primary lymphocytes express up to 32 different HERV-K envelopes, and that at least two of the most expressed Env proteins retain their ability to make a protein. Importantly, one of them, the envelope glycoprotein of HERV-K18, is incorporated into HIV-1 in an HIV matrix-specific fashion. The ramifications of such interactions are discussed, as the possibility of HIV-1 target tissue broadening and immune evasion are considered. PMID:24648457

  5. 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)

    Pschl, U.; Rudich, Y.; Ammann, M.

    2007-12-01

    Aerosols and clouds play central roles in atmospheric chemistry and physics, climate, air pollution, and public health. The mechanistic understanding and predictability of aerosol and cloud properties, interactions, transformations, and effects are, however, still very limited. This is due not only to the limited availability of measurement data, but also to the limited applicability and compatibility of model formalisms used for the analysis, interpretation, and description of heterogeneous and multiphase processes. To support the investigation and elucidation of atmospheric aerosol and cloud surface chemistry and gas-particle interactions, we present a comprehensive kinetic model framework with consistent and unambiguous terminology and universally applicable rate equations and parameters. It enables a detailed description of mass transport and chemical reactions at the gas-particle interface, and it allows linking aerosol and cloud surface processes with gas phase and particle bulk processes in systems with multiple chemical components and competing physicochemical processes. The key elements and essential aspects of the presented framework are: a simple and descriptive double-layer surface model (sorption layer and quasi-static layer); straightforward flux-based mass balance and rate equations; clear separation of mass transport and chemical reactions; well-defined and consistent rate parameters (uptake and accommodation coefficients, reaction and transport rate coefficients); clear distinction between gas phase, gas-surface, and surface-bulk transport (gas phase diffusion, surface and bulk accommodation); clear distinction between gas-surface, surface layer, and surface-bulk reactions (Langmuir-Hinshelwood and Eley-Rideal mechanisms); mechanistic description of concentration and time dependences (transient and steady-state conditions); flexible addition of unlimited numbers of chemical species and physicochemical processes; optional aggregation or resolution 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 Pschl, 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.

  6. Host-Parasite Interaction: Parasite-Derived and -Induced Proteases That Degrade Human Extracellular Matrix

    PubMed Central

    Piña-Vázquez, Carolina; Reyes-López, Magda; Ortíz-Estrada, Guillermo; de la Garza, Mireya; Serrano-Luna, Jesús

    2012-01-01

    Parasitic protozoa are among the most important pathogens worldwide. Diseases such as malaria, leishmaniasis, amoebiasis, giardiasis, trichomoniasis, and trypanosomiasis affect millions of people. Humans are constantly threatened by infections caused by these pathogens. Parasites engage a plethora of surface and secreted molecules to attach to and enter mammalian cells. The secretion of lytic enzymes by parasites into host organs mediates critical interactions because of the invasion and destruction of interstitial tissues, enabling parasite migration to other sites within the hosts. Extracellular matrix is a complex, cross-linked structure that holds cells together in an organized assembly and that forms the basement membrane lining (basal lamina). The extracellular matrix represents a major barrier to parasites. Therefore, the evolution of mechanisms for connective-tissue degradation may be of great importance for parasite survival. Recent advances have been achieved in our understanding of the biochemistry and molecular biology of proteases from parasitic protozoa. The focus of this paper is to discuss the role of protozoan parasitic proteases in the degradation of host ECM proteins and the participation of these molecules as virulence factors. We divide the paper into two sections, extracellular and intracellular protozoa. PMID:22792442

  7. 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

  8. 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

  9. Hepatitis C virus core-derived peptides inhibit genotype 1b viral genome replication via interaction with DDX3X.

    PubMed

    Sun, Chaomin; Pager, Cara T; Luo, Guangxiang; Sarnow, Peter; Cate, Jamie H D

    2010-01-01

    The protein DDX3X is a DEAD-box RNA helicase that is essential for the hepatitis C virus (HCV) life cycle. The HCV core protein has been shown to bind to DDX3X both in vitro and in vivo. However, the specific interactions between these two proteins and the functional importance of these interactions for the HCV viral life cycle remain unclear. We show that amino acids 16-36 near the N-terminus of the HCV core protein interact specifically with DDX3X both in vitro and in vivo. Replication of HCV replicon NNeo/C-5B RNA (genotype 1b) is significantly suppressed in HuH-7-derived cells expressing green fluorescent protein (GFP) fusions to HCV core protein residues 16-36, but not by GFP fusions to core protein residues 16-35 or 16-34. Notably, the inhibition of HCV replication due to expression of the GFP fusion to HCV core protein residues 16-36 can be reversed by overexpression of DDX3X. These results suggest that the protein interface on DDX3X that binds the HCV core protein is important for replicon maintenance. However, infection of HuH-7 cells by HCV viruses of genotype 2a (JFH1) was not affected by expression of the GFP fusion protein. These results suggest that the role of DDX3X in HCV infection involves aspects of the viral life cycle that vary in importance between HCV genotypes. PMID:20862261

  10. 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

  11. 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

  12. Identification of novel GAPDH-derived antimicrobial peptides secreted by Saccharomyces cerevisiae and involved in wine microbial interactions.

    PubMed

    Branco, Patrícia; Francisco, Diana; Chambon, Christophe; Hébraud, Michel; Arneborg, Nils; Almeida, Maria Gabriela; Caldeira, Jorge; Albergaria, Helena

    2014-01-01

    Saccharomyces cerevisiae plays a primordial role in alcoholic fermentation and has a vast worldwide application in the production of fuel-ethanol, food and beverages. The dominance of S. cerevisiae over other microbial species during alcoholic fermentations has been traditionally ascribed to its higher ethanol tolerance. However, recent studies suggested that other phenomena, such as microbial interactions mediated by killer-like toxins, might play an important role. Here we show that S. cerevisiae secretes antimicrobial peptides (AMPs) during alcoholic fermentation that are active against a wide variety of wine-related yeasts (e.g. Dekkera bruxellensis) and bacteria (e.g. Oenococcus oeni). Mass spectrometry analyses revealed that these AMPs correspond to fragments of the S. cerevisiae glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein. The involvement of GAPDH-derived peptides in wine microbial interactions was further sustained by results obtained in mixed cultures performed with S. cerevisiae single mutants deleted in each of the GAPDH codifying genes (TDH1-3) and also with a S. cerevisiae mutant deleted in the YCA1 gene, which codifies the apoptosis-involved enzyme metacaspase. These findings are discussed in the context of wine microbial interactions, biopreservation potential and the role of GAPDH in the defence system of S. cerevisiae. PMID:24292082

  13. Orally potent human renin inhibitors derived from angiotensinogen transition state: design, synthesis, and mode of interaction.

    PubMed

    Iizuka, K; Kamijo, T; Harada, H; Akahane, K; Kubota, T; Umeyama, H; Ishida, T; Kiso, Y

    1990-10-01

    A three-dimensional structure of the complex of human renin and the scissile site P4 Pro to P1' Val of angiotensinogen was deduced in order to design potent human renin inhibitors rationally. On the basis of this structure, an orally potent human renin inhibitor (1a) was designed from the angiotensinogen transition state and synthesized. The inhibitor 1a contains a (2R)-3-(morpholinocarbonyl)-2-(1-naphthylmethyl)propionyl residue (P4-P3) with a retro-inverso amide bond, L-histidine, and a novel amino acid, (2R,3S)-3-amino-4-cyclohexyl-2-hydroxybutyric acid, named cyclohexylnorstatine (2a). The optically pure cyclohexylnorstatine was efficiently prepared from Boc-L-cyclohexylalaninol (3), and the stereochemistry of 1a was established by X-ray crystal analysis. The analyses of interaction between 1a and human renin using modeling techniques indicated that (1) the cyclohexyl group of P1 and the naphthyl group of P3 were accommodated in large hydrophobic subsites S1 and S3, respectively; (2) the imidazole of P2 His was hydrogen bonded to the side chain OH of Ser-233 to contribute to the selectivity of renin inhibition; (3) cyclohexylnorstatine isopropyl ester residue was accommodated in S1-S1'. The importance of the stereochemistry in the potent and specific inhibitor was clearly shown. Oral administration to monkeys of this inhibitor resulted in a drop of 10-20 mmHg in mean blood pressure and a reduction of plasma renin activity for a 5-h period. PMID:2120440

  14. Influence of Fluid, Solid, and Geometric Parameters on the Fluid-Structure Interaction Response and Stability of Flexible Lifting Surfaces

    NASA Astrophysics Data System (ADS)

    Chae, Eun Jung; Akcabay, Deniz Tolga; Young, Yin Lu

    2013-11-01

    There is an increasing interest to use innovative passive/active flexible lifting surfaces to take advantage of the fluid-structure interaction (FSI) response to improve performance or harvest energy. However, design and testing of flexible lifting surfaces are quite complicated, particularly for lightweight structures in a dense, viscous fluid. The objectives of this work are to (1) investigate the influence of varying fluid, material, and geometric parameters on the FSI response and stability boundaries, and (2) to develop generic parametric maps to facilitate the design of flexible lifting surfaces In particular, the focus is on the influence of solid-to-fluid density ratio, Reynolds number, relative stiffness ratio, and relative excitation frequency ratio on the FSI response and static/dynamic divergence and flutter stability boundaries. The results show that the governing failure mode transitions from flutter to dynamic divergence to static divergence when the solid-to-fluid added mass ratio decreases. In addition, classic linear potential theory is severely under-conservative in predicting the flutter boundary, and cannot predict the transition to dynamic divergence for cases in the low mass ratio regimes due to the strong nonlinear, viscous FSI response that develops when the fluid forces are comparable or greater than the solid forces. The Office of Naval Research (Grant no. N00014-11-1-0833); the National Research Foundation of Korea (GCRC-SOP Grant no. 2012-0004783).

  15. 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.

  16. Estimation of a common effect parameter from follow-up data when there is no mechanistic interaction.

    PubMed

    Lee, Wen-Chung

    2014-01-01

    In a stratified analysis, the results from different strata if homogeneity assumption is met are pooled together to obtain a single summary estimate for the common effect parameter. However, the effect can appear homogeneous across strata using one measure but heterogeneous using another. Consequently, two researchers analyzing the same data can arrive at conflicting conclusions if they use different effect measures. In this paper, the author draws on the sufficient component cause model to develop a stratified-analysis method regarding a particular effect measure, the 'peril ratio'. When there is no mechanistic interaction between the exposure under study and the stratifying variable (i.e., when they do not work together to complete any sufficient cause), the peril ratio is constant across strata. The author presents formulas for the estimation of such a common peril ratio. Three real data are re-analyzed for illustration. When the data is consistent with peril-ratio homogeneity in a stratified analysis, researchers can use the formulas in this paper to pool the strata. PMID:24466062

  17. Statistical analysis of multipole-model-derived structural parameters and charge-density properties from high-resolution X-ray diffraction experiments.

    PubMed

    Kamiński, Radosław; Domagała, Sławomir; Jarzembska, Katarzyna N; Hoser, Anna A; Sanjuan-Szklarz, W Fabiola; Gutmann, Matthias J; Makal, Anna; Malińska, Maura; Bąk, Joanna M; Woźniak, Krzysztof

    2014-01-01

    A comprehensive analysis of various properties derived from multiple high-resolution X-ray diffraction experiments is reported. A total of 13 charge-density-quality data sets of α-oxalic acid dihydrate (C2H2O4·2H2O) were subject to Hansen-Coppens-based modelling of electron density. The obtained parameters and properties were then statistically analysed yielding a clear picture of their variability across the different measurements. Additionally, a computational approach (CRYSTAL and PIXEL programs) was utilized to support and examine the experimental findings. The aim of the study was to show the real accuracy and interpretation limits of the charge-density-derived data. An investigation of raw intensities showed that most of the reflections (60-70%) fulfil the normality test and the lowest ratio is observed for weak reflections. It appeared that unit-cell parameters are determined to the order of 10(-3) Å (for cell edges) and 10(-2) ° (for angles), and compare well with the older studies of the same compound and with the new 100 K neutron diffraction data set. Fit discrepancy factors are determined within a 0.5% range, while the residual density extrema are about ±0.16 (3) e Å(-3). The geometry is very well reproducible between different data sets. Regarding the multipole model, the largest errors are present on the valence shell charge-transfer parameters. In addition, symmetry restrictions of multipolar parameters, with respect to local coordinate systems, are well preserved. Standard deviations for electron density are lowest at bond critical points, being especially small for the hydrogen-bonded contacts. The same is true for kinetic and potential energy densities. This is also the case for the electrostatic potential distribution, which is statistically most significant in the hydrogen-bonded regions. Standard deviations for the integrated atomic charges are equal to about 0.1 e. Dipole moments for the water molecule are comparable with the ones presented in various earlier studies. The electrostatic energies should be treated rather qualitatively. However, they are quite well correlated with the PIXEL results. PMID:24419172

  18. Echocardiographic Parameters in Patients with Pulmonary Arterial Hypertension: Correlations with Right Ventricular Ejection Fraction Derived from Cardiac Magnetic Resonance and Hemodynamics

    PubMed Central

    Yang, Tao; Liang, Yu; Zhang, Yan; Gu, Qing; Chen, Guo; Ni, Xin-Hai; Lv, Xiu-Zhang; Liu, Zhi-Hong; Xiong, Chang-Ming; He, Jian-Guo

    2013-01-01

    Background Echocardiography is the most convenient method used to evaluate right ventricular function, and several echocardiographic parameters were studied in previous studies. But the value of these parameters to assess the right ventricular function in patients with pulmonary arterial hypertension (PAH) has not been well defined. Methods Patients with PAH were observed prospectively. Right heart catheterization, echocardiography and cardiac magnetic resonance (CMR) were performed within 1 week interval. The correlations between echocardiographic parameters and right ventricular ejection fraction (RVEF) derived from CMR as well as hemodynamics were analyzed. Results Thirty patients were enrolled including 24 with idiopathic PAH, 5 with PAH associated with connective tissue diseases and 1 with hereditary PAH. All echocardiographic parameters except right ventricular myocardial performance index (RVMPI) correlated significantly with RVEF (tricuspid annual plane systolic excursion [TAPSE], r = 0.440, P = 0.015; tricuspid annular systolic excursion velocity [S’], r = 0.444, P = 0.016; isovolumic acceleration [IVA], r = 0.600, P = 0.001; right ventricular fraction area change [RVFAC], r = 0.416, P = 0.022; ratio of right ventricular transverse diameter to left ventricular transverse diameter [RVETD/LVETD], r = −0.649, P<0.001; RVMPI, r = −0.027, P = 0.888). After adjusted for mean right atrial pressure, mean pulmonary arterial pressure and pulmonary vascular resistance (PVR), only IVA and RVETD/LVETD could independently predict RVEF. Four echocardiographic parameters displayed significant correlations with PVR (TAPSE, r = −0.615, P<0.001; S’, r = −0.557, P = 0.002; RVFAC, r = −0.454, P = 0.012; RVETD/LVETD, r = 0.543, P = 0.002). Conclusions The echocardiographic parameters IVA and RVETD/LVETD can reflect RVEF independently regardless of hemodynamics in patients with PAH. In addition, TAPSE, S’, RVFAC and RVETD/LVETD can also reflect PVR in PAH patients. PMID:23967181

  19. 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

  20. Design, Synthesis, and Biological Evaluation of 1-Benzyl-1H-pyrazole Derivatives as Receptor Interacting Protein 1 Kinase Inhibitors.

    PubMed

    Zou, Chan; Xiong, Yu; Huang, Lu-Yi; Song, Chun-Li; Wu, Xiao-Ai; Li, Lin-Li; Yang, Sheng-Yong

    2016-04-01

    Receptor interacting protein 1 (RIP1) kinase plays an important role in necroptosis, and inhibitors of the RIP1 kinase are thought to have a potential therapeutic value in the treatment of diseases related to necrosis. Herein, we report the structural optimization of a RIP1 kinase inhibitor, 1-(2,4-dichlorobenzyl)-3-nitro-1H-pyrazole (1a). A number of 1-benzyl-1H-pyrazole derivatives were synthesized and structure-activity relationship (SAR) analysis led to the discovery of a potent compound, 4b, which showed a Kd value of 0.078 μm against the RIP1 kinase and an EC50 value of 0.160 μm in a cell necroptosis inhibitory assay. Compound 4b also displayed considerable ability to protect the pancreas in an l-arginine-induced pancreatitis mouse model. PMID:26577270

  1. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA.

    PubMed

    Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

    2016-01-15

    A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging. PMID:26436845

  2. Effects and interactions of medium components on laccase from a marine-derived fungus using response surface methodology.

    PubMed

    D'Souza-Ticlo, Donna; Garg, Sandeep; Raghukumar, Chandralata

    2009-01-01

    The effects of various synthetic medium components and their interactions with each other ultimately impact laccase production in fungi. This was studied using a laccase-hyper-producing marine-derived basidiomycete, Cerrena unicolor MTCC 5159. Inducible laccases were produced in the idiophase only after addition of an inducer such as CuSO(4). Concentration of carbon and nitrogen acted antagonistically with respect to laccase production. A combination of low nitrogen and high carbon concentration favored both biomass and laccase production. The most favorable combination resulted in 917 U L(-1) of laccase. After sufficient growth had occurred, addition of a surfactant such as Tween 80 positively impacted biomass and increased the laccase activity to around 1,300 U L(-1). Increasing the surface to volume ratio of the culture vessel further increased its activity to almost 2,000 U L(-1). PMID:20098606

  3. 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.

  4. 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

  5. Multi-cellular interactions sustain long-term contractility of human pluripotent stem cell-derived cardiomyocytes

    PubMed Central

    Burridge, Paul W; Metzler, Scott A; Nakayama, Karina H; Abilez, Oscar J; Simmons, Chelsey S; Bruce, Marc A; Matsuura, Yuka; Kim, Paul; Wu, Joseph C; Butte, Manish; Huang, Ngan F; Yang, Phillip C

    2014-01-01

    Therapeutic delivery of cardiomyocytes derived from human pluripotent stem cells (hPSC-CMs) represents a novel clinical approach to regenerate the injured myocardium. However, poor survival and contractility of these cells are a significant bottleneck to their clinical use. To better understand the role of cell-cell communication in enhancing the phenotype and contractile properties of hPSC-CMs, we developed a three-dimensional (3D) hydrogel composed of hPSC-CMs, human pluripotent stem cell-derived endothelial cells (hPSC-ECs), and/or human amniotic mesenchymal stem cells (hAMSCs). The objective of this study was to examine the role of multi-cellular interactions among hPSC-ECs and hAMSCs on the survival and long-term contractile phenotype of hPSC-CMs in a 3D hydrogel. Quantification of spontaneous contractility of hPSC-CMs in tri-culture demonstrated a 6-fold increase in the area of contractile motion after 6 weeks with characteristic rhythmic contraction frequency, when compared to hPSC-CMs alone (P < 0.05). This finding was supported by a statistically significant increase in cardiac troponin T protein expression in the tri-culture hydrogel construct at 6 weeks, when compared to hPSC-CMs alone (P < 0.001). The sustained hPSC-CM survival and contractility in tri-culture was associated with a significant upregulation in the gene expression of L-type Ca2+ ion channel, Cav1.2, and the inward-rectifier potassium channel, Kir2.1 (P < 0.05), suggesting a role of ion channels in mediating these processes. These findings demonstrate that multi-cellular interactions modulate hPSC-CM phenotype, function, and survival, and they will have important implications in engineering cardiac tissues for treatment of cardiovascular diseases. PMID:25628783

  6. Deriving Macropore and Preferential Flow Parameters from Tracer and Time-lapse 3D GPR Experiments at the Plot-Scale

    NASA Astrophysics Data System (ADS)

    Jackisch, Conrad; Allroggen, Niklas; Tronicke, Jens; Zehe, Erwin

    2014-05-01

    "Hydrology - a science in which all processes are preferential" (Uhlenbrook, 2006) - as such preferential flow is known and discussed in hydrology since almost three decades. At the same time, preferential flow remains problematic as explicit descriptions are hard to define and upscale and implicit descriptions remain rather case sensitive. Moreover, our techniques to monitor preferential flow and especially flow structures are very limited. We conducted three multi-tracer plot-scale (1m x 1m) sprinkler experiments at a forested hillslope in the Attert Basin in Luxembourg with prevailing geogenic and biogenic preferential flow structures. It was accompanied by a 3D time-lapse GPR (Ground Penetrating Radar) survey covering an area of 3m x 3m. We present the results with special emphasis on the derivation of macropore parameters for further modelling. To do so, we developed an automated analysis of images from excavated Brilliant Blue stained profiles. Additionally, we analyse our time-lapse GPR data with respect to temporal changes and derive 3D strutural information of the preferential flow patterns. Superior to tracers, this high resolution subsurface imaging technique is non-invasive, repeatable and therefore helps to disentangle the dye stained patterns towards process observation. The results of the image analyses and the GPR surveys are compared and referenced to soil moisture monitoring, sampled Bromide profiles and stable isotope signatures. We further discuss implications for joint development of model concepts and observation methods.

  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. Bounds on the Time-Reversal Non-Invariant Nucleon - Interaction Derived from Transition-Strength Fluctuations.

    NASA Astrophysics Data System (ADS)

    Tomsovic, Steven Lee

    1987-10-01

    We deal here with Wigner's problem, i.e. the problem of determining, from the nuclear strength fluctuations (spectral. fluctuations can also be used and make up another part of the problem), values for or upper bounds upon the relative magnitude of the time-reversal non-invariant (TRNI) part of the nucleon-nucleon interaction. The solution of this problem proceeds in three main steps. First we develop a theory, relying on random-matrix methods,. for transition-strength fluctuation measures and their respective transitions as TRI is broken. We find that there is a universal transi- tion parameter (LAMDA)(' 1/2) which measures the TRI-breaking interaction. matrix elements on the scale of the local mean spacing (the same parameter bound in the earlier spectral fluctuation theory). Next, a good analysis of the data (mostly slow neutron resonance data). with the assumption of TRI, is undertaken. The goal of the data analysis then is to place a bound on (LAMDA)(' 1/2); we find that it indicates. (LAMDA)(' 1/2) <(, )0.10. Since the energy levels are detected via their strengths, it is necessary also to consider the consistency of the strength and spectral data. A discrepancy is found between the separate estimates of the degree of impurity (number of missing and wrongly. assigned levels) in the level sequences. This may be ascribed to deviation from the Porter-Thomas distribution (the GOE law for the strengths) in which case we would have (LAMDA)(' 1/2) (TURN) 0.03, but it may also. be due to a failure of the statistical model for small strengths. And finally we reduce the result to a statement about TRNI in the effective nuclear interaction. Using statistical spectroscopic methods and a bivariate Gaussian form for the density-weighted mean strength,. we can relate the (LAMDA)(' 1/2) bound to a bound on (alpha) which measures the relative norm of the TRI vs TRNI nucleon-nucleon interactions. This gives bounds of 1-4 parts per thousand for a. Further refinements in the data could lead to improvements, perhaps by a factor 4. The solution of this problem, will also enable us to assess the fundamental significance of other weakly broken symmetries (parity, isospin,...) and the techniques will be applicable to many other problems.

  10. Derivation of Orbital Parameters of Very Low-Mass Companions in Double Stars from Radial Velocities and Observations of Space-Astrometry Missions like HIPPARCOS, DIVA and GAIA

    NASA Astrophysics Data System (ADS)

    Bernstein, H.-H.

    Radial velocity measurements are a well known high-precision method to obtain the orbits of extrasolar planets or brown dwarfs. However, this method is not able to determine the inclination which could be derived from astrometry. The astrometric effects of those objects are very minute, wherefore the interest of astronomers in astrometric techniques was very poor. This situation changes fundamentally since space astrometry observations are available. HIPPARCOS demonstrated the power of space astrometry and the extremely high accuracy of the DIVA, and especially the GAIA observations allows one to detect Jupiter- and Earth-like objects. The optimal estimation of the parameters of the orbit of extrasolar planets or brown dwarfs is a combination of radial velocity measurements and space astrometry observations. Here it is possible to overcome problems which are inherent in both observation methods, so space astrometry complements radial velocity observations and vice versa. This paper gives a method for the parameter estimation using both tools of measurements and shows the limits of this procedure. In addition an error assessment gives the capability of the combination of radial velocity observations and space astrometry.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. Interactions and hybrid complex formation of anionic algal polysaccharides with a cationic glycine betaine-derived surfactant.

    PubMed

    Covis, Rudy; Vives, Thomas; Gaillard, Cédric; Benoit, Maud; Benvegnu, Thierry

    2015-05-01

    The interaction between anionic algal polysaccharides ((κ)-, (ι)-, (λ)-carrageenans, alginate and ulvan) and a cationic glycine betaine (GB) amide surfactant possessing a C18:1 alkyl chain has been studied using isothermal titration calorimetry (ITC), zeta-potential measurements, dynamic light scattering (DLS), transmission electron microscopy (TEM), atomic force microscopy (AFM), and surface tension measurements. It was observed that this cationic surfactant derived from renewable raw materials induced cooperative binding with the anionic polymers at critical aggregation concentration (CAC) and the CAC values are significantly lower than the corresponding critical micelle concentration (CMC) for the surfactant. The CMC of cationic GB surfactant was obtained at higher surfactant concentration in polysaccharide solution than in pure water. More interestingly, the presence of original polysaccharide/surfactant hybrid complexes formed above the CMC value was evidenced from (κ)-carrageenan by microscopy (TEM and AFM). Preliminary investigations of the structure of these complexes revealed the existence of surfactant nanoparticles surrounded with polysaccharide matrix, probably resulting from electrostatic attraction. In addition, ITC measurements clearly showed that the interactions of the κ-carrageenan was stronger than for other polysaccharides ((ι)-, (λ)-carrageenans, alginate and ulvan). These results may have important impact on the use of the GB amide surfactant in formulations based on algal polysaccharides for several applications such as in food, cosmetics, and detergency fields. PMID:25659719

  18. 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

  19. Interaction of zearalenone and soybean isoflavone in diets on the growth performance, organ development and serum parameters in prepubertal gilts.

    PubMed

    Wang, D F; Zhang, N Y; Peng, Y Z; Qi, D S

    2012-10-01

    The aim of the present research was to determine the interactive effect of zearalenone (ZEA) and soybean isoflavone (ISO) on the growth performance, development of organs and serum parameters in prepubertal gilts. Ninety 75-day-old female pigs (Duroc × Landrace × Yorkshire, 26.5 ± 0.60 kg) were randomly allocated to nine diet treatments during the 21-day study. The experiment employed a 3 × 3 factorial design using a non-soybean meal diet with the addition of 0, 0.5 or 2.0 mg/kg ZEA and 0, 300 or 600 mg/kg ISO. The results indicated that simultaneous addition of ZEA and ISO had no significant influence on the growth performance in prepubertal gilts. Zearalenone with 2 mg/kg increased (p < 0.05) the relative weight of the reproductive organs (including uterus and vagina) but had no obvious effects (p > 0.05) on the relative weight of the heart, liver, lung, kidney and spleen. Isoflavone at 600 mg/kg could offset the increased weight of the reproductive organs induced by ZEA. Simultaneous addition of ZEA and ISO to prepubertal gilts increased the level of alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase in the serum (p < 0.05) at day 14 but their levels decreased (p < 0.05) over time. Zearalenone increased the level of malondialdehyde and decreased the concentrations of superoxide dismutase and glutathione peroxidase (p < 0.05) in the serum. The results suggested that ISO added to diets at 600 mg/kg could reduce the increase in the relative weight of reproductive organs and relieve the oxidative stress induced by ZEA added at 2 mg/kg during the growth phase in prepubertal gilts. PMID:21883496

  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. Weak interactions in barbituric acid derivatives. Unusually steady intermolecular organic “sandwich” complexes. π π Stacking versus hydrogen bonding interactions

    NASA Astrophysics Data System (ADS)

    Khrustalev, Victor N.; Krasnov, Konstantin A.; Timofeeva, Tatiana V.

    2008-04-01

    The 4-methoxy-6,6-dimethyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5- g]isoquinolin-6-ium ( 1) and 2-(1 H-indol-3-yl)-1-ethanaminium (tryptaminium) ( 2) salts of 1,3-dimethyl-2,4,6-trioxoperhydro-pyrimidine-5-spiro-6'-{4'-methoxy-7'-(1,3-dimethyl-2,4,6-trioxoper-hydropyrimidin-5-yl)-5',6',7',8'-tetrahydro[1,3]dioxolo[4,5- g]naphthalene} ( 3) have been prepared and their structures have been investigated by single-crystal X-ray diffraction analysis. It has been found on the basis of the crystal packing arrangement as well as physical and chemical properties that derivatives 1 and 2 form unusually steady intermolecular sandwich-like complexes both in the crystal and in solution, which are stabilized by weak C sbnd H… n(O dbnd C) hydrogen bonds and π-π stacking. The interplay between the intermolecular π-π stacking and strong N sbnd H…O hydrogen bond interactions and its influence on the "sandwich" structures of 1 and 2 are discussed.

  2. Dependence of the average spatial and energy characteristics of the hadron-lepton cascade on the strong interaction parameters at superhigh energies

    NASA Technical Reports Server (NTRS)

    Boyadjian, N. G.; Dallakyan, P. Y.; Garyaka, A. P.; Mamidjanian, E. A.

    1985-01-01

    A method for calculating the average spatial and energy characteristics of hadron-lepton cascades in the atmosphere is described. The results of calculations for various strong interaction models of primary protons and nuclei are presented. The sensitivity of the experimentally observed extensive air showers (EAS) characteristics to variations of the elementary act parameters is analyzed.

  3. Interaction of cinnamic acid derivatives with commercial hypoglycemic drugs on 2-deoxyglucose uptake in 3T3-L1 adipocytes.

    PubMed

    Prabhakar, Pranav Kumar; Doble, Mukesh

    2011-09-28

    Hydroxycinnamic acid derivatives are naturally occurring substances found in fruits, vegetables, and flowers and are consumed as dietary phenolic compounds. The effect of cinnamic acid, ferulic acid, p-coumaric acid, eugenol, chlorogenic acid, and caffeic acid, alone and in combination with two commercial oral hypoglycemic drugs (OHD), namely, thiazolidinedione (THZ) and metformin, on the uptake of 2-deoxyglucose (2DG) by 3T3-L1 adipocytes is studied. All of the phytochemicals other than cinnamic acid show synergistic interaction in 2DG uptake with both of the OHDs. THZ (20 μM) in combination with ferulic acid (25 μM) or p-coumaric acid (25 μM) increases 2DG uptake by 7- or 6.34-fold, respectively, with respect to control, whereas metformin (20 μM), along with ferulic acid (25 μM) or cinnamic acid (25 μM), increases 2DG uptake by 6.45- or 5.87-fold, respectively, when compared to control. Chlorogenic and cinnamic acids increased the expression of PPARγ, whereas other hydroxycinnamic acids enhanced the expression of PI3K, indicating different mechanisms of action between these compounds. These phytochemicals were able to reduce the expressions of the fatty acid synthase and HMG CoA reductase genes, indicating that they may be able to reduce the secondary complications caused by the accumulation of lipids. These studies suggest that hydroxycinnamic acid derivatives may be beneficial for the treatment of diabetes mellitus. They may act as a supplement with commercial drugs and may reduce the secondary complications caused by OHDs. PMID:21870829

  4. 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 elements; the number of points; and the number of eigenfunctions required. Test run requires 4 MB Classification: 2.1, 2.4 External routines: GAULEG [3] Nature of problem: The three-dimensional boundary problem for the elliptic partial differential equation with an axial symmetry similar to the Schrödinger equation with the Coulomb and transverse oscillator potentials is reduced to the two-dimensional one. The latter finds wide applications in modeling of photoionization and recombination of oppositively charged particles (positrons, antiprotons) in the magnet-optical trap [4], optical absorption in quantum wells [5], and channeling of likely charged particles in thin doped films [6,7] or neutral atoms and molecules in artificial waveguides or surfaces [8,9]. In the adiabatic approach [10] known in mathematics as Kantorovich method [11] the solution of the two-dimensional elliptic partial differential equation is expanded over basis functions with respect to the fast variable (for example, angular variable) and depended on the slow variable (for example, radial coordinate ) as a parameter. An averaging of the problem by such a basis leads to a system of the second-order ordinary differential equations which contain potential matrix elements and the first-derivative coupling terms (see, e.g., [12,13,14]). The purpose of this paper is to present the finite element method procedure based on the use of high-order accuracy approximations for calculating 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 developed calculates potential matrix elements - integrals of the eigenfunctions multiplied by their derivatives with respect to the parameter. These matrix elements 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 [1,2]. Solution method: The parametric self-adjoined Sturm-Liouville problem with the parametric third type boundary conditions is solved by the finite element method using high-order accuracy approximations [15]. The generalized algebraic eigenvalue problem AF=EBF with respect to a pair of unknown ( E,F) arising after the replacement of the differential problem by the finite-element approximation is solved by the subspace iteration method using the SSPACE program [16]. First derivatives of the eigenfunctions with respect to the parameter which contained in potential matrix elements of the coupled system equations are obtained by solving the inhomogeneous algebraic equations. 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 described in [1,17,18], a 3D-model of a hydrogen atom in a homogeneous magnetic field described in [14,19] and a hydrogen atom on a three-dimensional sphere [20]. Restrictions: The computer memory requirements depend on: the number and order of finite elements; the number of points; and the number of eigenfunctions required. Restrictions due to dimension sizes may be easily alleviated by altering PARAMETER statements (see sections below and listing for details). The user must also supply DOUBLE PRECISION functions POTCCL and POTCC1 for evaluating potential function U(ρ,z) of Eq. (1) and its first derivative with respect to parameter ρ. The user should supply DOUBLE PRECISION functions F1FUNC and F2FUNC that evaluate functions f(z) and f(z) of Eq. (1). The user must also supply subroutine BOUNCF for evaluating the parametric third type boundary conditions. Running time: The running time depends critically upon: the number and order of finite elements; the number of points on interval [z,z]; and the number of eigenfunctions required. The test run which accompanies this paper took 2 s with calculation of matrix potentials on the Intel Pentium IV 2.4 GHz. References:O. Chuluunbaatar, A.A. Gusev, A.G. Abrashkevich, A. Amaya-Tapia, M.S. Kaschiev, S.Y. Larsen, S.I. Vinitsky, Comput. Phys. Comm. 177 (2007) 649-675 O. Chuluunbaatar, A.A. Gusev, S.I. Vinitsky, A.G. Abrashkevich, Comput. Phys. Comm. 179 (2008) 685-693. W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Numerical Recipes: The Art of Scientific Computing, Cambridge University Press, Cambridge, 1986. O. Chuluunbaatar, A.A. Gusev, S.I. Vinitsky, V.L. Derbov, L.A. Melnikov, V.V. Serov, Phys. Rev. A 77 (2008) 034702-1-4. E.M. Kazaryan, A.A. Kostanyan, H.A. Sarkisy