Science.gov

Sample records for derived interaction parameters

  1. 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.

  2. SimSphere model sensitivity analysis towards establishing its use for deriving key parameters characterising land surface interactions

    NASA Astrophysics Data System (ADS)

    Petropoulos, G. P.; Griffiths, H. M.; Carlson, T. N.; Ioannou-Katidis, P.; Holt, T.

    2014-01-01

    Being able to accurately estimate parameters characterising land surface interactions is of key scientific priority today due to their central role in the Earth's global energy and water cycle. To this end, some approaches have been based on utilising the synergies between land surface models and Earth Observation (EO) data to retrieve relevant parameters. One such model is SimSphere, the use of which is currently expanding, either as a stand-alone application or synergistically with EO data. The present study aims at exploring the effect of changing the atmospheric sounding profile to the sensitivity of key variables predicted by this model assuming different probability distribution functions (PDFs) for its inputs/outputs. To satisfy this objective and to ensure consistency and comparability to analogous studies conducted previously on the model, a sophisticated, cutting edge sensitivity analysis (SA) method adopting Bayesian theory is implemented herein on SimSphere. Our results did not show dramatic changes in the nature or ranking of influential model inputs in comparison to previous studies. Model outputs of which the SA was examined were sensitive to a small number of the inputs; a significant amount of first order interactions between the inputs was also found, suggesting strong model coherence. Results obtained suggest that the assumption of different PDFs for the model inputs/outputs did not have significant bearing on mapping the most responsive model inputs and interactions, but only the absolute SA measures. All in all, this study extends our understanding of SimSphere's structure and further establishes its coherence and correspondence to that of a natural system's behaviour. Consequently, the present work represents a significant step forward in the efforts globally on SimSphere verification, especially those focusing towards the development of global operational products from the synergy of SimSphere with EO data.

  3. SimSphere model sensitivity analysis towards establishing its use for deriving key parameters characterising land surface interactions

    NASA Astrophysics Data System (ADS)

    Petropoulos, G. P.; Griffiths, H. M.; Carlson, T. N.; Ioannou-Katidis, P.; Holt, T.

    2014-09-01

    Being able to accurately estimate parameters characterising land surface interactions is currently a key scientific priority due to their central role in the Earth's global energy and water cycle. To this end, some approaches have been based on utilising the synergies between land surface models and Earth observation (EO) data to retrieve relevant parameters. One such model is SimSphere, the use of which is currently expanding, either as a stand-alone application or synergistically with EO data. The present study aimed at exploring the effect of changing the atmospheric sounding profile on the sensitivity of key variables predicted by this model assuming different probability distribution functions (PDFs) for its inputs/outputs. To satisfy this objective and to ensure consistency and comparability to analogous studies conducted previously on the model, a sophisticated, cutting-edge sensitivity analysis (SA) method adopting Bayesian theory was implemented on SimSphere. Our results did not show dramatic changes in the nature or ranking of influential model inputs in comparison to previous studies. Model outputs examined using SA were sensitive to a small number of the inputs; a significant amount of first-order interactions between the inputs was also found, suggesting strong model coherence. Results showed that the assumption of different PDFs for the model inputs/outputs did not have an important bearing on mapping the most responsive model inputs and interactions, but only the absolute SA measures. This study extends our understanding of SimSphere's structure and further establishes its coherence and correspondence to that of a natural system's behaviour. Consequently, the present work represents a significant step forward in the global efforts on SimSphere verification, especially those focusing on the development of global operational products from the model synergy with EO data.

  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. 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.

  6. 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.

  7. 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

  8. 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.

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

    PubMed

    Bergner, Steven; Sedlmair, Michael; Mller, 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

  10. 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

  11. Determination of some thermodynamic parameters of dissociation of dihydropyrimidine derivatives

    NASA Astrophysics Data System (ADS)

    Bhalodia, Rahul; Gajera, Ravi; Baluja, Shipra

    2011-08-01

    Dissociation constant of dihydropyrimidine derivatives has been determined in dimethyl forma-midewater (60: 40 v/v) system at different temperatures. The data are discussed in terms of the electron nature of the substituents. Further, some thermodynamics parameters such as enthalpy of solution, Gibbs energy change and entropy of solution have also been evaluated for these systems.

  12. Interactions of benzodiazepine derivatives with annexins.

    PubMed

    Hofmann, A; Escherich, A; Lewit-Bentley, A; Benz, J; Raguenes-Nicol, C; Russo-Marie, F; Gerke, V; Moroder, L; Huber, R

    1998-01-30

    Human annexins III and V, members of the annexin family of calcium- and membrane-binding proteins, were complexed within the crystals with BDA452, a new 1,4-benzodiazepine derivative by soaking and co-crystallization methods. The crystal structures of the complexes were analyzed by x-ray crystallography and refined to 2.3- and 3.0-A resolution. BDA452 binds to a cleft which is located close to the N-terminus opposite to the membrane binding side of the proteins. Biophysical studies of the interactions of various benzodiazepine derivatives with annexins were performed to analyze the binding of benzodiazepines to annexins and their effects on the annexin-induced calcium influx into phosphatidylserine/phosphatidylethanolamine liposomes. Different effects were observed with a variety of benzodiazepines and different annexins depending on both the ligand and the protein. Almost opposite effects on annexin function are elicited by BDA250 and diazepam, its 7-chloro-derivative. We conclude that benzodiazepines modulate the calcium influx activity of annexins allosterically by stabilizing or destabilizing the conducting state of peripherally bound annexins in agreement with suggestions by Kaneko (Kaneko, N., Ago, H., Matsuda, R., Inagaki, E., and Miyano, M. (1997) J. Mol. Biol., in press). PMID:9446599

  13. Antiviral activity and interaction mechanisms study of novel glucopyranoside derivatives.

    PubMed

    Chen, Meihang; Hu, Deyu; Li, Xiangyang; Yang, Song; Zhang, Weiying; Li, Pei; Song, Baoan

    2015-09-15

    Novel glucopyranoside derivatives were synthesized and evaluated for their antiviral activities against tobacco mosaic virus (TMV). Bioassay results indicated that some of the target compounds exhibited good in vivo antiviral activities against TMV. Among the title compounds, f6 showed appreciable inactivation effect against TMV, with the 50% effective concentration value (EC50) of 52.9 ?g/mL, which was better than that of ribavirin (145.1 ?g/mL). In addition, interaction between f6 and TMV-CP was characterized by fluorescence spectroscopy, isothermal titration calorimetry (ITC), and microscale thermophoresis (MST). Results showed that f6 bound to TMV-CP with micromole affinity, and thermodynamic parameters suggested that this interaction was typically endothermic and spontaneous, with 1:1.53 ratio of TMV-CP to f6. Thus, the synthesized glucopyranoside derivatives containing 1,4-pentadien-3-one moiety could be promising antiviral agents. PMID:26243369

  14. 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.

  15. Derivation of genetic interaction networks from quantitative phenotype data

    PubMed Central

    Drees, Becky L; Thorsson, Vesteinn; Carter, Gregory W; Rives, Alexander W; Raymond, Marisa Z; Avila-Campillo, Iliana; Shannon, Paul; Galitski, Timothy

    2005-01-01

    We have generalized the derivation of genetic-interaction networks from quantitative phenotype data. Familiar and unfamiliar modes of genetic interaction were identified and defined. A network was derived from agar-invasion phenotypes of mutant yeast. Mutations showed specific modes of genetic interaction with specific biological processes. Mutations formed cliques of significant mutual information in their large-scale patterns of genetic interaction. These local and global interaction patterns reflect the effects of gene perturbations on biological processes and pathways. PMID:15833125

  16. 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.

  17. Predicting pharmacokinetic profiles using in silico derived parameters.

    PubMed

    Hosea, Natalie A; Jones, Hannah M

    2013-04-01

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

  18. 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.

  19. Counterintuitive interaction of anions with benzene derivatives

    NASA Astrophysics Data System (ADS)

    Quionero, David; Garau, Carolina; Frontera, Antonio; Ballester, Pau; Costa, Antonio; Dey, Pere M.

    2002-06-01

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

  20. 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.

  1. Faulting parameters derived from computer simulation of earthquakes

    NASA Technical Reports Server (NTRS)

    Cohen, S. C.

    1977-01-01

    Seismic source parameters, average displacement, rupture length, and strain energy release are investigated by computer simulation using a coupled massive block model of the sliding along an active fault. Average displacements and energy release vary considerably with the degree of heterogeneity in the friction and elastic parameters used in the model. Strain energy release is determined primarily by the product of dynamic friction, rupture length, and average displacement. Interrelationships among the faulting parameters are consistent with theoretical arguments and experimental data. The variation in the frequency of occurrence of simulation events with strain energy release is different from the variation in the frequency of naturally occurring events with seismic energy.

  2. 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.

  3. 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.

  4. 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...

  5. 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.

  6. Lidar conversion parameters derived from SAGE II extinction measurements

    NASA Technical Reports Server (NTRS)

    Thomason, L. W.; Osborn, M. T.

    1992-01-01

    SAGE II multiwavelength aerosol extinction measurements are used to estimate mass- and extinction-to-backscatter conversion parameters. The basis of the analysis is the principal component analysis of the SAGE II extinction kernels to estimate both total aerosol mass and aerosol backscatter at a variety of wavelengths. Comparisons of coincident SAGE II extinction profiles with 0.694-micron aerosol backscatter profiles demonstrate the validity of the method.

  7. Cloud optical parameters as derived from the multispectral cloud radiometer

    NASA Technical Reports Server (NTRS)

    Nakajima, Eruyuki; King, Michael D.

    1990-01-01

    Here, researchers analyze the data taken in the marine stratocumulus intensive field observation component of the First ISCCP Regional Experiment (FIRE), conducted off the California coast in July, 1987 using the Multispectral Cloud Radiometer (MCR). Researchers installed an efficient retrieval scheme for deriving the cloud optical thickness and droplet mode radius, and have described the behavior of the retrieval error. Generally the scheme can retrieve the optical thickness and mode radius adequately unless they are too small; the use of the forward scattering region is more sound than the use of the backscattering portion. Applying the method to real data, researchers derived the two-dimensional distribution of optical thickness and mode radius for a portion of one of the FIRE marine stratocumulus missions. In this case study, the droplet size showed a more uniform distribution than optical thickness with some correlation between large droplet size and small optical thickness. Although researchers can find microphysical reasons for these tendencies, they suspect that the remotely sensed droplet size may be overestimated. As a future problem, they will compare results with in situ data of the droplet size distribution. Also it will be very important to check several reasons why the droplet radius might be overestimated, e.g., soot contamination, effect of escaping photons from the lateral sides of broken clouds, and so on.

  8. 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.

  9. Do coinage metal anions interact with substituted benzene derivatives?

    PubMed

    Aliakbar Tehrani, Zahra; Jamshidi, Zahra; Farhangian, Hossein

    2013-11-01

    The nature of the anion-? interaction has been investigated by carrying out ab initio calculations of the complexes of coinage metal anions (Au(-), Ag(-), and Cu(-)) with different kinds of ?-systems. The binding energies indicate that gold anion has the highest and copper anion has the lowest affinity for interactions with ?-systems. Different aspects of the anion-? interaction in these systems have been investigated, including charge-transfer effects (using the Merz-Kollman method), "atoms-in-molecules" (AIM) topological parameters, and interaction energies (using energy decomposition analysis, EDA). Our results indicated that, for most M(-)? interactions, the electrostatic term provides the dominant contribution, whereas polarization, charge transfer, and dispersion effects contribute less than 25 % of the interaction. We believe that the present results should lead to a greater understanding of the basis for anion-? interactions of coinage metal anions. PMID:23989771

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

    PubMed

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

    2014-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  12. 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.

  13. Supramolecular Interactions of Terpyridine-Derived Cores of Metallomesogen Precursors

    PubMed Central

    Lee, Young Hoon; Harrowfield, Jack M.; Shin, Jong Won; Won, Mi Seon; Rukmini, Elisabeth; Hayami, Shinya; Min, Kil Sik; Kim, Yang

    2013-01-01

    Use of Hirshfeld surfaces calculated from crystal structure determinations on various transition metal ion complexes of three terpyridine ligands carrying trimethoxyphenyl substituents has enabled an assessment of the contribution made by the ligand components to the interactions determining the lattice structures, interactions expected also to be present in metallomesogens derived from similar ligands. The form of the link joining the trimethoxyphenyl substituent to the 4? position of 2,2?;6?,2?-terpyridine is of some importance. In the case of the Co(II) complexes of two of the ligands, their spin-crossover characteristics can be rationalised in terms of the different interactions seen in their lattices. PMID:24132156

  14. 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.

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

    PubMed

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

    2015-11-17

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

  16. 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.

  17. 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.

  18. 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

  19. 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-?-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

  20. Derivation of return stroke parameters from the electric and magnetic field derivatives

    SciTech Connect

    Cooray, V. )

    1989-01-01

    Recently, the transmission line model of the return stroke (Uman and McLain, 1970) has been used by several researchers to infer the characteristics of lightning return strokes. Equations are based on three assumptions: (a) the fields are pure radiation, (b) the maximum return stroke height at time t is much less than the distance to the point of observation, and (c) the ground is perfectly conducting. Any deviation from these assumptions will lead to an error in the inferred properties of the return stroke such as return stroke velocity and return stroke peak current derivative. In this paper the author calculates the electric and magnetic field derivatives from lightning return strokes at different distances over both perfectly conducting and finitely conducting ground, by using the transmission line model. The results will then be compared with those obtained from equations to investigate how far the electric and magnetic field peak derivatives deviate from those given by these equations in the presence of near field components and when the fields have propagated over finitely conducting earth.

  1. 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.

  2. Thermochemical and kinetic parameters for hydrogen bonded clusters, derived from avalanche condensation flux measurements

    NASA Astrophysics Data System (ADS)

    Bauer, S. H.; Zhang, Yi-Xue; Wilcox, C. F.

    2000-06-01

    The kinetic molecular model (KMM) was applied to recently reported extensive measurements of condensation flux levels developed under homogeneous conditions from supersaturated vapors of water and n-pentanol, in inert gas carriers. These data span wide ranges in temperatures and critical supersaturations (css). The calculated fluxes reproduced those observed (defined: number of droplets generated per cm3-s) within a factor 2, utilizing a narrow range of adjustable parameters. From the derived kinetic and thermochemical parameters one may derive estimates of size-dependent entropies for clusters. Thus, the derived entropy per mole of a 13 unit cluster of water molecules, at 233 K, is 233 eu.

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

    SciTech Connect

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

    1994-05-09

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

  4. Statistical comparisons between teleradiometer-derived and slide-derived visibility parameters

    SciTech Connect

    Johnson, C.E.; Malm, W.C.; Persha, G.; Molenar, J.V.; Hein, J.R.

    1985-12-01

    An automated scanning densitometer system developed to estimate visibility-related parameters from photographic slides was tested in comparison to similar teleradiometric measurements. Parameters such as target-sky contrast, visual range, atmospheric light extinction coefficient, and plume and layered contrast can be estimated using this system; however, only target-sky radiance ratios and standard visual ranges were compared. More than 1600 concurrent densitometer and teleradiometer data pairs from eight National Park Service air quality and visibility monitoring locations in the western US were analyzed using the techniques of correlation, linear regression, average bias and difference calculation, and cumulative frequency distribution generation. Correlation coefficients were good, especially with middle-range camera vistas around 50 km distant. Regression slopes approached unity with intercepts near zero. Average bias introduced into the determination of radiance ratios from slides ranged from near zero to 6%, depending on target distance. Standard visual range data distributions compared favorably at the low end with some minor differences at the high end.

  5. 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.

  6. Classification performance of the frequency-related parameters derived from uterine EMG signals.

    PubMed

    Moslem, B; Karlsson, B; Diab, M O; Khalil, M; Marque, C

    2011-01-01

    Frequency-related parameters derived from the uterine electromyogram (EMG) signals are widely used in many pregnancy monitoring and preterm delivery prediction studies. Although they are classical parameters, they are well suited for quantifying uterine EMG signals and have many advantages over amplitude-related parameters. The present work aims to compare various frequency-related parameters according to their classification performances (pregnancy vs. labor) using the receiver operating characteristic (ROC) curve analysis. The comparison between the parameters indicates that median frequency is the best frequency-related parameter that can be used for distinguishing between pregnancy and labor contractions. We conclude that median frequency can be the representative frequency-related parameter for classification problems of uterine EMG. PMID:22255062

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    The aeolian system sediment state is defined by three key components: (a) sediment supply, (b) sediment availability, and (c) the transport capacity of the wind (Kocurek and Lancaster, 1999). And the waves generated on the dune surface can produce a series of new smaller dunes, preventing sand seas from merging into a single giant dune (Elbelrhiti et al., 2005). Consequently, the development histories of sand seas should reflect the changing patterns of interactions between various geomorphological processes (supplying and transporting sediments) associated with local, regional and global environmental conditions. The aim of this paper is to investigate the distribution patterns of dunes and their triggering factors in the Badain Jaran Desert located in the western Inner Mongolia of China. Using satellite imageries, supported by ground controls, the forms of dunes in this ca. 50,000 square kilometer large sand sea are interpreted. The taller sand dunes, probably the highest on Earth, occur only in the southeastern portion of the region. Detailed geometrical survey shows that many of these dunes possess not only a steep lee but also a steep stoss side. The lee is due to the strong northwestern winds associated with Siberian-Mongolian high pressure while the stoss side is related to the southeastern winds controlled to a considerably degree by the pressure system in the Pacific. In addition to bringing moisture, the southeastern winds play a significant role in the shaping of the dunes, as indicated by the steep stoss side. Using geophysical methods, we mapped underground morphology of some megadunes, recognizing that bed rock morphologies have a certain influence on the height of dunes, but not in a linear relationship. Although the sediment availability decreases while the vegetation coverage increases during wetter epochs, the cementation surface formed during wetter periods appears to be advantageous to the increase of dune height while it acts as solid basis for the dunes from later generations. The final size and form of dunes in this desert appear to be decided indeed by interactions of multiple parameters including direction and strength of winds, bedrock landforms, as well as climatic fluctuations related to local, regional and global systems.

  9. 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.; Pschl, 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 ?m, which can be deconvoluted into a dilute intrinsic hygroscopicity parameter (?m,∞) 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 ?m-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 ?m 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 ?m,∞ 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.).

  10. 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

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

    PubMed

    Gagn, Olivier Charles; Hawthorne, Frank Christopher

    2015-10-01

    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? 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. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  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 ? =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. Reconstituting protein interaction networks using parameter-dependent domain-domain interactions

    PubMed Central

    2013-01-01

    Background We can describe protein-protein interactions (PPIs) as sets of distinct domain-domain interactions (DDIs) that mediate the physical interactions between proteins. Experimental data confirm that DDIs are more consistent than their corresponding PPIs, lending support to the notion that analyses of DDIs may improve our understanding of PPIs and lead to further insights into cellular function, disease, and evolution. However, currently available experimental DDI data cover only a small fraction of all existing PPIs and, in the absence of structural data, determining which particular DDI mediates any given PPI is a challenge. Results We present two contributions to the field of domain interaction analysis. First, we introduce a novel computational strategy to merge domain annotation data from multiple databases. We show that when we merged yeast domain annotations from six annotation databases we increased the average number of domains per protein from 1.05 to 2.44, bringing it closer to the estimated average value of 3. Second, we introduce a novel computational method, parameter-dependent DDI selection (PADDS), which, given a set of PPIs, extracts a small set of domain pairs that can reconstruct the original set of protein interactions, while attempting to minimize false positives. Based on a set of PPIs from multiple organisms, our method extracted 27% more experimentally detected DDIs than existing computational approaches. Conclusions We have provided a method to merge domain annotation data from multiple sources, ensuring large and consistent domain annotation for any given organism. Moreover, we provided a method to extract a small set of DDIs from the underlying set of PPIs and we showed that, in contrast to existing approaches, our method was not biased towards DDIs with low or high occurrence counts. Finally, we used these two methods to highlight the influence of the underlying annotation density on the characteristics of extracted DDIs. Although increased annotations greatly expanded the possible DDIs, the lack of knowledge of the true biological false positive interactions still prevents an unambiguous assignment of domain interactions responsible for all protein network interactions. Executable files and examples are given at: http://www.bhsai.org/downloads/padds/ PMID:23651452

  18. Cubic interaction parameters for t2g Wannier orbitals

    NASA Astrophysics Data System (ADS)

    Ribic, T.; Assmann, E.; Tth, A.; Held, K.

    2014-10-01

    Many-body calculations for multi-orbital systems at present typically employ Slater or Kanamori interactions which implicitly assume a full rotational invariance of the orbitals, whereas the real crystal has a lower symmetry. In cubic symmetry, the low-energy t2g orbitals have an on-site Kanamori interaction, albeit without the constraint U =U'+2J implied by spherical symmetry (U is the intra-orbital interaction, U' is the interorbital interaction, J is Hund's exchange). Using maximally localized Wannier functions we show that deviations from the standard, spherically symmetric interactions are indeed significant for 5d orbitals (25% for BaOsO3; 12% if screening is included) but are less important for 3d orbitals (6% for SrVO3; 1% if screened).

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

    PubMed

    Roth, Robert E

    2013-12-01

    Proposals to establish a 'science of interaction' have been forwarded from Information Visualization and Visual Analytics, as well as Cartography, Geovisualization, and GIScience. This paper reports on two studies to contribute to this call for an interaction science, with the goal of developing a functional taxonomy of interaction primitives for map-based visualization. A semi-structured interview study first was conducted with 21 expert interactive map users to understand the way in which map-based visualizations currently are employed. The interviews were transcribed and coded to identify statements representative of either the task the user wished to accomplish (i.e., objective primitives) or the interactive functionality included in the visualization to achieve this task (i.e., operator primitives). A card sorting study then was conducted with 15 expert interactive map designers to organize these example statements into logical structures based on their experience translating client requests into interaction designs. Example statements were supplemented with primitive definitions in the literature and were separated into two sorting exercises: objectives and operators. The objective sort suggested five objectives that increase in cognitive sophistication (identify, compare, rank, associate, & delineate), but exhibited a large amount of variation across participants due to consideration of broader user goals (procure, predict, & prescribe) and interaction operands (space-alone, attributes-in-space, & space-in-time; elementary & general). The operator sort suggested five enabling operators (import, export, save, edit, & annotate) and twelve work operators (reexpress, arrange, sequence, resymbolize, overlay, pan, zoom, reproject, search, filter, retrieve, & calculate). This taxonomy offers an empirically-derived and ecologically-valid structure to inform future research and design on interaction. PMID:24051802

  20. Deriving reliable fundamental parameters of pre-main-sequence-rich star clusters affected by differential reddening

    NASA Astrophysics Data System (ADS)

    Bonatto, C.; Bica, E.; Lima, E. F.

    2012-02-01

    We present an approach that improves the search for reliable astrophysical parameters (e.g. age, mass and distance) of differentially reddened, pre-main-sequence-rich star clusters. It involves simulating conditions related to the early-cluster phases, in particular the differential and foreground reddenings, and internal age spread. Given the loose constraints imposed by these factors, the derivation of parameters based only on photometry may be uncertain, especially for the poorly populated clusters. We consider a wide range of cluster (i) mass and (ii) age, and different values of (iii) distance modulus, (iv) differential and (v) foreground reddenings. Photometric errors and their relation with magnitude are also taken into account. We also investigate how the presence of unresolved binaries affect the derived parameters. For each set of (i)-(v) we build the corresponding model Hess diagram, and compute the root mean squared residual with respect to the observed Hess diagram. The parameters that produce the minimum residuals between model and observed Hess diagrams are searched by exploring the full parameter space of (i)-(v) by means of brute force, which may be time consuming but efficient. Control tests show that an adequate convergence is achieved allowing for solutions with residuals 10 per cent higher than the absolute minimum. Compared to a colour-magnitude diagram containing only single stars, the presence of 100 per cent of unresolved binaries has little effect on cluster age, foreground and differential reddenings; significant differences show up in the cluster mass and distance from the Sun. Our approach proves to be successful in minimizing the subjectiveness when deriving fundamental parameters of young star clusters.

  1. 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

  2. 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, ?n, of the Arrhenius equation. From the Arrhenius plot ln -?/? ? 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.

  3. An extension of Noether's theorem to transformations involving position-dependent parameters and their derivatives

    NASA Astrophysics Data System (ADS)

    Rund, Hanno

    1981-12-01

    Guided by the example of gauge transformations associated with classical Yang-Mills fields, a very general class of transformations is considered. The explicit representation of these transformations involves not only the independent and the dependent field variables, but also a set of position-dependent parameters together with their first derivatives. The stipulation that an action integral associated with the field variables be invariant under such transformations gives rise to a set of three conditions involving the Lagrangian and its derivatives, together with derivatives of the functions that define the transformations. These invariance identities constitute an extension of the classical theorem of Noether to general transformations of this kind. An application to the case of gauge fields demonstrates the existence of two distinct types of conservation laws for such fields.

  4. 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

  5. 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.

  6. 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

  7. Interaction of fluorescein derivatives with sulfonylurea binding in insulin-secreting cells.

    PubMed

    Schwanstecher, M; Bachmann, C; Lser, S; Panten, U

    1995-03-01

    Recently evidence was presented that fluorescein derivatives (e.g. phloxine B) inhibit glibenclamide binding by occupation of a nucleotide-binding site at the ATP-sensitive potassium channel (KATP channel). However, this conclusion was inconsistent with the results of previous studies testing the effects of nucleotides on glibenclamide binding. To elucidate the interaction mode of fluorescein derivatives with sulfonylurea binding, the effect of phloxine B on binding of [3H]glibenclamide to microsomes obtained from a pancreatic beta-cell line (HIT-T15) was examined. Phloxine B inhibited specific binding of glibenclamide half-maximally at 3.2 mumol/l. The slope parameter for the displacement curve was close to one, suggesting a competitive interaction between both drugs. In accordance with this assumption 4 mumol/l phloxine B did not show an effect on the number of high-affinity binding sites but increased the apparent dissociation constant for glibenclamide by 3.1-fold and 30 mumol/l phloxine B did not alter the rate of dissociation of [3H]glibenclamide. Moreover, MgATP (300 mumol/l) significantly reduced the apparent affinity for binding of phloxine B to the sulfonylurea receptor. This finding resembled the action of MgATP on binding of sulfonylureas to their receptor site. It is concluded that fluorescein derivatives inhibit glibenclamide binding due to competition for the same site at the sulfonylurea receptor. PMID:7746835

  8. 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

  9. 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.

  10. CONSTRAINING THE SYMMETRY PARAMETERS OF THE NUCLEAR INTERACTION

    SciTech Connect

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

    2013-07-01

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

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

    PubMed

    Morse, Peter K; Corwin, Eric I

    2016-01-20

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

  12. 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.

  13. 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.

  14. 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

  15. Use of a weather buoy to derive improved heat and mass balance parameters for Ruapehu Crater Lake

    NASA Astrophysics Data System (ADS)

    Hurst, Tony; Christenson, Bruce; Cole-Baker, Jeremy

    2012-08-01

    Heat and mass balance calculations are important for monitoring volcanoes with heated crater lakes, but for these lakes the critical process of evaporation can be substantially affected by the lake's influence on the air mass above it. Measurements in 2010 using a weather station on a buoy floating in Ruapehu Crater Lake enabled us to derive a relation between wind velocity above the lake and that measured at nearby weather stations, as well as providing direct evidence of the effect of the warm lake on the air above it. This supported the use of evaporation equations that allowed for the changing air conditions as incoming air became warmer and wetter from interaction with the lake, so decreasing the overall evaporation rate. Heat and mass balance calculations using these parameters and equations during the period 2003 to early 2007, as Crater Lake filled before it overflowed, confirm the previously observed high ratio of total heat flow to steam volume.

  16. 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):853858. PMID:26163465

  17. 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.

  18. Spatial Interdependency Between Kinematic Source Parameters Derived From Dynamic Rupture Simulations

    NASA Astrophysics Data System (ADS)

    Schmedes, J.; Archuleta, R. J.; Lavallee, D.

    2008-12-01

    For a kinematic model to accurately predict ground motion, it is necessary to know not only the spatial distribution of the source parameters but also the spatial interdependency among the parameters. Because there are limitations to the kinematic parameters derived from inversions of seismic data, we determine the spatial interdependency between source parameters from physically based dynamic ruptures. We have computed and analyzed hundreds of dynamic rupture models to get a quantitative understanding of the spatial interdependency and amplitude distributions of parameters describing the earthquake source, such as stress drop, rupture velocity, and rise time. We use a slip weakening friction law combined with different approaches to create random heterogeneous initial stress and strength distributions on the fault as the basic ingredients for our dynamic ruptures. While there is much to be learned by looking at differences among all the models, we focus on features that are common among all models, that is, features that show the least dependence on the choice of the initial model. Using all dynamic ruptures, we are able to construct probability density functions (PDF's) for the amplitude distributions of the source parameters as well as for the spatial correlation between the source parameters. In addition we compute joint probability density functions to determine if there is a linear relationship between different source parameters, and cross spectral densities to determine if there is correlation at all scales. We find: (1) slip amplitude does not show systematic correlations with rupture velocity, and it is positively correlated with rise time; (2) peak slip rate shows strong correlation with rupture velocity and rise time; (3) the PDF of rupture velocity has a well defined maximum between 80%-90% of the shear wave velocity. The value of this maximum probability density increases with distance from the hypocenter, while the width of the PDF decreases, i.e., the rupture velocity tends toward a more constant value farther from the hypocenter. A similar dependence is found for the PDF of the rise times, which has a width that decreases with increasing distance from the nucleation zone; moreover, the mean value of the rise time shifts to a smaller value.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  20. 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 ...

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. Banding of NMR-derived methyl order parameters: implications for protein dynamics.

    PubMed

    Sharp, Kim A; Kasinath, Vignesh; Wand, A Joshua

    2014-09-01

    Our understanding of protein folding, stability, and function has begun to more explicitly incorporate dynamical aspects. Nuclear magnetic resonance has emerged as a powerful experimental method for obtaining comprehensive site-resolved insight into protein motion. It has been observed that methyl-group motion tends to cluster into three "classes" when expressed in terms of the popular Lipari-Szabo model-free squared generalized order parameter. Here the origins of the three classes or bands in the distribution of order parameters are examined. As a first step, a Bayesian based approach, which makes no a priori assumption about the existence or number of bands, is developed to detect the banding of Oaxis2 values derived either from NMR experiments or molecular dynamics simulations. The analysis is applied to seven proteins with extensive molecular dynamics simulations of these proteins in explicit water to examine the relationship between O2 and fine details of the motion of methyl bearing side chains. All of the proteins studied display banding, with some subtle differences. We propose a very simple yet plausible physical mechanism for banding. Finally, our Bayesian method is used to analyze the measured distributions of methyl group motions in the catabolite activating protein and several of its mutants in various liganded states and discuss the functional implications of the observed banding to protein dynamics and function. PMID:24677353

  11. Relations between Optically Derived Aerosol Parameters, Humidity, and Air-Quality Data in an Urban Atmosphere.

    NASA Astrophysics Data System (ADS)

    O'Neill, N. T.; Royer, A.; Cot, P.; McArthur, L. J. B.

    1993-09-01

    This paper deals with diurnal and mensual correlations between ground-based atmospheric observations of columnar and surface optical parameters, standard surface humidity parameters, and surface air-quality data. The implications of a significant portion of small, Rayleigh-free optical depths being attributable to continuum water vapor absorption are analyzed in terms of the impact on the computation of aerosol optical depth and ngstrm spectral coefficients in relatively clear atmospheres. Multiwavelength correlation analysis between aerosol optical depth and precipitable water indicators (surface vapor pressure or vertically integrated precpitable water) yielded a systematic, inverse-wavelength type of dependency in the extracted slopes (apparent attenuation coefficients) that was suggestive of a simple correlation between precipitable water and the accumulation-mode number density of the aerosols. On a diurnal basis, increasing trends in aerosol optical depth were negatively correlated with surface relative humidity and thus resulted either from variations in the nature or abundance of dry aerosol or possibly from convection-induced increases in relative humidity at higher altitudes in the aerosol scattering layer. The diurnal trend in aerosol optical depth plus the limited correlation between surface volume extinction coefficients derived from visibility measurements and relative humidity indicated that the aerosol optical scale height, on a diurnal basis, varied in an inverse fashion with surface relative humidity. Correlations between diurnally averaged aerosol optical depths and 24-h averaged surface sulfate measurements indicated the potential of satellite-based pollution monitoring using passive remote sensing data.

  12. 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.

  13. Ellipsometric Investigation of Optical Parameters and Characterization of Spray Pyrolysis-Derived ZnO Films

    NASA Astrophysics Data System (ADS)

    Geny?lmaz, Olcay; Atay, Ferhunde; Akyz, ?dris

    2015-09-01

    The pH value of solution is an important parameter in thin film production. In this work, ZnO films were successfully produced for various pH values (6.9 ? pH ? 3.2) by spray pyrolysis. The effects of the pH value on the optical parameters such as thickness, refractive index and extinction coefficient, structural, surface, and electrical properties were investigated by spectroscopic ellipsometry and other characterization technique. Thickness, refractive index, and extinction coefficient values were defined by spectroscopic ellipsometry technique using Cauchy-Urbach model. The thickness values of ZnO films were found to be in the range of 345 to 376 nm. The crystalline structure, orientation, and lattice parameters of the films were determined using XRD patterns. X-ray diffraction revealed that the crystallization level increased prominently with decreasing of the pH value and the best crystallization was found for pH 3.5 value. The average optical transmittance of the films was improved with changing of the pH values. Atomic force microscopic image was shown that the surface morphology improved and roughness value decreased with decrease of pH values. Electrical resistivity values of ZnO films decreased as the pH value decreased and the lowest resistivity value was found 1.1 10-3 ? cm for pH 3.5 deposited films. As a result, the low pH values have a strong effect on the mentioned properties of spray pyrolysis-derived ZnO films.

  14. 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.

  15. 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.

  16. 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 0C and the -10C 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 (0C, 10C) 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 0C level and showed just a slight oscillation. In the case of the thunderstorms' volume the height was even located above the -10C 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.

  17. 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.

  18. 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

  19. 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.

  20. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  2. Deriving hydrogeological parameters through time series analysis of groundwater head fluctuations around well fields

    NASA Astrophysics Data System (ADS)

    Obergfell, Christophe; Bakker, Mark; Zaadnoordijk, Willem Jan; Maas, Kees

    2013-08-01

    A method is presented by which time series analysis is applied to support groundwater system conceptualization and provide calibration targets for a steady groundwater model. The method is demonstrated for heads measured in the vicinity of a drinking-water well field. The estimated steady response to pumping was used to classify the monitoring wells as semi-confined or phreatic. Based on this conceptualization, the aquifer system was represented by two layers separated by a leaky bed, which represents the resistance to vertical flow of the layers. The model could be calibrated satisfactorily using the drawdowns estimated by time series analysis. This approach was more successful than deriving the aquifer parameters directly from the analytical well function of Hantush, which was successful for a limited number of monitoring wells only and required the a priori choice of the elevation of a confining layer which was not clear from bore logs. This study shows that time series analysis can lead to qualitative and quantitative insights regarding the local hydrogeology, providing complementary information to available bore logs to design a conceptual groundwater model. Time series analysis provides a cost-effective alternative to pumping tests when measured head fluctuations influenced by pumping wells are available.

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

    SciTech Connect

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

    2014-09-10

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

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

    SciTech Connect

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

    1997-11-01

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

  5. 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 .

  6. 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

  7. Crystal lattice properties fully determine short-range interaction parameters for alkali and halide ions

    NASA Astrophysics Data System (ADS)

    Mao, Albert H.; Pappu, Rohit V.

    2012-08-01

    Accurate models of alkali and halide ions in aqueous solution are necessary for computer simulations of a broad variety of systems. Previous efforts to develop ion force fields have generally focused on reproducing experimental measurements of aqueous solution properties such as hydration free energies and ion-water distribution functions. This dependency limits transferability of the resulting parameters because of the variety and known limitations of water models. We present a solvent-independent approach to calibrating ion parameters based exclusively on crystal lattice properties. Our procedure relies on minimization of lattice sums to calculate lattice energies and interionic distances instead of equilibrium ensemble simulations of dense fluids. The gain in computational efficiency enables simultaneous optimization of all parameters for Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I- subject to constraints that enforce consistency with periodic table trends. We demonstrate the method by presenting lattice-derived parameters for the primitive model and the Lennard-Jones model with Lorentz-Berthelot mixing rules. The resulting parameters successfully reproduce the lattice properties used to derive them and are free from the influence of any water model. To assess the transferability of the Lennard-Jones parameters to aqueous systems, we used them to estimate hydration free energies and found that the results were in quantitative agreement with experimentally measured values. These lattice-derived parameters are applicable in simulations where coupling of ion parameters to a particular solvent model is undesirable. The simplicity and low computational demands of the calibration procedure make it suitable for parametrization of crystallizable ions in a variety of force fields.

  8. 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.

  9. 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.

  10. 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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    PubMed

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

    2014-11-20

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

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

    PubMed

    Wang, Shu; Robertson, Megan L

    2015-06-10

    Vegetable oils and their fatty acids are promising sources for the derivation of polymers. Long-chain poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) are readily derived from fatty acids through conversion of the carboxylic acid end-group to an acrylate or methacrylate group. The resulting polymers contain long alkyl side-chains with around 10-22 carbon atoms. Regardless of the monomer source, the presence of alkyl side-chains in poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) provides a convenient mechanism for tuning their physical properties. The development of structured multicomponent materials, including block copolymers and blends, containing poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) requires knowledge of the thermodynamic interactions governing their self-assembly, typically described by the Flory-Huggins interaction parameter ?. 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

  15. 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.

  16. 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.

  17. 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...

  18. 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.

  19. Inter- and intramolecular CFc?o interactions on aliphatic and cyclohexane carbonyl derivatives.

    PubMed

    Cormanich, Rodrigo A; Rittner, Roberto; O'Hagan, David; Bhl, Michael

    2016-01-01

    Weak inter- and intra- molecular C(?+) F(?-) C(?+) ?O(?-) interactions were theoretically evaluated in 4 different sets of compounds at different theoretical levels. Intermolecular CH3 FC?O interactions were stabilizing by about 1 kcal mol(-1) for various carbonyl containing functional groups. Intramolecular CFC?O interactions were also detected in aliphatic and fluorinated cyclohexane carbonyl derivatives. However, the stabilization provided by intramolecular CFC?O interactions was not enough to govern the conformational preferences of compounds 2-4. 2015 Wiley Periodicals, Inc. PMID:25903504

  20. 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.

  1. 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.

  2. Derivation of the Time Dependent Gross-Pitaevskii Equation Without Positivity Condition on the Interaction

    NASA Astrophysics Data System (ADS)

    Pickl, Peter

    2010-07-01

    Using a new method (Pickl in A simple derivation of mean field limits for quantum systems, 2010) it is possible to derive mean field equations from the microscopic N body Schrdinger evolution of interacting particles without using BBGKY hierarchies. In this paper we wish to analyze scalings which lead to the Gross-Pitaevskii equation which is usually derived assuming positivity of the interaction (Erds et al. in Commun. Pure Appl. Math. 59(12):1659-1741, 2006; Invent. Math. 167:515-614, 2007). The new method for dealing with mean field limits presented in Pickl (2010) allows us to relax this condition. The price we have to pay for this relaxation is however that we have to restrict the scaling behavior of the interaction and that we have to assume fast convergence of the reduced one particle marginal density matrix of the initial wave function ?^{?0} to a pure state | ? 0>< ? 0|.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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 Berrys 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. Berrys connection is given by a WuYang-like magnetic monopole in SU(2) YangMills.

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

    PubMed Central

    2012-01-01

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

  9. 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.

  10. Automated Optimization of WaterWater 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 NelderMead 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

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    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.

  13. 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.

  14. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  16. 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

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

    PubMed

    Lehnert, Teresa; Timme, Sandra; Pollmcher, Johannes; Hnniger, 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

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

    PubMed Central

    Lehnert, Teresa; Timme, Sandra; Pollmcher, Johannes; Hnniger, 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

  19. 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.

  20. 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

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

    NASA Astrophysics Data System (ADS)

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

    2004-04-01

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

  2. 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 (?E) 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 ?E 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 ?E values of the ?- and ?-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

  3. 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

  4. New Model Parameters for the Production of Cosmic-Ray-produced Nuclides Derived from Measurements in Knyahinya

    NASA Astrophysics Data System (ADS)

    Graf, Th.; Nishiizumi, K.; Finkel, R. C.; Caffee, M. W.; Southon, J.; Toe, S.; Lavielle, B.; Gilabert, E.; Simonoff, G. N.

    1993-07-01

    A model for the production of cosmogenic nuclides in chondrites based on a production rate equation with two free parameters (A(sub)i, B(sub)i) for each nuclide i has been presented earlier [1]. The model parameters were determined by fitting measured depth profiles in the large Knyahinya chondrite [2]. New measurements of ^26Al, ^10Be, and ^36Cl in metal separates and Kr in bulk samples of Knyahinya have been carried out [3,4]. Here, we present model calculations for these newly measured nuclides. The A(sub)i and B(sub)i parameters for the production of ^10Be, ^36Cl from metal and ^78,81,83Kr in bulk samples were fitted to the measured depth profiles in Knyahinya and are given in Table 1. The model predictions for ^36Cl are in good agreement with the nearly constant activities observed for St. Severin [5], if corrections for the high Ni content in the metal of this meteorite are applied. However, ^78,83Kr profiles measured in St. Severin [6] show larger variations with shielding depth than predicted by the model. This may partly be due to the complex preatmospheric shape of St. Severin and to uncertainties arising from corrections for the low Rb content of this meteorite. The model predicts that any two production rate ratios are correlated in a way independent of the size and shape of a particular meteoroid. The calculated correlation line in a ^81Kr/^83Kr vs. ^22Ne/^21Ne diagram agrees well (+-3%) with the line obtained from data of many different chondrites [7]. On the other hand, the calculated correlation of ^78Kr/^83Kr vs. ^22Ne/^21Ne yields ^78Kr/^83Kr ratios that are 5-10% lower compared to those observed in samples from near surface locations in small meteorites (^22Ne/^21Ne>1.15) [7]. A(sub)i and B(sub)i parameters for the production of ^36Ar in metal (Table 1) can be derived from those of ^36Cl because >80% of ^36Ar in metal is produced indirectly via decay of ^36Cl and the ratio of the cross-sections for the production of ^36Cl and ^36Ar from Fe is quite constant. Parameters for ^38Ar in metal are obtained from those of ^36Ar by using the known shielding dependence of the ^36Ar/^38Ar ratios. A comparison of the calculated production rates of ^38Ar in bulk samples and metal separates indicates that the production rate ratio P(sub)38(Ca,K)/P(sub)38(Fe,Ni) increases by ~40% with increasing shielding (^22Ne/^21Ne ratios of 1.2 and 1.06, respectively). ^10Be activities in metal show a small decrease with increasing shielding depth except for one unusually low value in a near surface sample. The resulting value for B(sub)10 is 0.77. Model calculations based on ^10Be measurements in the Grant iron meteorite [8] yielded B(sub)10=0, indicating that ^10Be is produced solely by high energy particles. Therefore, the Grant model should be applicable to the Knyahinya data if the interaction mean free path for high energy particles is adjusted properly. The activities predicted in this way show a much larger decrease with increasing shielding (~50%) than observed. A possible solution to the problem may be that the preatmospheric radius of Grant was larger than the 40 cm derived in [9]. References: [1] Graf Th. et al. (1990) GCA, 54, 2521-2534. [2] Graf et al. (1990) GCA, 54, 2511-2520. [3] Reedy et al. (1993) LPSC XXIV, 1195-1196. [4] Toe et al. (1993) Meteoritics, this issue. [5] Nishiizumi et al. (1989) LPSC XIX, 305-312. [6] Lavielle B. and Marti K. (1988) LPSC XVIII, 565-572. [7] Eugster O. (1988) GCA, 52, 1649-1662. [8] Graf et al. (1987) Nucl. Instr. and Methods, B29, 262-265. [9] Signer P. and Nier A. O. (1960) JGR, 65, 2947-2964. Table 1, which appears here in the hard copy, shows model parameters.

  5. 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

  6. 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...

  7. 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

  8. 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.

  9. 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

  10. Astrocyte-Derived Tissue Transglutaminase Interacts with Fibronectin: A Role in Astrocyte Adhesion and Migration?

    PubMed Central

    van Strien, Miriam E.; Brev, John J. P.; Fratantoni, Silvina; Schreurs, Marco W. J.; Bol, John G. J. M.; Jongenelen, Cornelis A. M.; Drukarch, Benjamin; van Dam, Anne-Marie

    2011-01-01

    An important neuropathological feature of neuroinflammatory processes that occur during e.g. Multiple Sclerosis (MS) is the formation of an astroglial scar. Astroglial scar formation is facilitated by the interaction between astrocytes and extracellular matrix proteins (ECM) such as fibronectin. Since there is evidence indicating that glial scars strongly inhibit both axon growth and (re)myelination in brain lesions, it is important to understand the factors that contribute to the interaction between astrocytes and ECM proteins. Tissue Transglutaminase (TG2) is a multifunctional enzyme with an ubiquitous tissue distribution, being clearly present within the brain. It has been shown that inflammatory cytokines can enhance TG2 activity. In addition, TG2 can mediate cell adhesion and migration and it binds fibronectin with high affinity. We therefore hypothesized that TG2 is involved in astrocyte-fibronectin interactions. Our studies using primary rat astrocytes show that intracellular and cell surface expression and activity of TG2 is increased after treatment with pro-inflammatory cytokines. Astrocyte-derived TG2 interacts with fibronectin and is involved in astrocyte adhesion onto and migration across fibronectin. TG2 is involved in stimulating focal adhesion formation which is necessary for the interaction of astrocytes with ECM proteins. We conclude that astrocyte-derived TG2 contributes to the interaction between astrocytes and fibronectin. It might thereby regulate ECM remodeling and possibly glial scarring. PMID:21949843

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

    USGS Publications Warehouse

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

    2008-01-01

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

  12. 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.

  13. 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.

  14. Comparison of floodplain surface roughness parameters derived from land cover data and field measurements

    NASA Astrophysics Data System (ADS)

    Medeiros, Stephen C.; Hagen, Scott C.; Weishampel, John F.

    2012-07-01

    SummaryParameterizing surface roughness is a key element in the application of tidal and storm surge inundation models. In this context, surface roughness refers to the ability of the terrain to act as a momentum sink to the overland water flow and also the prevailing winds that help drive this flow. These effects are typically parameterized using estimates of Manning's n, surface canopy coverage and effective aerodynamic roughness length which vary spatially across the modeling domain as a function of the physical landscape. The current methodology for coastal inundation in the United States assigns these parameters based on published land use/land cover data such as the National Land Cover Dataset. This paper compares those assigned values to values computed based on field measurements at 24 sites in Florida that are representative of land use/land cover classes affected by storm surge. It is shown that while the land use/land cover method is capable of automatically parameterizing surface roughness over a large model domain, parameter prediction errors due to variability within land cover types, misclassification, and parameter value selection for specific land cover classes at the local level are significant which could result in inaccurate estimates of inundation extent and duration.

  15. 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, Franois

    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.

  16. 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.

  17. [Study on the interaction between DNR-D3 (daunorubicin derivative)and ctDNA by spectroscopic methods].

    PubMed

    L, Juan; Wang, Gong-Ke; Zhang, Gui-Sheng; Liu, Qing-Feng; Lu, Yan

    2010-05-01

    The interaction of DNR-D3 (daunorubicin derivative) synthesized in our laboratory with ctDNA was investigated by UV spectrum and fluorescence spectrum under physiological conditions (pH 7.4) for the first time. The red shifts and hypochromicities were observed from the absorption titration experiments. These results suggest that DNR-D3 was intercalated into the DNA base pairs. Through the fluorescence quenching data measured at different temperatures (20 degrees C, 30 degrees C and 37 degrees C), it is known that the quenching mechanism of fluorescence of DNR-D3 by ctDNA is a static quenching type. On the other hand, the binding constant, the number of binding sites and thermodynamic parameters were also obtained. These data also indicate that the binding mode of the interaction between DNR-D3 and ctDNA is intercalation. Additionally, the types of interaction force are mainly hydrogen bonding and electrostatic interaction, and the binding is exothermic enthalpy-entropy cooperative driven process. When the degree of fluorescence quenching of DNR-D3 is 50%, the ratio of the molar concentration of DNR-D3 to ctDNA is 7/25, which indicates that the DNR-D3 anthracycline was intercalated into the DNA base pairs and that DNR-D3 showed a strong anti-cancer activity. DNR-D3 is expected to become one of the drug candidates from our investigations. PMID:20672627

  18. 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 ? of the Flory-Huggins interaction parameter ?wp(?) describing the free energy of mixing of polymers in water is obtained by exploiting the connection of ?wp(?) 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), ?wp(?) depends strongly on ?, 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

  19. Using Isothermal Titration Calorimetry to Determine Thermodynamic Parameters of ProteinGlycosaminoglycan Interactions

    PubMed Central

    Dutta, Amit K.; Rsgen, Jrg; 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 proteinglycosaminoglycan (GAG) complexes. Isothermal titration calorimetry (ITC) is the only technique that can provide various thermodynamic parametersenthalpy, entropy, free energy (binding constant), and stoichiometryfrom 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 proteinGAG interactions. PMID:25325962

  20. 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.

  1. 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.

  2. 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.

  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. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

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

    NASA Astrophysics Data System (ADS)

    Bulko, Roman; Drusa, Marin; Vl?ek, Jozef; Me?r, 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.

  13. 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.

  14. Current noise parameters derived from voltage noise and impedance in embryonic heart cell aggregates.

    PubMed Central

    Clay, J R; DeFelice, L J; DeHaan, R L

    1979-01-01

    We have recorded membrane impedance and voltage noise in the pacemaker range of potentials (-70 to -59 mV) from spheroidal aggregates of 7-d embryonic chick ventricle cells made quiescent by exposure to tetrodotoxin in medium containing 4.5 mM K+. The input capacitance is proportional to aggregate volume and therefore to total membrane area. The specific membrane capacitance is 1.24 microF/cm2. The input resistance at constant potential is inversely proportional to aggregate volume and therefore to total membrane area. The specific membrane resistance in 18 k omega . cm2 at -70 mV and increases to 81 k omega . cm2 at -59 mV. The RC time constant is 22 ms at -70 mV and increases to 146 ms at -59 mV. The aggregate transmembrane small-signal impedance can be represented by a parallel RC circuit itself in parallel with an inductive branch consisting of a resistor (rL) and an inductor (L) in series. The time constant of the inductive branch (L/rL) is 340 ms, and is only weakly dependent on potential. Correlation functions of aggregate voltage noise and the impedance data were modeled by a population of channels with simple open-close kinetics. The time constant of a channel (tau s) derived from the noise analysis is 300 ms. The low frequency limit of the pacemaker current noise (SI[0]), derived from the voltage noise and impedance, increases from 10(-20) A2/Hz . cm2 at -67 mV to 10(-19) A2/Hz . cm2 at -61 mV. PMID:262547

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  16. 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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    SciTech Connect

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

    1992-12-01

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Moeser, D.; Sthli, 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  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-HO 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. 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.

  10. 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 1.0031.044). 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

  11. 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

  12. Spectroscopic investigations of the binding interaction of a new indanedione derivative with human and bovine serum albumins.

    PubMed

    Stan, Dana; Matei, Iulia; Mihailescu, Carmen; Savin, Mihaela; Hillebrand, Mihaela; Baciu, Ion; Matache, Mihaela

    2009-01-01

    Binding of a newly synthesized indanedione derivative, 2-(2-hydroxy-3-ethoxybenzylidene)-1,3-indanedione (HEBID), to human and bovine serum albumins (HSA and BSA), under simulated physiological conditions was monitored by fluorescence spectroscopy. The binding parameters (binding constants and number of binding sites) and quenching constants were determined according to literature models. The quenching mechanism was assigned to a Frster non-radiative energy transfer due to the HEBID-SA complex formation. A slightly increased affinity of HEBID for HSA was found, while the number of binding sites is approximately one for both albumins. The molecular distance between donor (albumin) and acceptor (HEBID) and the energy transfer efficiency were estimated, in the view of Frster's theory. The effect of HEBID on the protein conformation was investigated using circular dichroism and synchronous fluorescence spectroscopies. The results revealed partial unfolding in the albumins upon interaction, as well as changes in the local polarity around the tryptophan residues. PMID:19396020

  13. 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.

  14. 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.

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

    SciTech Connect

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

    2011-11-01

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

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

    PubMed

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

    2012-03-01

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

  17. 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.

    2016-01-01

    For a set of equation of state (EoS) models involving interacting strange quark matter, characterized by an effective bag constant (Beff) and a perturbative QCD 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 (?) at least up to ?3.0 M?; and ?1250 Hz respectively, and hence are fully consistent with measured MG and ? 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 ?, 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. Derivation of Spatial Parameters to Estimate Mass Delivery of Pesticides to Ground Water in Morgan Creek, Maryland

    NASA Astrophysics Data System (ADS)

    Wieczorek, M. E.; Webb, R. M.

    2006-05-01

    Water and solutes in the unsaturated zone are being intensively monitored at multiple sites in Morgan Creek, Maryland as part of the U.S. Geological Survey?s National Water- Quality Assessment (NAWQA) program. The observations are being used to calibrate simple and complex one-dimensional models that simulate the movement of water and the transformation pesticides in the unsaturated zone beneath the monitored sites. However, the monitored sites are limited in their representation of pesticide fluxes through the larger watershed encompassing the sites. This paper describes how ensembles of spatially distributed model parameters were derived to predict mass delivery of pesticides to the ground water in the larger watershed of Morgan Creek. Model parameters describing pesticide solubility, dispersion, sorbtivity, and transformation rates were calibrated to match concentrations of pesticides and metabolites observed in lysimeter samples installed at the intensive monitoring sites. The parameters describing the pesticide properties were then held fixed in a suite of models built to represent the variety of land use, soils, and unsaturated-zone thicknesses found in the Morgan Creek watershed. Land-use data were compiled from the Geographic Information Retrieval Analysis System (GIRAS), the National Land Cover Dataset (NLCD), and field surveys. Soil-erodibility and bulk-density information was obtained from the State Survey Geographic (STATSGO) database, whereas descriptions of soil texture, organic material, permeability, and available water-capacity values were obtained from the more detailed Soil Survey Geographic (SSURGO) database. Unsaturated-thickness information was created from the difference between a 30-meter resolution grid of head values, created using the results of a steady-state modular three-dimensional ground-water flow model (MODFLOW), and a 3-meter resolution digital elevation model (DEM, resampled to 30-meter), derived from Light Detection and Ranging (LIDAR). A point coverage of 100-meter spacing was overlaid onto the resulting maps of land use, soils, and unsaturated-zone thickness to identify the characteristics of the watershed surrounding the intensive monitoring sites. The approximately 3,300 sampled points were then subjected to a cluster analysis to identify regions with similar characteristics and to estimate the statistical distribution of specific model parameters within each region. Where nominal values were encountered, a noise model was added to provide a range in expected values. The mean and variance for each parameter in a cluster were then used to define the parameter space for input to models simulating the unsaturated-zone processes within each cluster. Finally, model predictions and confidence intervals were weighted by the area of each cluster to arrive at estimates of fluxes of water and sediment in the larger watershed.

  20. 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.

  1. 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

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

    PubMed

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

    2014-06-01

    In this work, we report a computational study of the interactions between metal cations and imidazole derivatives in the gas phase. We first performed a systematic assessment of various density functionals and basis sets for predicting the binding energies between metal cations and the imidazoles. We find that the M11L functional in combination with the 6-311++G(d,p) basis set provides the best compromise between accuracy and computational cost with our metalimidazole complexes. We then evaluated the binding of a series of metal cations, including Li(+), Na(+), K(+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Ba(2+), Hg(2+), and Pb(2+), with several substituted imidazole derivatives. We find that electron-donating groups increase the metal-binding energy, whereas electron-withdrawing groups decrease the metal-binding energy. Furthermore, the binding energy trends can be rationalized by the hardness of the metal cations and imidazole derivatives, providing a quick way to estimate the metalimidazole binding strength. This insight can enable efficient screening protocols for identifying effective imidazole-based solvents and membranes for metal adsorption and provide a framework for understanding metalimidazole interactions in biological systems. PMID:24824821

  3. 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

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

    PubMed

    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; Ma, Xiao-Chi; Fang, Zhong-Ze

    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 (Ki) 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 (Ki) 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. PMID:24631340

  5. 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

  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. 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

  8. 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.

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

    PubMed

    Langer, Andreas; Schrml, 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

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

    PubMed Central

    Langer, Andreas; Schrml, 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

  11. 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

  12. Studies on the interaction mechanism of aminopyrene derivatives with human tumor-related DNA.

    PubMed

    Li, Li; Lu, Jia; Zhou, Wenshu; Li, Huihui; Yang, Xiaodi

    2013-06-01

    Polycyclic aromatic hydrocarbons derivatives (PAHs) have been confirmed to be carcinogenic, teratogenic and mutagenic, and have the potential to cause human malignant diseases. In this work, interactions of two selected amino-PAHs (aminopyrene derivatives) and human tumor-related DNA were evaluated using spectroscopic and polyacrylamide gel electrophoresis (PAGE) methods. Spectroscopic results demonstrated that there were remarkable interactions between PAHs and the targeted DNA with the order of the binding ability as 1-AP>1-PBA. The binding constants of 1-AP with the targeted DNA were at the level of about 10(6) L/mol, while that of 1-PBA only to about 10(3) L/mol. 1-AP with a short side-chain acted mainly as an intercalator, and its interactions with DNA were strengthened with electrostatic forces. As for 1-PBA with a flexible long side-chain, the intercalation mode was dominated with an auxiliary role of Van der Wals forces and hydrogen bonds. Besides, the binding abilities of amino-PAHs to p53 DNA seemed stronger than that for C-myc DNA. PAGE results showed that the binding of amino-PAHs could further change the conformation of DNA sequences from the duplex to the antiparallel G-quadruplex. PMID:23608671

  13. 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

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

    PubMed Central

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

    2014-01-01

    The development of novel antimicrobial agents is urgently required to curb the widespread emergence of multidrug-resistant bacteria like colistin-resistant Pseudomonas aeruginosa. We previously synthesized a series of amphiphilic neamine derivatives active against bacterial membranes, among which 3?,6-di-O-[(2?-naphthyl)propyl]neamine (3?,6-di2NP), 3?,6-di-O-[(2?-naphthyl)butyl]neamine (3?,6-di2NB), and 3?,6-di-O-nonylneamine (3?,6-diNn) showed high levels of activity and low levels of cytotoxicity (L. Zimmermann et al., J. Med. Chem. 56:76917705, 2013). We have now further characterized the activity of these derivatives against colistin-resistant P. aeruginosa and studied their mode of action; specifically, we characterized their ability to interact with lipopolysaccharide (LPS) and to alter the bacterial outer membrane (OM). The three amphiphilic neamine derivatives were active against clinical colistin-resistant strains (MICs, about 2 to 8 ?g/ml), The most active one (3?,6-diNn) was bactericidal at its MIC and inhibited biofilm formation at 2-fold its MIC. They cooperatively bound to LPSs, increasing the outer membrane permeability. Grafting long and linear alkyl chains (nonyl) optimized binding to LPS and outer membrane permeabilization. The effects of amphiphilic neamine derivatives on LPS micelles suggest changes in the cross-bridging of lipopolysaccharides and disordering in the hydrophobic core of the micelles. The molecular shape of the 3?,6-dialkyl neamine derivatives induced by the nature of the grafted hydrophobic moieties (naphthylalkyl instead of alkyl) and the flexibility of the hydrophobic moiety are critical for their fluidifying effect and their ability to displace cations bridging LPS. Results from this work could be exploited for the development of new amphiphilic neamine derivatives active against colistin-resistant P. aeruginosa. PMID:24867965

  15. 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.

  16. 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

  17. Solubility and interaction parameters as references for solution properties. I. Exceptional mixing and excess functions.

    PubMed

    Rosenholm, Jarl B

    2009-02-28

    In order to focus on salient interactions it is customary to design a parameter network representing the reference (ideal) molecular behavior. Such reference properties are subtracted from the experimental data and the difference is analyzed. Each network is based on generally agreed thermodynamic dependent and independent variables defining unambiguously the state of the system. Unfortunately, more correction terms have been introduced making the relationship with traditional thermodynamic networks dependent on each system investigated. A critical comparison is made on the conceptual constraints introduced when developing the two most utilized reference thermodynamic networks. The first is represented by the standard mixing and excess functions of Gibbs free energy. The second represents tailored models involving van der Waals liquids and polymer solutions. Although the mixing and excess functions are formally same, their definition varies dramatically. Unfortunately this influences the analysis of divergence from the reference function, resulting in serious consequences as shown by the entropy and enthalpy obtained from temperature dependency. Moreover, entirely new functions relating to multiple solubility parameters in excess of standard van der Waals behavior are developed since reference data for these models are easily accessible. PMID:19007920

  18. 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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  1. 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

  2. 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...

  3. Evidence for a strong sulfur-aromatic interaction derived from crystallographic data.

    PubMed

    Zauhar, R J; Colbert, C L; Morgan, R S; Welsh, W J

    2000-03-01

    We have uncovered new evidence for a significant interaction between divalent sulfur atoms and aromatic rings. Our study involves a statistical analysis of interatomic distances and other geometric descriptors derived from entries in the Cambridge Crystallographic Database (F. H. Allen and O. Kennard, Chem. Design Auto. News, 1993, Vol. 8, pp. 1 and 31-37). A set of descriptors was defined sufficient in number and type so as to elucidate completely the preferred geometry of interaction between six-membered aromatic carbon rings and divalent sulfurs for all crystal structures of nonmetal-bearing organic compounds present in the database. In order to test statistical significance, analogous probability distributions for the interaction of the moiety X-CH(2)-X with aromatic rings were computed, and taken a priori to correspond to the null hypothesis of no significant interaction. Tests of significance were carried our pairwise between probability distributions of sulfur-aromatic interaction descriptors and their CH(2)-aromatic analogues using the Smirnov-Kolmogorov nonparametric test (W. W. Daniel, Applied Nonparametric Statistics, Houghton-Mifflin: Boston, New York, 1978, pp. 276-286), and in all cases significance at the 99% confidence level or better was observed. Local maxima of the probability distributions were used to define a preferred geometry of interaction between the divalent sulfur moiety and the aromatic ring. Molecular mechanics studies were performed in an effort to better understand the physical basis of the interaction. This study confirms observations based on statistics of interaction of amino acids in protein crystal structures (R. S. Morgan, C. E. Tatsch, R. H. Gushard, J. M. McAdon, and P. K. Warme, International Journal of Peptide Protein Research, 1978, Vol. 11, pp. 209-217; R. S. Morgan and J. M. McAdon, International Journal of Peptide Protein Research, 1980, Vol. 15, pp. 177-180; K. S. C. Reid, P. F. Lindley, and J. M. Thornton, FEBS Letters, 1985, Vol. 190, pp. 209-213), as well as studies involving molecular mechanics (G. Nemethy and H. A. Scheraga, Biochemistry and Biophysics Research Communications, 1981, Vol. 98, pp. 482-487) and quantum chemical calculations (B. V. Cheney, M. W. Schulz, and J. Cheney, Biochimica Biophysica Acta, 1989, Vol. 996, pp.116-124; J. Pranata, Bioorganic Chemistry, 1997, Vol. 25, pp. 213-219)-all of which point to the possible importance of the sulfur-aromatic interaction. However, the preferred geometry of the interaction, as determined from our analysis of the small-molecule crystal data, differs significantly from that found by other approaches. PMID:10679628

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

    PubMed

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

    2014-03-01

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

  5. Deriving the four-string and open-closed string interactions from geometric string field theory

    SciTech Connect

    Kaku, M. )

    1990-02-20

    One of the questions concerning the covariant open string field theory is why there are two distinct BRST theories and why the four-string interaction appears in one version but not the other. The authors solve this mystery by showing that both theories are gauge-fixed versions of a higher gauge theory, called the geometric string field theory, with a new field, a string verbein e{sub {mu}{sigma}}{sup {nu}{rho}}, which allows us to gauge the string length and {sigma} parametrization. By fixing the gauge, the authors can derive the endpoint gauge (the covariantized light cone gauge), the midpoint gauge of Witten, or the interpolating gauge with arbitrary string length. The authors show explicitly that the four-string interaction is a gauge artifact of the geometric theory (the counterpart of the four-fermion instantaneous Coulomb term of QED). By choosing the interpolating gauge, they produce a new class of four-string interactions which smoothly interpolate between the endpoint gauge and the midpoint gauge (where it vanishes). Similarly, they can extract the closed string as a bound state of the open string, which appears in the endpoint gauge but vanishes in the midpoint gauge. Thus, the four-string and open-closed string interactions do not have to be added to the action as long as the string vierbein is included.

  6. 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.

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

    PubMed Central

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

    2015-01-01

    Optimization of the chemical structure of antitumor photosensitizers (PSs) is aimed at increasing their affinity to a transport protein, albumin and irreversible light-induced tumor cell damage. Bacteriopurpurinimide derivatives are promising PSs thanks to their ability to absorb light in the near infrared spectral region. Using spectrophotometry, we show that two new bacteriopurpurinimide derivatives with different substituents at the N atoms of the imide exocycle and the pyrrole ring A are capable of forming non-covalent complexes with human serum albumin (HSA). The association constant (calculated with the Benesi-Hildebrand equation) for N-ethoxybacteriopurpurinimide ethyloxime (compound 1) is higher than that for the methyl ether of methoxybacteriopurpurinimide (compound 2) (1.18105 M-1 vs. 1.26104 M-1, respectively). Molecular modeling provides details of the atomic interactions between 1 and 2 and amino acid residues in the FA1 binding site of HSA. The ethoxy group stabilizes the position of 1 within this site due to hydrophobic interaction with the protein. The higher affinity of 1 for HSA makes this compound more potent than 2 in photodynamic therapy for cultured human colon carcinoma cells. Photoactivation of 1 and 2 in cells induces rapid (within a few minutes of irradiation) necrosis. This mechanism of cell death may be efficient for eliminating tumors resistant to other therapies. PMID:25927008

  8. Interaction with serum albumin as a factor of the photodynamic efficacy of novel bacteriopurpurinimide derivatives.

    PubMed

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

    2015-01-01

    Optimization of the chemical structure of antitumor photosensitizers (PSs) is aimed at increasing their affinity to a transport protein, albumin and irreversible light-induced tumor cell damage. Bacteriopurpurinimide derivatives are promising PSs thanks to their ability to absorb light in the near infrared spectral region. Using spectrophotometry, we show that two new bacteriopurpurinimide derivatives with different substituents at the N atoms of the imide exocycle and the pyrrole ring A are capable of forming non-covalent complexes with human serum albumin (HSA). The association constant (calculated with the Benesi-Hildebrand equation) for N-ethoxybacteriopurpurinimide ethyloxime (compound 1) is higher than that for the methyl ether of methoxybacteriopurpurinimide (compound 2) (1.1810(5) M-1 vs. 1.2610(4) M(-1), respectively). Molecular modeling provides details of the atomic interactions between 1 and 2 and amino acid residues in the FA1 binding site of HSA. The ethoxy group stabilizes the position of 1 within this site due to hydrophobic interaction with the protein. The higher affinity of 1 for HSA makes this compound more potent than 2 in photodynamic therapy for cultured human colon carcinoma cells. Photoactivation of 1 and 2 in cells induces rapid (within a few minutes of irradiation) necrosis. This mechanism of cell death may be efficient for eliminating tumors resistant to other therapies. PMID:25927008

  9. Interaction between neural stem cells and bone marrow derived-mesenchymal stem cells during differentiation

    PubMed Central

    RONG, JU; WEN, ZENG; RONG, WU; ZHICHUN, FENG

    2015-01-01

    Due to their capacity to self-replicate or produce specific differentiated cell types, neural stem cells (NSCs) and bone marrow derived-mesenchymal stem cells (BMSCs) are potential sources for cell transplantation therapies, particularly for neural injury. However, the interaction between NSCs and BMSCs during differentiation has not yet been defined. The interaction is believed to improve the effectiveness and efficiency of cell therapy. In the present study, human NSCs and BMSCs were cultured and the Transwell co-culture system was used to observe the interplay between NSCs and BMSCs during differentiation. The results revealed that NSCs promoted BMSCs to differentiate into neurons and NSCs; whereas, BMSCs did not affect the differentiation of NSCs. Simultaneously, co-culture increased the concentration of brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF), which are secreted by NSCs and BMSCs. The present findings suggest that co-culture of NSCs and BMSCs can promote the differentiation and this process may be modulated by BDNF and NGF. PMID:25798249

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Suckow, A.

    2012-04-01

    Several tracers for dating groundwater (18O/2H, 3H, CFCs, SF6, 85Kr) need lumped parameter modeling (LPM) to convert measured values into numbers with unit time. Other tracers (T/3He, 39Ar, 14C, 81Kr) allow the computation of apparent ages with a mathematical formula using radioactive decay without defining the age mixture that any groundwater sample represents. Also interpretation of the latter profits significantly from LPM tools that allow forward modeling of input time series to measurable output values assuming different age distributions and mixtures in the sample. This talk presents a Lumped Parameter Modeling code, Lumpy, combining up to two LPMs in parallel. The code is standalone and freeware. It is based on MS Access and Access Basic (AB) and allows using any number of measurements for both input time series and output measurements, with any, not necessarily constant, time resolution. Several tracers, also comprising very different timescales like e.g. the combination of 18O, CFCs and 14C, can be modeled, displayed and fitted simultaneously. Lumpy allows for each of the two parallel models the choice of the following age distributions: Exponential Piston flow Model (EPM), Linear Piston flow Model (LPM), Dispersion Model (DM), Piston flow Model (PM) and Gamma Model (GM). Concerning input functions, Lumpy allows delaying (passage through the unsaturated zone) shifting by a constant value (converting 18O data from a GNIP station to a different altitude), multiplying by a constant value (geochemical reduction of initial 14C) and the definition of a constant input value prior to the input time series (pre-bomb tritium). Lumpy also allows underground tracer production (4He or 39Ar) and the computation of a daughter product (tritiugenic 3He) as well as partial loss of the daughter product (partial re-equilibration of 3He). These additional parameters and the input functions can be defined independently for the two sub-LPMs to represent two different recharge areas. For a user defined choice of up to five parameters (mean residence times and dispersion parameters of the two sub-LPM plus the mixing ratios of the two models) the best fit can be determined. Fits can be assessed using different methods for the Goodness Of Fit. Input and output data are send to MS Excel for interactive display of modeling result and comparison with measurements. Excel only serves as data display; computations are performed in AB throughout. Lumpy allows display of time series and any combination of tracer vs. tracer plot. In the latter, the possible output data space assessable by the input variables can be displayed, to check if any of the model combinations under consideration is able to explain the measured data. Comparison and fit to measurements is possible after each of the two sub-models and after mixing these two. The talk will demonstrate the usefulness of this approach with examples from the Croatian Karst (Babinka 2007), the Fischa tracer test (Stolp et al., 2010) and the 30 years monthly tritium time series of the Danube (Aggarwal et al., 2010).

  19. 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

  20. Weak interactions in barbituric acid derivatives. Unusually steady intermolecular organic sandwich complexes. ? ? 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 ?-? stacking. The interplay between the intermolecular ?-? stacking and strong N sbnd HO hydrogen bond interactions and its influence on the "sandwich" structures of 1 and 2 are discussed.

  1. 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.

  2. 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.

  3. 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.

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

    SciTech Connect

    Behbahani, Siavosh R.; Mirbabayi, Mehrdad; Senatore, Leonardo; Smith, Kendrick M. E-mail: mehrdadm@ias.edu E-mail: kmsmith@perimeterinstitute.ca

    2014-11-01

    Given the fantastic experimental effort, it is important to thoroughly explore the signature space of inflationary models. The fact that higher derivative operators do not renormalize lower derivative ones allows us to find a large class of technically natural single-clock inflationary models where, in the context of the Effective Field Theory of Inflation, the leading interactions have many derivatives. We systematically explore the 3-point function induced by these models and their overlap with the standard equilateral and orthogonal templates. We find that in order to satisfactorily cover the signature space of these models, two new additional templates need to be included. We then perform the optimal analysis of the WMAP 9-year data for the resulting four templates, finding that the overall significance of a non-zero signal is between 22.5?, depending on the choice of parameter space, partially driven by the preference for nonzero f{sub NL}{sup orth} in WMAP9.

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

    PubMed Central

    2013-01-01

    Background Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of action. From a risk assessment perspective, alterations in biological pathways are a rich resource for setting toxicant thresholds, which may be more sensitive and mechanism-informed than traditional toxicity endpoints. Here we developed a novel differential networks (DNs) approach to connect pathway perturbation with toxicity threshold setting. Methods Our DNs approach consists of 6 steps: time-series gene expression data collection, identification of altered genes, gene interaction network reconstruction, differential edge inference, mapping of genes with differential edges to pathways, and establishment of causal relationships between chemical concentration and perturbed pathways. A one-sample Gaussian process model and a linear regression model were used to identify genes that exhibited significant profile changes across an entire time course and between treatments, respectively. Interaction networks of differentially expressed (DE) genes were reconstructed for different treatments using a state space model and then compared to infer differential edges/interactions. DE genes possessing differential edges were mapped to biological pathways in databases such as KEGG pathways. Results Using the DNs approach, we analyzed a time-series Escherichia coli live cell gene expression dataset consisting of 4 treatments (control, 10, 100, 1000 mg/L naphthenic acids, NAs) and 18 time points. Through comparison of reconstructed networks and construction of differential networks, 80 genes were identified as DE genes with a significant number of differential edges, and 22 KEGG pathways were altered in a concentration-dependent manner. Some of these pathways were perturbed to a degree as high as 70% even at the lowest exposure concentration, implying a high sensitivity of our DNs approach. Conclusions Findings from this proof-of-concept study suggest that our approach has a great potential in providing a novel and sensitive tool for threshold setting in chemical risk assessment. In future work, we plan to analyze more time-series datasets with a full spectrum of concentrations and sufficient replications per treatment. The pathway alteration-derived thresholds will also be compared with those derived from apical endpoints such as cell growth rate. PMID:24268022

  6. 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

  7. Interactions between 33 solutes and four cyano-containing stationary phases: gas chromatographic activity coefficients and the solvation parameter model.

    PubMed

    Santiuste, Jos M; Takcs, Jzsef M

    2003-07-01

    Infinite-dilution gas-liquid chromatographic activity coefficients at 393.15 K (with their thermal and athermal components) and derived excess partial molar Gibbs energies, enthalpies, and entropies have been determined for each of 33 solutes of different polarity on four stationary phases with cyano groups, using retention data taken from the literature. The strongest interactions predicted by the solvation model are the dipolarity/polarizability, the acidic solute-basic stationary phase interaction, and nonpolar cavity formation and dispersion. These interactions were compared with those evaluated from the solute activity coefficients; the effect of the solute connectivity index and dipole moment on nonpolar and polar interactions, respectively, is discussed. The dependence of the thermal activity coefficient on nonpolar interactions, and the influence of stationary phase polarity on the four solute-stationary phase interactions, were evaluated. The nonpolar interaction increases with increasing connectivity and with increasing athermal activity coefficient. The dipolarity/polarizability interaction increases with increasing solute dipole moment. Finally, polar interactions increase with increasing stationary phase polarity whereas the nonpolar interaction is independent of stationary phase polarity. PMID:12819849

  8. 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

  9. 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.

  10. 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

  11. 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.

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

    PubMed

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

    2015-11-11

    We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 10(5) M(-1), 4.7 10(5) M(-1), and 6.6 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications. PMID:26506886

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

    NASA Astrophysics Data System (ADS)

    Weber, Jeffrey K.; Pande, Vijay S.

    2013-02-01

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

  14. 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

  15. 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 Vam3Syk 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. Effect of various parameters on viability and growth of bacteria immobilized in sol-gel-derived silica matrices.

    PubMed

    Alvarez, Gisela S; Foglia, Mara L; Copello, Guillermo J; Desimone, Martn F; Diaz, Luis E

    2009-03-01

    Immobilized bacteria are being extensively used for metabolite production, biocatalysts, and biosensor construction. However, long-term viability and metabolic activity of entrapped bacteria is affected by several conditions such as their physiological state, the presence of high-osmolarity environments, porous structure and shrinkage of the matrix. The aim of this work was to evaluate the effect of various parameters on bacteria immobilized in sol-gel-derived silica matrices. With this purpose, we evaluated the stress of immobilization over bacteria cultures obtained from different growing states, the effect of cell density and bacteria capability to proliferate inside matrices. Best results to attain longer preservation times were obtained when we immobilized suspensions with an optimized bacterial number of 1 x 10(7) cfu/gel in the presence of LB medium using aqueous silica precursors. Furthermore, the impact of osmotic stress with the subsequent intracellular trehalose accumulation and the addition of osmolites were investigated. Shorter preservation times were found for bacteria immobilized in the presence of osmolites while trehalose accumulation in stressed cells did not produce changes on entrapped bacteria viability. Finally, nutrient addition in silica matrices was studied indicating that the presence of a carbon source without the simultaneous addition of nitrogen was detrimental for immobilized E. coli. However, when both carbon and nitrogen sources were present, bacteria were able to survive longer periods of time. PMID:19034444

  1. Interaction between antimalarial 2-aryl-3H-indol-3-one derivatives and human serum albumin.

    PubMed

    Rakotoarivelo, Nambinina V; Perio, Pierre; Najahi, Ennaji; Nepveu, Franoise

    2014-11-26

    Binding of drugs to plasma proteins, such as albumin, is a major factor which determines their pharmacokinetics and pharmacological effects. Therefore, the interactions between human serum albumin (HSA) and four antimalarial compounds selected in the 2-aryl-3H-indol-3-one series have been investigated using UV-visible, fluorescence and circular dichroism (CD) spectroscopies. Compounds produced a static quenching of the intrinsic fluorescence of HSA. The thermodynamic parameters have shown that the binding reaction is endothermic for three compounds while exothermic for the 2-phenyl-3H-indol-3-one, 3. The interaction is entropically driven with predominant hydrophobic forces with binding affinities of the order of 10(4) M(-1). The highest binding constant is observed for 3 (K?=280nm = 4.53 10(4) M(-1)) which is also the less active compound against Plasmodium falciparum. Synchronous fluorescence gave qualitative information on the conformational changes of HSA while quantitative data were obtained with CD. Displacement experiments with site markers indicated that drugs bind to HSA at site I (subdomain IIA). In addition, the apparent binding constant and the binding site number were calculated in the presence of different ions. PMID:25360713

  2. 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 ?(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

  3. Interactive 3-D Immersive Visualization for Analysis of Large Multi-Parameter Atmospheric Data Sets

    NASA Astrophysics Data System (ADS)

    Frenzer, J. B.; Hoell, J. M.; Holdzkom, J. J.; Jacob, D.; Fuelberg, H.; Avery, M.; Carmichael, G.; Hopkins, D. L.

    2001-12-01

    Significant improvements in the ability of atmospheric chemistry models to predict the transport and production of atmospheric constituents on regional and global scales have been realized over the past decade. Concurrent with the model improvements, has been an increase in the size and complexity of atmospheric observational data sets. As a result, the challenge to provide efficient and realistic visualization of atmospheric data "products" has increased dramatically. Over the past several years, personnel from the Atmospheric Sciences Data Center (ASDC) at NASA's Langley Research Center have explored the merits of visualizing atmospheric data products using interactive, immersive visualization hardware and software. As part of this activity, the Virtual Global Explorer and Observatory (vGeo) software, developed by VRCO, Inc., has been utilized to support the visual analysis of large multivariate data sets. The vGeo software provides an environment in which the user can create, view, navigate, and interact with data, models, and images in an immersive 3-D environment. The vGeo visualization capability was employed during the March/April 2001, NASA Global Tropospheric Experiment Transport and Chemical Evolution over the Pacific (TRACE-P) mission [(GTE) http://www-gte.larc.nasa.gov] to support day-to-day flight-planning activities through the creation of virtual 3-D worlds containing modeled data and proposed aircraft flight paths. The GTE, a major activity within NASA's Earth Science Enterprise, is primarily an aircraft-based measurement program, supplemented by ground-based measurements and satellite observations, focused on understanding the impact of human activity on the global troposphere. The TRACE-P is the most recent campaign conducted by GTE and was deployed to Hong Kong and then to the Yokota Airbase, Japan. TRACE-P is the third in a series of GTE field campaigns in the northwestern Pacific region to understand the chemical composition of air masses emerging from the Asian Continent and their impact on the region. Since completing the field deployment phase of TRACE-P, the 3-D visualization capability has been used as a tool to combine and visually analyze TRACE-P data from multiple sources (e.g. model, airborne and ground based measurements, ozone sondes, and satellite observations). This capability to merge measurements into model data fields in a virtual 3-D world is perhaps the most exciting aspect of this new visualization capability. This allows for a more realistic contextual representation of the model/measurement results. The measured parameters along specific flights (of typical duration of 8 hrs) along with supporting ancillary measurements provide the "real" representation of the atmosphere at that specific point in time and space. The models provide the time evolution, and three-dimensional structure during the measurement period. When these are merged together the context of the observations is documented, and model predictions can be validated and/or improved. Specific TRACE-P case studies will be presented showing results from global and regional models coupled with airborne measurements for which the influence of transport on the spatial distribution of species measured on the aircraft was more clearly discerned within the 3-D environment than from conventional visualization techniques.

  4. 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

  5. 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.

  6. 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 ?sca and backscatter ?backsca) 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. ?sca is a factor of two higher in the east (Bhubaneshwar, Chennai) than in the west (Trivandrum, Goa). ?sca is about 5-10 10-5 m-1 over Bhubaneshwar and Chennai. ?backsca is about an order of magnitude lower than ?sca. 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 ngstrm exponent (?) 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 ?, 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.

  7. Relationship between Levels of Brain-Derived Neurotrophic Factor and Metabolic Parameters in Patients with Type 2 Diabetes Mellitus

    PubMed Central

    Boyuk, Banu; Degirmencioglu, Serife; Atalay, Hande; Guzel, Savas; Acar, Ayse; Celebi, Aslan; Ekizoglu, Ismail; Simsek, Caglar

    2014-01-01

    Background and Aim. Studies have suggested that brain-derived neurotrophic factor (BDNF) plays a role in glucose and lipid metabolism and inflammation. The aim of this study was to evaluate the relationship between serum BDNF levels and various metabolic parameters and inflammatory markers in patients with type 2 diabetes mellitus (T2DM). Materials and Methods. The study included 88 T2DM patients and 33 healthy controls. Fasting blood samples were obtained from the patients and the control group. The serum levels of BDNF were measured with an ELISA kit. The current paper introduces a receiver-operating characteristic (ROC) generalization curve to identify cut-off for the BDNF values in type 2 diabetes patients. Results. The serum levels of BDNF were significantly higher in T2DM patients than in the healthy controls (206.81??107.32?pg/mL versus 130.84??59.81?pg/mL; P < 0.001). They showed a positive correlation with the homeostasis model assessment of insulin resistance (HOMA-IR) (r = 0.28; P < 0.05), the triglyceride level (r = 0.265; P < 0.05), and white blood cell (WBC) count (r = 0.35; P < 0.001). In logistic regression analysis, age (P < 0.05), body mass index (BMI) (P < 0.05), C-reactive protein (CRP) (P < 0.05), and BDNF (P < 0.01) were independently associated with T2DM. In ROC curve analysis, BDNF cut-off was 137. Conclusion. The serum BDNF level was higher in patients with T2DM. The BDNF had a cut-off value of 137. The findings suggest that BDNF may contribute to glucose and lipid metabolism and inflammation. PMID:25587547

  8. Derivatives of any order of the confluent hypergeometric function {sub 1}F{sub 1}(a,b,z) with respect to the parameter a or b

    SciTech Connect

    Ancarani, L. U.; Gasaneo, G.

    2008-06-15

    The derivatives to any order of the confluent hypergeometric (Kummer) function F={sub 1}F{sub 1}(a,b,z) with respect to the parameter a or b are investigated and expressed in terms of generalizations of multivariable Kampe de Feriet functions. Various properties (reduction formulas, recurrence relations, particular cases, and series and integral representations) of the defined hypergeometric functions are given. Finally, an application to the two-body Coulomb problem is presented: the derivatives of F with respect to a are used to write the scattering wave function as a power series of the Sommerfeld parameter.

  9. 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

  10. Self-Assembled Monolayers of an Azobenzene Derivative on Silica and Their Interactions with Lysozyme.

    PubMed

    Wei, Tao; Sajib, Md Symon Jahan; Samieegohar, Mohammadreza; Ma, Heng; Shing, Katherine

    2015-12-22

    The capability of the photoresponsive isomerization of azobenzene derivatives in self-assembled monolayer (SAM) surfaces to control protein adsorption behavior has very promising applications in antifouling materials and biotechnology. In this study, we performed an atomistic molecular dynamics (MD) simulation in combination with free-energy calculations to study the morphology of azobenzene-terminated SAMs (Azo-SAMs) grafted on a silica substrate and their interactions with lysozyme. Results show that the Azo-SAM surface morphology and the terminal benzene rings' packing are highly correlated with the surface density and the isomer state. Higher surface coverage and the trans-isomer state lead to a more ordered polycrystalline backbone as well as more ordered local packing of benzene rings. On the Azo-SAM surface, water retains a high interfacial diffusivity, whereas the adsorbed lysozyme is found to have extremely low mobility but a relative stable secondary structure. The moderate desorption free energy (?60 kT) from the trans-Azo-SAM surface was estimated by using both the nonequilibrium-theorem-based Jarzynski's equality and equilibrium umbrella sampling. PMID:26597057

  11. Lens Epithelium-derived Growth Factor/p75 Interacts with the Transposase-derived DDE Domain of PogZ*S?

    PubMed Central

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

    2009-01-01

    Lens epithelium-derived growth factor/p75 (LEDGF/p75) is a prominent cellular interaction partner of human immunodeficiency virus-1 (HIV-1) integrase, tethering the preintegration complex to the host chromosome. In light of the development of LEDGF/p75-integrase interaction inhibitors, it is essential to understand the cell biology of LEDGF/p75. We identified pogZ as new cellular interaction partner of LEDGF/p75. Analogous to lentiviral integrase, pogZ, a domesticated transposase, carries a DDE domain, the major determinant for LEDGF/p75 interaction. Using different in vitro and in vivo approaches, we corroborated the interaction between the C terminus of LEDGF/p75 and the DDE domain of pogZ, revealing an overlap in the binding of pogZ and HIV-1 integrase. Competition experiments showed that integrase is efficient in displacing pogZ from LEDGF/p75. Moreover, pogZ does not seem to play a role as a restriction factor of HIV. The finding that LEDGF/p75 is capable of interacting with a DDE domain protein that is not a lentiviral integrase points to a profound role of LEDGF/p75 in DDE domain protein function. PMID:19244240

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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 (?) 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.

  19. 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.

  20. 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

  1. 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...

  2. Plasma-derived mannose-binding lectin shows a direct interaction with C1-inhibitor.

    PubMed

    Keizer, Mischa P; Kamp, Angela M; Brouwer, Nannette; van de Wetering, Marianne D; Wouters, Diana; Kuijpers, Taco W

    2014-04-01

    MBL-deficiency has been associated with an increased frequency and severity of infection, in particular in children and under immunocompromized conditions. In an open uncontrolled safety and pharmacokinetic MBL-substitution study using plasma-derived MBL (pdMBL) in MBL-deficient pediatric oncology patients, we found that despite MBL trough levels above 1.0?g/ml MBL functionality was not efficiently restored upon ex vivo testing. PdMBL showed C4-converting activity by itself, indicating the presence of MASPs. Upon incubation of pdMBL with MBL-deficient sera this C4-converting activity was significantly reduced. Depletion of the MASPs from pdMBL, paradoxically, restored the C4-converting activity. Subsequent depletion or inhibition of C1-inh, the major inhibitor of the lectin pathway, in the recipient serum restored the C4-converting activity as well. Complexes between MBL/MASPs and C1-inh (MMC-complexes) were detected after ex vivo substitution of MBL-deficient serum with pdMBL. These MMC-complexes could also be detected in the sera of the patients included in the MBL-substitution study shortly after pdMBL infusion. Altogether, we concluded that active MBL-MASP complexes in pdMBL directly interact with C1-inh in the recipient, leading to the formation of a multimolecular complex between C1-inh and MBL/MASPs, in contrast to the classical pathway where C1r and C1s are dissociated from C1q by C1-inh. Because of the presence of activated MASPs in the current pdMBL products efficient MBL-mediated host protection cannot be expected because of the neutralizing capacity by C1-inh. PMID:24368318

  3. Toward a non-invasive screening tool for differentiation of pancreatic lesions based on intra-voxel incoherent motion derived parameters.

    PubMed

    Graf, Markus; Simon, Dirk; Lemke, Andreas; Grnberg, Katharina; Mang, Sarah

    2013-02-01

    Early recognition of and differential diagnosis between pancreatic cancer and chronic pancreatitis is an important step in successful therapy. Parameters of the IVIM (intra-voxel incoherent motion) theory can be used to differentiate between those lesions. The objective of this work is to evaluate the effects of rigid image registration on IVIM derived parameters for differentiation of pancreatic lesions such as pancreatic cancer and solid mass forming pancreatitis. The effects of linear image registration methods on reproducibility and accuracy of IVIM derived parameters were quantified on MR images of ten volunteers. For this purpose, they were evaluated statistically by comparison of registered and unregistered parameter data. Further, the perfusion fraction f was used to differentiate pancreatic lesions on eleven previously diagnosed patient data sets. Its diagnostic power with and without rigid registration was evaluated using receiver operating curves (ROC) analysis. The pancreas was segmented manually on MR data sets of healthy volunteers as well as the patients showing solid pancreatic lesions. Diffusion weighted imaging was performed in 10 blocks of breath-hold phases. Linear registration of the weighted image stack leads to a 3.7% decrease in variability of the IVIM derived parameter f due to an improved anatomical overlap of 5%. Consequently, after registration the area under the curve in the ROC-analysis for the differentiation approach increased by 2.7%. In conclusion, rigid registration improves the differentiation process based on f-values. PMID:23154146

  4. 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.

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

    PubMed Central

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

    2013-01-01

    Overbinding of ions to lipid head groups is a potentially serious artifact in simulations of charged lipid bilayers. In this study, the Lennard-Jones radii in the CHARMM force field for interactions of Na+ and lipid oxygen atoms of carboxyl, phosphate and ester groups were revised to match osmotic pressure data on sodium acetate, and electrophoresis data on palmitoyloleoyl phosphatidylcholine (POPC) vesicles. The new parameters were then validated by successfully reproducing previously published experimental NMR deuterium order parameters for dimyristoyl phosphatidylglycerol (DMPG) and newly obtained values for palmitoyloleoyl phosphatidylserine (POPS). Although the increases in Lennard-Jones diameters are only 0.02 to 0.12 , they are sufficient to reduce Na+ binding, and thereby increase surface areas per lipid by 510% compared with the unmodified parameters. PMID:23924441

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

    NASA Technical Reports Server (NTRS)

    Carlson, T. N. (principal investigator)

    1981-01-01

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

  7. 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.

  8. 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.

  9. 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.

  10. Five-Parameter Grain Boundary Inclination Recovery with EBSD and Interaction Volume Models

    NASA Astrophysics Data System (ADS)

    Sorensen, Caroline; Basinger, John A.; Nowell, Matthew M.; Fullwood, David T.

    2014-08-01

    While electron backscatter diffraction (EBSD) patterns are often used to present two-dimensional information about a material microstructure, they are in fact a product of the three-dimensional electron interaction volume. Consequently, 3D spatial information exists in EBSD images, which is generally not accessed. Specifically, the inclination of the grain boundary plane may be observed in EBSD patterns taken near grain boundaries. If, at the same time, the shape of an electron interaction volume in the material is known, a grain boundary plane normal direction can be obtained from a sequence of EBSD images taken stepwise in a line crossing the grain boundary. Here, these two principles are used for demonstrating the determination of grain boundary normal vectors from EBSD images. Coherent twin boundaries and focused ion beam serial scan data are used for validation. Results indicate a mean error for this approach of 3 deg with a standard deviation of 3.8 deg.

  11. Parameter dependence of vortex interactions on a two-dimensional plunging plate

    NASA Astrophysics Data System (ADS)

    Eslam Panah, Azar; Buchholz, James H. J.

    2014-03-01

    The structure and dynamics of the flow field created by a plunging flat-plate airfoil are investigated at a chord Reynolds number of 10,000 while varying plunge amplitude and Strouhal number. Digital particle image velocimetry measurements are used to characterize the shedding patterns and the interactions between the leading- and trailing-edge vortex structures (LEV and TEV), resulting in the development of a wake classification system based on the nature and timing of interactions between the leading- and trailing-edge vortices. The streamwise advancement of the LEV during a plunge cycle and its resulting interaction with the TEV is primarily dependent on reduced frequency; however, for Strouhal numbers above approximately 0.4, significant changes are observed in the formation of vortices shed from the leading and trailing edges, as well as the circulation of the leading-edge vortex. The functional form of the relationship between leading-edge vortex circulation and Strouhal number suggests that the Strouhal number dependence is more specifically a manifestation of the effective angle of attack. Comparison with low-Reynolds-number studies of plunging airfoil aerodynamics reveals a high degree of consistency and suggests applicability of the classification system beyond the range examined in the present work.

  12. 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.

  13. 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.

  14. 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.

  15. Solute-solvent interactions from gas chromatographic activity coefficients and the solvation parameter model for nitrogen-containing stationary phases.

    PubMed

    Santiuste, Jos M

    2003-04-01

    Infinite dilution gas-liquid chromatographic activity coefficients (gamma) and excess thermodynamic molar partial magnitudes [Gibbs energy (G(E)), enthalpy (H(E)), and entropy (S(E))] for 37 solutes of varied polarity on four stationary phases with -NH groups are obtained from partition coefficients taken from literature. Relationships between G(E) and S(E) with the 37 solutes' structure in terms of the molecular connectivity index ((1)chi(v)) are investigated. Correlations of solute-solvent interactions calculated in light of the solvation parameter model for selected solutes and stationary phases are tested. The effect of the solute's structure, expressed as the molecular connectivity index, on the nonpolar (cavity formation and dispersion interaction) [c+l. log L(16)] and the effect of the dipole moment and of the activity coefficient on the dipolarity-polarizability interaction (spi(2)(H)) are studied. The correlation between the nonpolar interaction with the athermal activity coefficient on the nonpolymeric stationary phases is also attempted. In addition, the influence of the stationary phase polarity on the solute-stationary phase interactions for a series of solutes is studied. PMID:12803811

  16. 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.

  17. Coarse-grain simulations of skin ceramide NS with newly derived parameters clarify structure of melted phase.

    PubMed

    Sovov, ofie; Berka, Karel; Otyepka, Michal; Jure?ka, Petr

    2015-03-12

    Ceramides are lipids that are involved in numerous biologically important structures (e.g., the stratum corneum and ceramide-rich platforms) and processes (e.g., signal transduction and membrane fusion), but their behavior is not fully understood. We report coarse-grain force field parameters for N-lignocerylsphingosine (ceramide NS, also known as ceramide 2) that are consistent with the Martini force field. These parameters were optimized for simulations in the gel phase and validated against atomistic simulations. Coarse-grained simulations with our parameters provide areas per lipid, membrane thicknesses, and electron density profiles that are in good agreement with atomistic simulations. Properties of the simulated membranes are compared with available experimental data. The obtained parameters were used to model the phase behavior of ceramide NS as a function of temperature and hydration. At low water content and above the main phase transition temperature, the bilayer melts into an irregular phase, which may correspond to the unstructured melted-chain phase observed in X-ray diffraction experiments. The developed parameters also reproduce the extended conformation of ceramide, which may occur in the stratum corneum. The parameters presented herein will facilitate studies on important complex functional structures such as the uppermost layer of the skin and ceramide-rich platforms in phospholipid membranes. PMID:25679231

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

    PubMed Central

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

    2014-01-01

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

  19. A computational parameter study for the three-dimensional shock?bubble interaction

    NASA Astrophysics Data System (ADS)

    Niederhaus, John H. J.; Greenough, J. A.; Oakley, J. G.; Ranjan, D.; Anderson, M. H.; Bonazza, R.

    The morphology and time-dependent integral properties of the multifluid compressible flow resulting from the shock0.8 0.2, three-dimensional (non-axisymmetric) effects become particularly significant in the total enstrophy at late times. A new model for the total velocity circulation is proposed, also based on properties derived from one-dimensional gasdynamics, which compares favourably with circulation data obtained from calculations, relative to existing models. The action of nonlinear-acoustic effects and primary and secondary vorticity production is depicted in sequenced visualizations of the density and vorticity fields, which indicate the significance of both secondary vorticity generation and turbulent effects, particularly for M > 2 and A > 0.2. Movies are available with the online version of the paper.

  20. Ab initio analysis of the tight-binding parameters and magnetic interactions in Na2IrO3

    NASA Astrophysics Data System (ADS)

    Foyevtsova, Kateryna; Jeschke, Harald O.; Mazin, I. I.; Khomskii, D. I.; Valent, Roser

    2013-07-01

    By means of density functional theory (DFT) calculations [with and without inclusion of spin-orbit (SO) coupling] we present a detailed study of the electronic structure and corresponding microscopic Hamiltonian parameters of Na2IrO3. In particular, we address the following aspects: (i) We investigate the role of the various structural distortions and show that the electronic structure of Na2IrO3 is exceptionally sensitive to structural details. (ii) We discuss both limiting descriptions for Na2IrO3quasimolecular orbitals (small SO limit, itinerant) versus relativistic orbitals (large SO limit, localized)and show that the description of Na2IrO3 lies in an intermediate regime. (iii) We investigate whether the nearest neighbor Kitaev-Heisenberg model is sufficient to describe the electronic structure and magnetism in Na2IrO3. In particular, we verify the recent suggestion of an antiferromagnetic Kitaev interaction and show that it is not consistent with actual or even plausible electronic parameters. Finally, (iv) we discuss correlation effects in Na2IrO3. We conclude that while the Kitaev-Heisenberg Hamiltonian is the most general expression of the quadratic spin-spin interaction in the presence of spin-orbit coupling (neglecting single-site anisotropy), the itinerant character of the electrons in Na2IrO3 makes other terms beyond this model (including, but not limited to, 2nd and 3rd neighbor interactions) essential.

  1. A flexible, interactive software tool for fitting the parameters of neuronal models.

    PubMed

    Friedrich, Pter; Vella, Michael; Gulys, Attila I; Freund, Tams F; Kli, 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

  2. 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.

  3. Kinetic model framework for aerosol and cloud surface chemistry and gas-particle interactions: Part 1 - general equations, parameters, and terminology

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

    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 allows to describe mass transport and chemical reactions at the gas-particle interface and to link 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 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 correction, 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 dependencies; flexible inclusion/omission of chemical species and physicochemical processes; flexible convolution/deconvolution of species and processes; and full compatibility with traditional resistor model formulations. Exemplary practical applications and model calculations illustrating the relevance of the above aspects will be presented in a companion paper (Ammann and Pschl, 2005). We expect that the presented model framework will serve as a useful tool and basis for experimental and theoretical studies investigating and describing atmospheric aerosol and cloud surface chemistry and gas-particle interactions. In particular, it is meant to support the planning and design of laboratory experiments for the elucidation and determination of kinetic parameters; the establishment, evaluation, and quality assurance of comprehensive and self-consistent collections of rate parameters; and the development of detailed master mechanisms for process models and the derivation of simplified but yet realistic parameterizations for atmospheric and climate models.

  4. 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.

  5. [Biophysical parameters of erythrocyte membranes and mechanisms of interaction with non-opioid analgesics under acute pain syndrome].

    PubMed

    Hubs'ky?, Iu I; Bukhtiarova, T A; Horiushko, H H; Litvinova, N V; Paramonova, H I; Kurapova, T M; Velychko, O M; Babenko, L P

    2014-01-01

    Methods of fluorescent probing, spectrophotometry and microcalorimetry were applied to investigate the alterations in biophysical parameters of erythrocytes membranes, and specifically microviscosity, surface charge, molecular organization of lipid bilayer and lipid-protein interactions under conditions of acute pain syndrome produced by experimental chemical lesion. The distinctive features of non-opiod analgesics interactions and binding to the erythrocytes membranes of rats subjected to acute nociceptive pain accompanied with oxidative stress development were investigated. The abilities of analgesics under research, and namely paracetamol, aspirin, phenazone, ketorolac, pyrodazole, ketoprofenum, natrium mefenaminate, indometacin, nimesulide to make up physico-chemical complexes with lipoperoxidation modified erythrocytes surface and protein-lipid bilayer showed marked changes. The significance of oxidative damage of biophase under conditions of acute pain syndrome for analgesics effective pharmacodynamics and pharmacokinetics realization is under consideration. PMID:25033559

  6. Bianchi type-III minimally interacting holographic dark energy model with linearly varying deceleration parameter in Brans-Dicke theory

    NASA Astrophysics Data System (ADS)

    Kiran, M.; Reddy, D. R. K.; Rao, V. U. M.

    2015-12-01

    In this paper, we study the minimally interacting fields; matter and holographic dark energy components in Bianchi type-III space-time in the frame work of Brans-Dicke (Phys. Rev. 125:961, 1961) scalar-tensor theory of gravitation. We present a Bianchi type-III holographic dark energy model with the help of linearly varying deceleration parameter proposed by Akarsu and Dereli (Int. J. Theor. Phys. 51:612, 2012). Some physical and kinematical properties of the model are also discussed.

  7. Dynamic calibration of higher eigenmode parameters of a cantilever in atomic force microscopy by using tipsurface interactions

    PubMed Central

    Forchheimer, Daniel; Haviland, David B

    2014-01-01

    Summary We present a theoretical framework for the dynamic calibration of the higher eigenmode parameters (stiffness and optical lever inverse responsivity) of a cantilever. The method is based on the tipsurface force reconstruction technique and does not require any prior knowledge of the eigenmode shape or the particular form of the tipsurface interaction. The calibration method proposed requires a single-point force measurement by using a multimodal drive and its accuracy is independent of the unknown physical amplitude of a higher eigenmode. PMID:25383301

  8. The effect of structural parameters and positive charge distance on the interaction free energy of antimicrobial peptides with membrane surface.

    PubMed

    Ghahremanpour, Mohammad Mehdi; Sardari, Soroush

    2015-01-01

    Many attempts have been made to find hints explaining the relationship between physicochemical and structural properties of antimicrobial peptides (AMPs) which are relevant to their antimicrobial activities. We here found that there is a difference in the percentages of hydrophobic, hydrophilic, and charged residues between AMPs killing both bacteria and fungi (Group A) and AMPs that only kill bacteria (Group B). The percentage of charged residues in Group A AMPs is highly elevated, while in Group B the percentage of hydrophobic residues is increased. This result suggests a sequence-based mechanism of selectivity for AMPs. Moreover, we examined how the distance between basic residues affects the interaction free energy of AMPs with the membrane surface, since most of the known AMPs act by membrane perturbation. We measured the average distance between basic residues throughout the 3D structure of AMPs by defining Dpr parameter and calculated the interaction free energy for 10 AMPs that interacted with the DPPC membrane using molecular dynamics simulation. We found that the changes of the interaction free energy correlates with the change of Dpr by a linear regression coefficient of r(2?)=?.47 and a cubic regression coefficient of r(2?)=?.70. PMID:24621111

  9. 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.

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

    PubMed

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

    2015-11-01

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

  11. Precision measurements of the Co60 ?-asymmetry parameter in search for tensor currents in weak interactions

    NASA Astrophysics Data System (ADS)

    Wauters, F.; Kraev, I.; Zkouck, D.; Beck, M.; Breitenfeldt, M.; de Leebeeck, V.; Golovko, V. V.; Kozlov, V. Yu.; Phalet, T.; Roccia, S.; Soti, G.; Tandecki, M.; Towner, I. S.; Traykov, E.; van Gorp, S.; Severijns, N.

    2010-11-01

    The ?-asymmetry parameter for the Gamow-Teller decay of Co60 was measured by polarizing the radioactive nuclei with the brute-force low-temperature nuclear-orientation method. The Co60 activity was cooled down to milliKelvin temperatures in a He3-He4 dilution refrigerator in an external 13-T magnetic field. The ? particles were observed by a 500-?m-thick Si PIN diode operating at a temperature of about 10 K in a magnetic field of 0.6 T. Extensive geant4 Monte Carlo simulations were performed to gain control over the systematic effects. Our result, =-1.014(12)stat(16)syst, is in agreement with the standard-model value of -0.987(9), which includes recoil-order corrections that were addressed for the first time for this isotope. Further, it enables limits to be placed on possible tensor-type charged weak currents, as well as other physics beyond the standard model.

  12. 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, ...

  13. In vitro histological investigation of interactions between rat decellularized large intestine scaffold and human adipose derived mesenchymal stem cells

    PubMed Central

    Naderi, Somayeh; Akbarzadeh Niaki, Malihe; Mahdavi Shahri, Nasser; Moghaddam Matin, Maryam; Fereidoni, Masoud; Naseri, Fatemeh

    2015-01-01

    The aim of this study was to investigate the interactions between rat intestine decellularized scaffold and human adipose derived mesenchymal stem cells. Rat large intestine was dissected in fragments and decellularized by physicochemical methods. The scaffolds were loaded by human adipose derived mesenchymal stem cells expressing green fluorescent protein. Microscopic sections were prepared from the scaffolds after two weeks of culture with stem cells and studied by histological methods. The interactions of scaffolds with MSCs were also studied by electron microscopy. Histological and electron microscopy studies revealed human mesenchymal stem cell adhesion, migration, division and maintenance during the 14 days of culture in vitro. According to the results, scaffolds prepared from rat intestine matrix could be a suitable scaffold for studying in vitro cell behaviors such as division, migration and attachment. These various behaviors of cultured cells might be due to inductive effects of the extracellular matrix derived scaffold. However, more investigations are required to discover the exact effects of this scaffold and its interactions with mesenchymal stem cells.

  14. 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.

  15. 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 ?M while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD?=?1553 ?M). 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

  16. 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

  17. 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.

  18. 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

  19. Ionic composition of seawaters and derived saline solutions determined by ion chromatography and its relation to other water quality parameters.

    PubMed

    Gros, Natasa; Cames, M F; Oliveira, Cristina; Silva, M C R

    2008-11-01

    Ion chromatography (IC) presents new possibilities for assessing information about environmental samples, namely waters of various compositions, ranging from high-purity water to highly saline ones. Constant proportion between major ions present in seawater, has been assumed in the past, from which the first practical equation relating chlorinity and salinity has been developed, being later substituted by a practical salinity scale, derived from conductivity measurements relative to a standard seawater, according to internationally accepted recommended procedures. Seawaters are characterized by salinity values around 35 while derived saline solutions may present considerable changes in ionic composition, conductivity, hence on salinity. Natural and anthropogenic phenomena may introduce new issues requiring clarification for which qualitative and quantitative information from additional sources is useful, e.g. ionic composition from IC. The different ranges of concentration of major and minor species present in seawater and derived saline solutions are a challenge for the optimization of a practical methodology for composition assessment in two single IC runs, one for anions and another one for cations, which has been attained in this work. Composition of saline solutions determined by IC was critically assessed in terms of anion-cation balance and further related to conductivity and salinity measurements aiming to evaluate the quality/completeness of ion chromatographic analyses performed at preselected conditions and to search for other meaningful relations for efficient recognition/distinction between saline solutions of different types. PMID:18829032

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

    PubMed

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

    2013-01-01

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

  1. 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 (?G) 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 ?G. 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 ??G 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 ??G with QMPC for the complexes formed by ER? 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

  2. Fundamental parameters of the close interacting binary HD 170582 and its luminous accretion disc

    NASA Astrophysics Data System (ADS)

    Mennickent, R. E.; Djuraevi?, G.; Cabezas, M.; Cski, A.; Rosales, J. G.; Niemczura, E.; Araya, I.; Cur, M.

    2015-04-01

    We present a spectroscopic and photometric study of the double period variable HD 170582. Based on the study of the ASAS V-band light curve, we determine an improved orbital period of 16.871 77 0.020 84 d and a long period of 587 d. We disentangled the light curve into an orbital part, determining ephemerides and revealing orbital ellipsoidal variability with unequal maxima, and a long cycle, showing quasi-sinusoidal changes with amplitude ?V= 0.1 mag. Assuming synchronous rotation for the cool stellar component and semidetached configuration we find a cool evolved star of M2 = 1.9 0.1 M?, T2 = 8000 100 K and R2 = 15.6 0.2 R?, and an early B-type dwarf of M1 = 9.0 0.2 M?. The B-type star is surrounded by a geometrically and optically thick accretion disc of radial extension 20.8 0.3 R? contributing about 35 per cent to the system luminosity at the V band. Two extended regions located at opposite sides of the disc rim, and hotter than the disc by 67 and 46 per cent, fit the light-curve asymmetries. The system is seen under inclination 67.4 0.4 and it is found at a distance of 238 10 pc. Specially interesting is the double line nature of He I 5875; two absorption components move in antiphase during the orbital cycle; they can be associated with the shock regions revealed by the photometry. The radial velocity of one of the He I 5875 components closely follows the donor radial velocity, suggesting that the line is formed in a wind emerging near the stream-disc interacting region.

  3. Using force covariance to derive effective stochastic interactions in dissipative particle dynamics.

    PubMed

    Eriksson, Anders; Jacobi, Martin Nilsson; Nystrm, Johan; Tunstrm, Kolbjrn

    2008-01-01

    There exist methods for determining effective conservative interactions in coarse-grained particle-based mesoscopic simulations. The resulting models can be used to capture thermal equilibrium behavior, but the model system we study does not correctly represent transport properties. We suggest the use of force covariance to determine the full functional form of dissipative and stochastic interactions. We show that a combination of the RDF and a force covariance function can be used to determine all interactions in dissipative particle dynamics (DPD). Furthermore, we use the method to test whether the effective interactions in DPD can be adjusted to produce a force covariance consistent with the projection of a microscopic Lennard-Jones simulation. The results indicate that the DPD ansatz may not be consistent with the underlying microscopic dynamics. We discuss how this result relates to theoretical studies reported in the literature. PMID:18351960

  4. Design, synthesis, and physico-chemical interactions of bile acid derived dimeric phospholipid amphiphiles with model membranes.

    PubMed

    Kumar, Sandeep; Bhargava, Priyanshu; Sreekanth, Vedagopuram; Bajaj, Avinash

    2015-06-15

    Understanding of amphiphile-membrane interactions is crucial in design and development of novel amphiphiles for drug delivery, gene therapy, and biomedical applications. Structure and physico-chemical properties of amphiphiles determine their interactions with biomembranes thereby influencing their drug delivery efficacies. Here, we unravel the interactions of bile acid derived dimeric phospholipid amphiphiles with model membranes using Laurdan-based hydration, DPH-based membrane fluidity, and differential scanning calorimetry studies. We synthesized three dimeric bile acid amphiphiles where lithocholic acid, deoxycholic acid, and cholic acid are conjugated to cholic acid phospholipid using click chemistry. Interactions of these dimeric amphiphiles with model membranes showed that these amphiphiles form different structural assemblies and molecular packing in model membranes depending on the number and position of free hydroxyl groups on bile acids. We discovered that cholic acid-cholic acid dimeric phospholipid form self-assembled aggregates in model membranes without changing membrane fluidity; whereas cholic acid-deoxycholic acid derived amphiphile induces membranes fluidity and hydration of model membranes. PMID:25746193

  5. 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.

  6. Mathematical Model Relating Uniaxial Compressive Behavior of Manufactured Sand Mortar to MIP-Derived Pore Structure Parameters

    PubMed Central

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

    The uniaxial compression response of manufactured sand mortars proportioned using different water-cement ratio and sand-cement ratio is examined. Pore structure parameters such as porosity, threshold diameter, mean diameter, and total amounts of macropores, as well as shape and size of micropores are quantified by using mercury intrusion porosimetry (MIP) technique. Test results indicate that strains at peak stress and compressive strength decreased with the increasing sand-cement ratio due to insufficient binders to wrap up entire sand. A compression stress-strain model of normal concrete extending to predict the stress-strain relationships of manufactured sand mortar is verified and agreed well with experimental data. Furthermore, the stress-strain model constant is found to be influenced by threshold diameter, mean diameter, shape, and size of micropores. A mathematical model relating stress-strain model constants to the relevant pore structure parameters of manufactured sand mortar is developed. PMID:25133257

  7. 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. 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.

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

    PubMed

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

    2007-10-28

    Relativistic effects on the (129)Xe nuclear magnetic resonance shielding and (131)Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe(2) system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift delta, the anisotropy of the shielding tensor Deltasigma, and the NQC constant along the internuclear axis chi( parallel) are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Moller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for delta and Deltasigma by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for delta and Deltasigma in Xe(2). For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For chi( parallel), the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the (129)Xe nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe(2), are in excellent agreement with the experiment for the first time. PMID:17979344

  10. 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.

  11. 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.

  12. 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

  13. 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)...

  14. Interactions of Jet Fuels with Nitrile O-Rings: Petroleum-Derived versus Synthetic Fuels

    SciTech Connect

    Gormley, Robert J.; Link, Dirk D.; Baltrus, John P.; Zandhuis, Paul H.

    2009-02-19

    A transition from petroleum-derived jet fuels to blends with Fischer-Tropsch (F-T) fuels, and ultimately fully synthetic hydro-isomerized F-T fuels has raised concern about the fate of plasticizers in nitrile-butadiene rubber o-rings that are contacted by the fuels as this transition occurs. The partitioning of plasticizers and fuel molecules between nitrile o-rings and petroleum-derived, synthetic, and additized-synthetic jet fuels has been measured. Thermal desorption of o-rings soaked in the various jet fuels followed by gas chromatographic analysis with a mass spectrometric detector showed many of the plasticizer and stabilizer compounds were removed from the o-rings regardless of the contact fuel. Fuel molecules were observed to migrate into the o-rings for the petroleum-derived fuel as did both the fuel and additive for a synthetic F-T jet fuel additized with benzyl alcohol, but less for the unadditized synthetic fuel. The specific compounds or classes of compounds involved in the partitioning were identified and a semiquantitative comparison of relative partitioning of the compounds of interest was made, The results provide another step forward in improving the confidence level of using additized, fully synthetic jet fuel in the place of petroleum-derived fuel.

  15. Targeting diverse protein-protein interaction interfaces with ?/?-peptides derived from the Z-domain scaffold.

    PubMed

    Checco, James W; Kreitler, Dale F; Thomas, Nicole C; Belair, David G; Rettko, Nicholas J; Murphy, William L; Forest, Katrina T; Gellman, Samuel H

    2015-04-14

    Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. Here, we describe a strategy for designing oligomers containing both ?- and ?-amino acid residues ("?/?-peptides") that mimic several peptides derived from the three-helix bundle "Z-domain" scaffold. We show that ?/?-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding ?/?-peptide inhibits the VEGF165-induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain-mimetic ?/?-peptides that bind to two other protein partners, IgG and tumor necrosis factor-?. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable ?/?-peptides that bind tightly and specifically to diverse targets of biomedical interest. Such reagents would be useful for diagnostic and therapeutic applications. PMID:25825775

  16. 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.

  17. 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.

  18. Novel insights into host-fungal pathogen interactions derived from live-cell imaging.

    PubMed

    Bain, Judith; Gow, Neil A R; Erwig, Lars-Peter

    2015-03-01

    The theoretical physicist and Nobel laureate Richard Feynman outlined in his 1959 lecture, "There's plenty of room at the bottom", the enormous possibility of producing and visualising things at smaller scales. The advent of advanced scanning and transmission electron microscopy and high-resolution microscopy has begun to open the door to visualise host-pathogen interactions at smaller scales, and spinning disc confocal and two-photon microscopy has improved our ability to study these events in real time in three dimensions. The aim of this review is to illustrate some of the advances in understanding host-fungal interactions that have been made in recent years in particular those relating to the interactions of live fungal pathogens with phagocytes. Dynamic imaging of host-pathogen interactions has recently revealed novel detail and unsuspected mechanistic insights, facilitating the dissection of the phagocytic process into its component parts. Here, we will highlight advances in our knowledge of host-fungal pathogen interactions, including the specific effects of fungal cell viability, cell wall composition and morphogenesis on the phagocytic process and try to define the relative contributions of neutrophils and macrophages to the clearance of fungal pathogens in vitro and the infected host. PMID:25398200

  19. 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.

  20. 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

  1. 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

  2. Quantitative analysis of the interaction between l-methionine derivative and oligonucleotides.

    PubMed

    Mota, lia; Sousa, Fani; Queiroz, Joo A; Cruz, Carla

    2015-04-01

    This study explores the use of l-methionine derivative as a potential affinity ligand for nucleic acids purification. The l-methionine derivative is synthesized by activation of the carboxylic acid group with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide follow by immobilization on amine sensor surface, previously activated and treated with ethylenediamine. Their affinity towards oligonucleotides has been determined by surface plasmon resonance biosensor. The highest affinity is found for cytosine and thymine, followed by adenine, whereas the lowest affinity is found for guanine. For hetero-oligonucleotides the affinity order is CCCTTT > CCCAAA ? AAATTT > GGGTTT, showing that nucleotides with cytosine have the highest affinity, and the presence of guanine reduces the affinity, corroborating with the results obtained with homo-oligonucleotides. PMID:25425656

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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…

  8. 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.

  9. 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

  10. 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.

  11. 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, Bjrn; Moene, Arnold F.; van Dinther, Danille; 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.

  12. 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.

  13. 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.

  14. 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 matrixand 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.

  15. nd Scattering Observables Derived from the Quark-Model Baryon-Baryon Interaction

    SciTech Connect

    Fujiwara, Y.; Fukukawa, K.

    2010-05-12

    We solve the nd scattering in the Faddeev formalism, employing the NN sector of the quark-model baryon-baryon interaction fss2. The energy-dependence of the NN interaction, inherent to the (3q)-(3q) resonating-group formulation, is eliminated by the standard off-shell transformation utilizing the 1/sq root(N) factor, where N is the normalization kernel for the (3q)-(3q) system. This procedure yields an extra nonlocality, whose effect is very important to reproduce all the scattering observables below E{sub n}<=65 MeV. The different off-shell properties from the standard meson-exchange potentials, related to the non-locality of the quark-exchange kernel, yields appreciable effects to the differential cross sections and polarization observables of the nd elastic scattering, which are usually attributed to the specific properties of three-body forces.

  16. 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.

  17. The 27-28 October 1986 FIRE IFO cirrus case study: Cirrus parameter relationships derived from satellite and lidar data

    NASA Technical Reports Server (NTRS)

    Minnis, Patrick; Young, David F.; Sassen, Kenneth; Alvarez, Joseph M.; Grund, Christian J.

    1989-01-01

    Cirrus cloud radiative and physical characteristics are determined using a combination of ground-based, aircraft, and satellite measurements taken as part of the First ISCCP Regional Experiment (FIRE) Cirrus Intensive Field Observations (IFO) during October and November 1986. Lidar backscatter data are used to define cloud base, center, and top heights and the corresponding temperatures. Coincident GOES 4 km visible (0.65 microns) and 8 km infrared window (11.5 microns) radiances are analyzed to determine cloud emittances and reflectances. Infrared optical depth is computed from the emittance results. Visible optical depth is derived from reflectance using a theoretical ice crystal scattering model and an empirical bidirectional reflectance mode. No clouds with visible optical depths greater than 5 or infrared optical depths less than 0.1 were used in the analysis. Average cloud thickness ranged from 0.5 km to 8 km for the 71 scenes. An average visible scattering efficiency of 2.1 was found for this data set. The results reveal a significant dependence of scattering efficiency on cloud temperature.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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

  3. Genome-wide genetic interaction analysis of glaucoma using expert knowledge derived from human phenotype networks.

    PubMed

    Hu, Ting; Darabos, Christian; Cricco, Maria E; Kong, Emily; Moore, Jason H

    2015-01-01

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

  4. Interactions of Anopheles gambiae Odorant-binding Proteins with a Human-derived Repellent

    PubMed Central

    Murphy, Emma J.; Booth, Jamie C.; Davrazou, Foteini; Port, Alex M.; Jones, David N. M.

    2013-01-01

    The Anopheles gambiae mosquito, which is the vector for Plasmodium falciparum malaria, uses a series of olfactory cues emanating from human sweat to select humans as their source for a blood meal. Perception of these odors within the mosquito olfactory system involves the interplay of odorant-binding proteins (OBPs) and odorant receptors and disrupting the normal responses to those odorants that guide mosquito-human interactions represents an attractive approach to prevent the transmission of malaria. Previously, it has been shown that DEET targets multiple components of the olfactory system, including OBPs and odorant receptors. Here, we present the crystal structure of A. gambiae OBP1 (OBP1) in the complex it forms with a natural repellent 6-methyl-5-heptene-2-one (6-MH). We find that 6-MH binds to OBP1 at exactly the same site as DEET. However, key interactions with a highly conserved water molecule that are proposed to be important for DEET binding are not involved in binding of 6-MH. We show that 6-MH and DEET can compete for the binding of attractive odorants and in doing so disrupt the interaction that OBP1 makes with OBP4. We further show that 6-MH and DEET can bind simultaneously to OBPs with other ligands. These results suggest that the successful discovery of novel reagents targeting OBP function requires knowledge about the specific mechanism of binding to the OBP rather than their binding affinity. PMID:23261834

  5. 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".

  6. 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.

  7. Early Epidemic Dynamics of the West African 2014 Ebola Outbreak: Estimates Derived with a Simple Two-Parameter Model

    PubMed Central

    Fisman, David; Khoo, Edwin; Tuite, Ashleigh

    2014-01-01

    The 2014 West African Ebola virus outbreak, now more correctly referred to as an epidemic, is the largest ever to occur. As of August 28, 2014, concerns have been raised that control efforts, particularly in Liberia, have been ineffective, as reported case counts continue to increase. Limited data are available on the epidemiology of the outbreak. However, reported cumulative incidence data as well as death counts are available for Guinea, Sierra Leone, Liberia and Nigeria. We utilized a simple, two parameter mathematical model of epidemic growth and control, to characterize epidemic growth patterns in West Africa, to evaluate the degree to which the epidemic is being controlled, and to assess the potential implications of growth patterns for epidemic size. Models demonstrated good fits to data. Overall basic reproductive number (R0) for the epidemic was estimated to be between 1.6 and 2.0, consistent with prior outbreaks. However, we identified only weak evidence for the occurrence of epidemic control in West Africa as a whole, and essentially no evidence for control in Liberia (though slowing of growth was seen in Guinea and Sierra Leone). It is projected that small reductions in transmission would prevent tens of thousands of future infections. These findings suggest that there is an extraordinary need for improved control measures for the 2014 Ebola epidemic, especially in Liberia, if catastrophe is to be averted. PMID:25642358

  8. 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-cellmediated 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

  9. 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

  10. 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

  11. Synergistic interaction between endothelium-derived NO and prostacyclin in pulmonary artery: potential role for K+ATP channels

    PubMed Central

    Gambone, Linda M; Murray, Paul A; Flavahan, Nicholas A

    1997-01-01

    The aim of the present study was to assess interactions between nitric oxide (NO) and prostacyclin (PGI2) during endothelium-dependent relaxations evoked by bradykinin, calcium ionophore (A23187) and acetylcholine in canine isolated pulmonary artery. Relaxations to low concentrations of bradykinin and A23187 were abolished by combined inhibition of NO-synthase (by N?-nitro-L-arginine methyl ester L-NAME, 30??M) and cyclo-oxygenase (indomethacin, 10??M), suggesting mediation by NO and PGI2. The individual contributions of NO and PGI2 to the dilator responses were quantified by use of areas above the separate indomethacin-insensitive and L-NAME-insensitive components of the concentration-effect curves, respectively. Individually, NO and PGI2 accounted for only 535% and 169% of total bradykinin-induced relaxation, and 4610% and 209% of total A23187-induced relaxation, suggesting that NO and PGI2 acted synergistically to cause endothelium-dependent relaxation. Relaxation to low concentrations of acetylcholine was abolished by L-NAME but not affected by indomethacin, suggesting the response was mediated solely by NO with no interaction from PGI2. Glibenclamide (1??M), an inhibitor of ATP-sensitive potassium (K+ATP) channels, inhibited responses to bradykinin or A23187 but did not affect relaxations evoked by acetylcholine. Glibenclamide did not affect endothelium-independent relaxations to PGI2 or the NO-donor, 3-morpholinosydnonimine (SIN-1). With bradykinin, glibenclamide attenuated total relaxation by 498%, but did not alter the individual NO and PGI2-mediated components of the response. Glibenclamide abolished the synergistic interaction between endothelium-derived NO and PGI2. At high concentrations, bradykinin, A23187 or acetylcholine caused endothelium-dependent relaxation that was insensitive to L-NAME + indomethacin. With bradykinin or A23187, this component of relaxation was inhibited by glibenclamide, whereas with acetylcholine, glibenclamide had no effect. The synergistic interaction between endothelium-derived NO and PGI2 in canine pulmonary artery is mediated by activation of K+ATP channels, presumably by an endothelium-derived hyperpolarizing factor (EDHF). The pattern of endothelial dilator mediators and the presence of this synergistic interaction is dependent on the nature of the endothelial stimulus. PMID:9154337

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. Screening of the most relevant parameters for method development in ultra-high performance hydrophilic interaction chromatography.

    PubMed

    Periat, Aurlie; Debrus, Benjamin; Rudaz, Serge; Guillarme, Davy

    2013-03-22

    The goal of the present work was to provide some guidelines for method development in hydrophilic interaction chromatography (HILIC). For this purpose, a training set of 82 representative pharmaceutical compounds possessing diverse polarity and including acidic, basic and neutral properties was analyzed. All these drugs were injected on five short HILIC columns packed with sub-2?m particles and dedicated for UHPLC (ultra-high performance liquid chromatography) operation. Four different pH conditions ranging from pH 3 to 6 were tested at two ionic strengths (10 and 50mmol/L) and finally, the reference organic modifier in HILIC, namely acetonitrile was modified with small amounts of methanol or isopropanol. From these experiments and using multivariate data analysis, it is clear that the stationary phase was the most relevant parameters for tuning selectivity in HILIC, since the types of interactions (i.e. dipole-dipole, hydrogen bonding and ion exchange) with analytes strongly vary between columns. Among the selected phases, the diol phase was the less interesting one, in terms of selectivity and peak shape. The zwitterionic phase was attractive, as it allowed a better retention of acidic compounds. Finally, the bare silica phase was the most versatile HILIC column packed with sub-2?m particles in terms of retention, peak shape and selectivity. Mobile phase pH was the other important parameter to achieve an appropriate selectivity and retention, even if it remains always difficult to assess precisely the mobile phase pH, analyte pKa and silanols pKa, when working with more 70% acetonitrile. Finally, buffer ionic strength and organic modifier nature could be considered as secondary parameters for HILIC method development. In conclusion, screening four different columns packed with sub-2?m particles at two mobile phase pH, using a fast gradient seems to be a good generic approach for initial HILIC method development. The total time for such a screening was estimated at ?1h, including reequilibration. PMID:23411147

  17. 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

  18. Study on the interaction of amino phosphine ester derivatives with DNA by spectroscopy, modeling and calorimetry

    NASA Astrophysics Data System (ADS)

    Lu, Yan; Wang, Gongke; Tang, Wen; Hao, Xiaoxiao; Xu, Meihua; Li, Xiang

    2011-11-01

    The binding properties of amino phosphate ester derivatives, compound 1 and 2 with calf thymus DNA (CT-DNA) were investigated by UV spectra, fluorescence spectra, molecular modeling and isothermal titration calorimetry (ITC). The intrinsic binding constants Kb of compound 1 and 2 with CT-DNA were determined by fluorescence spectroscopy and ITC, respectively. The results indicated that the two compounds bind to CT-DNA with different binding affinity, which is in the order of compound 1 > compound 2. At the same time, fluorescence spectra suggested that the mechanism of the binding of the two compounds to CT-DNA is a static enhancing type. According to the ethidium bromide displacement experiments, UV spectra, molecular modeling and ITC studies, it can be concluded that compound 1 and 2 are intercalators that can slide into the G-C rich region of CT-DNA. Furthermore, ITC data showed that compound/DNA binding is enthalpy controlled.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. Real-time fluorescence polarization measurements: interaction of phospholipase A2 with a fluorescent lecithin derivative.

    PubMed

    Monti, J A; McBride, M R; Barker, S A; Linton, J L; Christian, S T

    1985-05-01

    We have modified an SLM 4800 fluorometer to allow continuous measurement of fluorescence polarization. The modifications included construction of simple mechanical and electronic accessories which allowed polarizer position to be program-controlled by an HP 9815 calculator. With these modifications we were able to follow the interaction of the fluorescent lipid analog 1-acyl-2-(N-4-nitrobenzo-2-oxa-1,3-diazole)-aminododecanoyl phosphatidylcholine (I) with Naja-naja venom phospholipase A2 (PLA2) (E.C.3.1.1.4). Upon addition of aliquots of PLA2 containing up to 85 ng protein to a cuvette containing 1-2 microM I, the total measured polarization decreased linearly with time for at least 1000 s. Concomitant analyses of equivalent incubation mixtures and analyses of the contents of the cuvette after incubation and collection of fluorescence data revealed time-dependent formation of N-4-nitrobenzo-2-oxa-1,3-diazole-aminododecanoic acid (II). The decrease in total measured polarization was accelerated by Ca2+ and inhibited by EDTA. These data suggest that PLA2 activity in Naja-naja venom can be measured rapidly at low concentrations of both enzyme (0.01 microgram protein) and substrate (1 microM). Since this technique can be used to collect polarization data over time intervals as short as 4 s, it should be possible to measure the early changes in polarization during the interaction of fluorescent probes with proteins or membranes. PMID:3924989

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

    NASA Astrophysics Data System (ADS)

    Friedl, Peter; Hppner, 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.

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

    SciTech Connect

    Chvetsov, Alexei V.

    2013-03-15

    Purpose: The main goal of this paper is to reconstruct a distribution of cell survival fractions from tumor-volume variation for a heterogeneous group of head and neck cancer patients and compare this distribution to the data from predictive assays. Methods: To characterize the tumor-volume variation during radiation therapy treatment, the authors use a two-level tumor-volume model of cell population that separates the entire tumor cell population into two subpopulations of viable cells and lethally damaged cells. This parameterized radiobiological model is integrated with a least squares objective function and a simulated annealing optimization algorithm to describe time-dependent tumor-volume variation rates in individual patients. Several constraints have been used in the optimization problem because tumor-volume variation during radiotherapy is described by a sum of exponentials; therefore, the problem of accurately fitting a model to measured data is ill-posed. The model was applied to measured tumor-volume variation curves from a clinical study on tumor-volume variation during radiotherapy for 14 head and neck cancer patients in which an integrated CT/linear particle accelerator (LINAC) system was used for tumor-volume measurements. Results: The two-level cell population tumor-volume modeling is capable of describing tumor-volume variation throughout the entire treatment for 11 of the 14 patients. For three patients, the tumor-volume variation was described only during the initial part of treatment, a fact that may be related to the neglected hypoxia in the two-level approximation. The predicted probability density distribution for the survival fractions agrees with the data obtained using in vitro studies with predictive assays. The mean value 0.35 of survival fraction obtained in this study is larger than the value 0.32 from in vitro studies, which could be expected because of greater repair in vivo. The mean half-life obtained in this study for the head-and-neck squamous cell carcinoma (SCC) is equal to 3.8 mean potential doubling times, which agrees with 4.0 mean potential doubling times obtained previously for lung SCC. Conclusions: The distribution of cell survival fractions obtained in this study support the hypothesis that the tumor-volume variation during radiotherapy treatment for head and neck cancer can be described by the two-level cell population tumor-volume model. This model can be used for in vivo evaluation of patient-specific radiobiological parameters that are needed for tumor-control probability evaluation.

  7. 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

  8. 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

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

    NASA Astrophysics Data System (ADS)

    Perfetto, E.; Stefanucci, G.

    2012-08-01

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

  10. Accuracy of Quantum Mechanically Derived Force-Fields Parameterized from Dispersion-Corrected DFT Data: The Benzene Dimer as a Prototype for Aromatic Interactions.

    PubMed

    Prampolini, Giacomo; Livotto, Paolo Roberto; Cacelli, Ivo

    2015-11-10

    A multilevel approach is presented to assess the ability of several popular dispersion corrected density functionals (M06-2X, CAM-B3LYP-D3, BLYP-D3, and B3LYP-D3) to reliably describe two-body interaction potential energy surfaces (IPESs). To this end, the automated Picky procedure ( Cacelli et al. J. Comput. Chem. 2012 , 33 , 1055 ) was exploited, which consists in parametrizing specific intermolecular force fields through an iterative approach, based on the comparison with quantum mechanical data. For each of the tested functionals, the resulting force field was employed in classical Monte Carlo and Molecular Dynamics simulations, performed on systems of up to 1000 molecules in ambient conditions, to calculate a number of condensed phase properties. The comparison of the resulting structural and dynamic properties with experimental data allows us to assess the quality of each IPES and, consequently, even the quality of the DFT functionals. The methodology is tested on the benzene dimer, commonly used as a benchmark molecule, a prototype of aromatic interactions. The best results were obtained with the CAM-B3LYP-D3 functional. Besides assessing the reliability of DFT functionals in describing aromatic IPESs, this work provides a further step toward a robust protocol for the derivation of sound force field parameters from quantum mechanical data. This method can be relevant in all those cases where standard force fields fail in giving accurate predictions. PMID:26574315

  11. Interface contributions to the spin-orbit interaction parameters of electrons at the (001) GaAs/AlGaAs interface

    NASA Astrophysics Data System (ADS)

    Devizorova, Zh. A.; Shchepetilnikov, A. V.; Nefyodov, Yu. A.; Volkov, V. A.; Kukushkin, I. V.

    2014-09-01

    One-body mechanisms of spin splitting of the energy spectrum of 2D electrons in a one-side doped (001) GaAs/Al x Ga1 - x As quantum well have been studied theoretically and experimentally. The interfacial spin splitting has been shown to compensate (enhance) considerably the contribution of the bulk Dresselhaus (Bychkov-Rashba) mechanism. The theoretical approach is based on the solution of the effective mass equation in a quasi-triangular well supplemented by a new boundary condition at a high and atomically sharp hetero-barrier. The model takes into account the spin-orbit interaction of electrons with both bulk and interfacial crystal potential having C 2 v symmetry, as well as the lack of inversion symmetry and nonparabolicity of the conduction band in GaAs. The effective 2D spin Hamiltonian including both bulk and interface contributions to the Dresselhaus (?BIA) and Rashba (?SIA) constants has been derived. The analytical relation between these constants and the components of the anisotropic nonlinear g-factor tensor in an oblique quantizing magnetic field has been found. The experimental approach is based, on one hand, on the detection of electron spin resonance in the microwave range and, on the other hand, on photoluminescence measurements of the nonparabolicity parameter. The interface contributions to ?BIA and ?SIA have been found from comparison with the theory.

  12. 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 ?4 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 ?4 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 ?4 as well as of other proteins and peptides. PMID:24732115

  13. 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.

  14. TRADES: A new software to derive orbital parameters from observed transit times and radial velocities. Revisiting Kepler-11 and Kepler-9

    NASA Astrophysics Data System (ADS)

    Borsato, L.; Marzari, F.; Nascimbeni, V.; Piotto, G.; Granata, V.; Bedin, L. R.; Malavolta, L.

    2014-11-01

    Aims: With the purpose of determining the orbital parameters of exoplanetary systems from observational data, we have developed a software, named TRADES (TRAnsits and Dynamics of Exoplanetary Systems), to simultaneously fit observed radial velocities and transit times data. Methods: We implemented a dynamical simulator for N-body systems, which also fits the available data during the orbital integration and determines the best combination of the orbital parameters using grid search, ?2 minimization, genetic algorithms, particle swarm optimization, and bootstrap analysis. Results: To validate TRADES, we tested the code on a synthetic three-body system and on two real systems discovered by the Kepler mission: Kepler-9 and Kepler-11. These systems are good benchmarks to test multiple exoplanet systems showing transit time variations (TTVs) due to the gravitational interaction among planets. We have found that orbital parameters of Kepler-11 planets agree well with the values proposed in the discovery paper and with a a recent work from the same authors. We analyzed the first three quarters of Kepler-9 system and found parameters in partial agreement with discovery paper. Analyzing transit times (T0s), covering 12 quarters of Kepler data, that we have found a new best-fit solution. This solution outputs masses that are about 55% of the values proposed in the discovery paper; this leads to a reduced semi-amplitude of the radial velocities of about 12.80 ms-1.

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

    PubMed Central

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

    1996-01-01

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

  16. 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

  17. 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

  18. Influence of gold(I) complexes involving adenine derivatives on major drug-drug interaction pathway.

    PubMed

    Dvo?k, Zden?k; Novotn, Aneta; Van?o, Jn; Trvn?ek, Zden?k

    2013-12-01

    A series of considerably anti-inflammatory active gold(I) mixed-ligand complexes, involving the benzyl-substituted derivatives of N6-benzyladenine (HLn) and triphenylphosphine (PPh3) as ligands and having the general formula [Au(Ln)(PPh3)]xH2O (1-4; n=1-4 and x=0-1), was evaluated for the ability to influence the expression of CYP1A1/2 and CYP3A4 and transcriptional activity of glucocorticoid (GR) and aryl hydrocarbon (AhR) receptors in primary human hepatocytes and HepG2 cells. In both tests, evaluating the ability of the complexes to modulate the expression of CYP1A1, CYP1A2 and CYP3A4 in primary human hepatocytes and influence the transcriptional activity of AhR and GR in the reporter cell lines, no negative influence on the major drug-metabolizing cytochrome P450 isoenzymes and their signaling pathway (through GR and AhR receptors) was observed. These positive findings revealed another substantial evidence that could lead to utilization of the complexes as effective and relatively safe drugs for the treatment of hard-to-treat inflammation-related diseases, such as rheumatoid arthritis, comparable or even better than clinically used gold-containing drug Auranofin. PMID:24157406

  19. 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

  20. 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

  1. 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

  2. Interaction of artesunate with ?-cyclodextrin: Characterization, thermodynamic parameters, molecular modeling, effect of PEG on complexation and antimalarial activity

    PubMed Central

    Chadha, Renu; Gupta, Sushma; Shukla, Geeta; Jain, D.V.S.; Pissurlenkar, Raghuvir R.S.; Coutinho, Evans C.

    2011-01-01

    Inclusion of artesunate in the cavity of ?-cyclodextrin (?-CD) as well as its methyl and hydroxypropyl derivatives was investigated experimentally and by molecular modeling studies. The effect of PEG on the inclusion was also studied. A 1:1 stoichiometry was indicated by phase-solubility studies both in the presence and absence of PEG and suggested by the mass spectrometry. The mode of inclusion was supported by 2D NMR and results were further verified by docking studies utilizing Fast Rigid Exhaustive Docking acronym. The thermodynamic parameters were determined for both binary and ternary systems using solution calorimetry and were found to be best for the methyl-?-cyclodextrin (Me-?-CD) system. However, the presence of PEG improves the complexation ability as evident from elevation in the numerical value of the stability constant (K). Solubility and dissolution profile of binary complex is enhanced in the presence of PEG, which is approximately at par with drug Me-?-CD complexes. In vivo studies showed 100% survivability in artesunateMe-?-CD complexes. PMID:25755980

  3. The interaction of adipose-derived human mesenchymal stem cells and polyether ether ketone.

    PubMed

    Wang, Weiwei; Kratz, Karl; Behl, Marc; Yan, Wan; Liu, Yue; Xu, Xun; Baudis, Stefan; Li, Zhengdong; Kurtz, Andreas; Lendlein, Andreas; Ma, Nan

    2015-09-10

    Polyether ether ketone (PEEK) as a high-performance, thermoplastic implant material entered the field of medical applications due to its structural function and commercial availability. In bone tissue engineering, the combination of mesenchymal stem cells (MSCs) with PEEK implants may accelerate the bone formation and promote the osseointegration between the implant and the adjacent bone tissue. In this concept the question how PEEK influences the behaviour and functions of MSCs is of great interest. Here the cellular response of human adipose-derived MSCs to PEEK was evaluated and compared to tissue culture plate (TCP) as the reference material. Viability and morphology of cells were not altered when cultured on the PEEK film. The cells on PEEK presented a high proliferation activity in spite of a relatively lower initial cell adhesion rate. There was no significant difference on cell apoptosis and senescence between the cells on PEEK and TCP. The inflammatory cytokines and VEGF secreted by the cells on these two surfaces were at similar levels. The cells on PEEK showed up-regulated BMP2 and down-regulated BMP4 and BMP6 gene expression, whereas no conspicuous differences were observed in the committed osteoblast markers (BGLAP, COL1A1 and Runx2). With osteoinduction the cells on PEEK and TCP exhibited a similar osteogenic differentiation potential. Our results demonstrate the biofunctionality of PEEK for human MSC cultivation and differentiation. Its clinical benefits in bone tissue engineering may be achieved by combining MSCs with PEEK implants. These data may also provide useful information for further modification of PEEK with chemical or physical methods to regulate the cellular processes of MSCs and to consequently improve the efficacy of MSC-PEEK based therapies. PMID:26410880

  4. Food plant derived disease tolerance and resistance in a natural butterfly-plant-parasite interactions.

    PubMed

    Sternberg, Eleanore D; Lefvre, 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

  5. 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

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

    PubMed Central

    Pia-Vzquez, Carolina; Reyes-Lpez, Magda; Ortz-Estrada, Guillermo; de la Garza, Mireya; Serrano-Luna, Jess

    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. Cooperative interaction between metallosurfactants, derived from the [Ru(2,2'-bpy)3](2+) complex, and DNA.

    PubMed

    Lebrn, J A; Ostos, F J; Moy, M L; Lpez-Lpez, M; Carrasco, C J; Lpez-Cornejo, P

    2015-11-01

    With the idea of improving and advancing the design and preparation of new reagents based on cationic surfactants for gene therapy, two luminescent metallosurfactants derived from the [Ru(2,2'-bpy)3](2+) complex were synthesized. Their interaction with DNA and the effect they exert on the conformation of the polynucleotide were studied by using different techniques. The equilibrium binding constants, Kb, of the two surfactants to DNA were obtained at different molar ratios X=[surfactant]/[DNA]. The observed sigmoidal dependence of Kb on X confirms the cooperative character of the binding. After the addition of a determined surfactant concentration, the condensation of the polymer was observed. The amount of surfactant needed to produce this conformational change is lower for the double stranded surfactant than for the single chain surfactant due to a stronger hydrophobic interaction. The addition of ?-cyclodextrin molecules to the metallosurfactant/DNA solutions results in polynucleotide decompaction, which confirms the importance of the hydrophobic interactions in the condensation of the polynucleotide. Results also show the importance of choosing both a proper system to study and the most seeming measuring technique to use. It is demonstrated that, in some cases, the use of several techniques is desirable to obtain reliable and accurate results. PMID:26344065

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

  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. Experimental and theoretical electron-density study of three isoindole derivatives: topological and Hirshfeld surface analysis of weak intermolecular interactions.

    PubMed

    Ch?ci?ska, Lilianna; Grabowsky, Simon; Ma?ecka, Magdalena; Rybarczyk-Pirek, Agnieszka J; J?wiak, Andrzej; Paulmann, Carsten; Luger, Peter

    2011-12-01

    A combined experimental and theoretical study of three isoindole derivatives was made on the basis of a topological analysis of their electron-density distributions. Experimental electron densities were determined from high-resolution X-ray diffraction data sets measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using DFT methods at the B3LYP\\6-311++G(3df,3pd) level of approximation. Both experimental and theoretical models are in good agreement with each other. Since the analysed structures possess a variety of hydrogen-bonding interactions, weak intermolecular contacts of C-HC(?), C,N(?)C,N(?) and HH types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment. PMID:22101546

  11. 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.

  12. Measurement of the ?-asymmetry parameter of Cu67 in search for tensor-type currents in the weak interaction

    NASA Astrophysics Data System (ADS)

    Soti, G.; Wauters, F.; Breitenfeldt, M.; Finlay, P.; Herzog, P.; Knecht, A.; Kster, U.; Kraev, I. S.; Porobic, T.; Prashanth, P. N.; Towner, I. S.; Tramm, C.; Zkouck, D.; Severijns, N.

    2014-09-01

    Background: Precision measurements at low energy search for physics beyond the standard model in a way complementary to searches for new particles at colliders. In the weak sector the most general ?-decay Hamiltonian contains, besides vector and axial-vector terms, also scalar, tensor, and pseudoscalar terms. Current limits on the scalar and tensor coupling constants from neutron and nuclear ? decay are on the level of several percent. Purpose: Extracting new information on tensor coupling constants by measuring the ?-asymmetry parameter in the pure Gamow-Teller decay of Cu67, thereby testing the V-A structure of the weak interaction. Method: An iron sample foil into which the radioactive nuclei were implanted was cooled down to mK temperatures in a 3He-4He dilution refrigerator. An external magnetic field of 0.1 T, in combination with the internal hyperfine magnetic field, oriented the nuclei. The anisotropic ? radiation was observed with planar high-purity germanium detectors operating at a temperature of about 10 K. An on-line measurement of the ? asymmetry of Cu68 was performed as well for normalization purposes. Systematic effects were investigated using geant4 simulations. Results: The experimental value, =0.587(14), is in agreement with the standard model value of 0.5991(2) and is interpreted in terms of physics beyond the standard model. The limits obtained on possible tensor-type charged currents in the weak interaction Hamiltonian are -0.045<(CT+CT')/CA<0.159 (90% C.L.). Conclusions: The obtained limits are comparable to limits from other correlation measurements in nuclear ? decay and contribute to further constraining tensor coupling constants.

  13. Temporal variation and interaction of full size spectrum Alcian blue stainable materials and water quality parameters in a reservoir.

    PubMed

    Thuy, Nguyen Thi; Lin, Justin Chun-Te; Juang, Yaju; Huang, Chihpin

    2015-07-01

    This paper reports on the fate of different fractions of Alcian blue (AB) stainable material in Pao-Shan reservoir, Taiwan, in a one-year study (2013-2014) and an intensive study during phytoplankton bloom (2014). The interactions between the fractions, including AB stained particles, particle and colloidal transparent exopolymer particles (pTEP and cTEP), dissolved acid polysaccharide (dAPS), and their relationship to other water quality parameters were analyzed. The Flow Cytometer and Microscope (FlowCAM) was for first time used to characterize AB stained particles. The results of the one-year study likely showed relationships of pTEP concentration to phytoplankton count and chlorophyll a, while in the intensive study, AB stained particles abundance and pTEP concentration were correlated neither phytoplankton count nor chlorophyll a, but strongly positively correlated with some phytoplankton species' abundance. The difference indicates that sampling frequency and phytoplankton composition should be addressed for studying the links between AB stained fractions and phytoplankton. The interaction between different AB stained fractions further suggests that the majority of AB stained particles and pTEP would be directly generated by some phytoplankton species, whereas their abiotic generation by cTEP or dAPS may only have contributed partly to their formation. This differs from previous studies which generally posited that pTEP are mainly formed abiotically from dissolved precursors. Successful application of FlowCAM for visualization of AB stained particles recommends this technique by which particle morphologies can be conserved and morphological features of particle can be simultaneously elucidated. PMID:25835149

  14. Predicting forest structural parameters using the image texture derived from WorldView-2 multispectral imagery in a dryland forest, Israel

    NASA Astrophysics Data System (ADS)

    Ozdemir, Ibrahim; Karnieli, Arnon

    2011-10-01

    Estimation of forest structural parameters by field-based data collection methods is both expensive and time consuming. Satellite remote sensing is a low-cost alternative in modeling and mapping structural parameters in large forest areas. The current study investigates the potential of using WordView-2 multispectral satellite imagery for predicting forest structural parameters in a dryland plantation forest in Israel. The relationships between image texture features and the several structural parameters such as Number of Trees (NT), Basal Area (BA), Stem Volume (SV), Clark-Evans Index (CEI), Diameter Differentiation Index (DDI), Contagion Index (CI), Gini Coefficient (GC), and Standard Deviation of Diameters at Breast Heights (SDDBH) were examined using correlation analyses. These variables were obtained from 30 m 30 m square-shaped plots. The Standard Deviation of Gray Levels (SDGL) as a first order texture feature and the second order texture variables based on Gray Level Co-occurrence Matrix (GLCM) were calculated for the pixels that corresponds to field plots. The results of the correlation analysis indicate that the forest structural parameters are significantly correlated with the image texture features. The highest correlation coefficients were calculated for the relationships between the SDDBH and the contrast of red band ( r = 0.75, p < 0.01), the BA and the entropy of blue band ( r = 0.73, p < 0.01), and the GC and the contrast of blue band ( r = 0.71, p < 0.01). Each forest structural parameter was modeled as a function of texture measures derived from the satellite image using stepwise multi linear regression analyses. The determination coefficient ( R2) and root mean square error (RMSE) values of the best fitting models, respectively, are 0.38 and 109.56 ha -1 for the NT; 0.54 and 1.79 m 2 ha -1 for the BA; 0.42 and 27.18 m 3 ha -1 for the SV; 0.23 and 0.16 for the CEI; 0.32 and 0.05 for the DDI; 0.25 and 0.06 for the CI; 0.50 and 0.05 for the GC; and 0.67 and 0.70 for the SDDBH. The leave-one-out cross-validation technique was applied for validation of the best-fitted models ( R2 > 0.50). In conclusion, cross-validated statistics confirmed that the structural parameters including the BA, SDDBH, and GC can be predicted and mapped with a reasonable accuracy using the texture features extracted from the spectral bands of WorldView-2 image.

  15. Interaction of plasma-derived lipid transfer protein with macrophages in culture.

    PubMed

    Morton, R E

    1988-10-01

    This study investigates the ability of human plasma-derived lipid transfer protein to facilitate lipid transfer to and from intact viable cells in culture. Mouse peritoneal macrophages or J774 macrophages were preincubated with acetylated low density lipoprotein and [3H]oleate/albumin to promote the intracellular synthesis and accumulation of cholesteryl [3H]oleate and 3H-labeled triglyceride. The addition of partially purified lipid transfer protein to cultures of lipid-loaded macrophages resulted in a time and concentration-dependent transfer of radiolabeled cholesteryl ester and triglyceride from macrophages to the medium. At 48 hr, lipid transfer protein facilitated the net transfer of 16 and 11% of cellular cholesteryl ester and triglyceride radioactivity, respectively, to the medium; transfer in the absence of the lipid transfer protein was less than 2%. The transfer of cholesteryl ester radioactivity was accompanied by a similar decrease in cellular cholesteryl ester mass indicating a net transfer event. Lipid transfer from cells was not dependent on the presence of a lipoprotein acceptor in the medium; however, low and high density lipoproteins present at 200 micrograms cholesterol/ml did significantly stimulate the transfer protein-facilitated efflux of these lipids. Lipid transfer protein did not appear capable of transferring radiolabeled lipid from low density or high density lipoprotein to macrophages. Radiolabeled cholesteryl ester and triglyceride transferred from cells to the medium by lipid transfer protein were associated with large molecular weight (greater than 2 x 10(6)) components in the medium with an average density greater than 1.21 g/ml; these lipids were not associated with lipid transfer protein itself. However, these radiolabeled lipids were readily incorporated into low or high density lipoproteins when these lipoproteins were added to the medium either during or after its incubation with cells. It is concluded that lipid transfer protein can facilitate the net efflux of cholesteryl esters from intact, living macrophages. These studies suggest a novel and potentially antiatherogenic role for lipid transfer protein. PMID:3235919

  16. 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).

  17. Cost-effective health services for interactive continuous monitoring of vital signs parameters--the e-Vital concept.

    PubMed

    Prentza, Andriana; Angelidis, Pantelis; Leondaridis, Lefteris; Koutsouris, Dimitris

    2004-01-01

    The objective of the e-Vital project is the validation of the market concerning the provision of a novel remote telemedicine service aimed at large sensitive parts of the European population, the "at-risk" citizens, who are usually patients with a stable medical condition that allow a near normal life but may suddenly deteriorate and put life at risk. This service will increase their quality of life and their feeling of safety concerning their health. The e-Vital project focuses on the implementation and exploitation of a modular and ambulatory secure telemedicine platform, which is using easily wearable vital signs monitoring devices, causing minimal discomfort to patients, and which transfer in real time and on-line critical vital parameters to doctors and/or medical experts/consultants, regardless of their location, while getting feedback to increase their feeling of comfort or in case of alarm. The interactive continuous monitoring promises cost effective health services, more active involvement of patients in their own care, and a new sense of realism in making a diagnosis. PMID:15747940

  18. Relationship between diffusion parameters derived from intravoxel incoherent motion MRI and perfusion measured by dynamic contrast-enhanced MRI of soft tissue tumors.

    PubMed

    Marzi, Simona; Stefanetti, Linda; Sperati, Francesca; Anelli, Vincenzo

    2016-01-01

    Our aim was to evaluate the link between diffusion parameters measured by intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) and the perfusion metrics obtained with dynamic contrast-enhanced (DCE) MRI in soft tissue tumors (STTs). Twenty-eight patients affected by histopathologically confirmed STT were included in a prospective study. All patients underwent both DCE MRI and IVIM DWI. The perfusion fraction f, diffusion coefficient D and perfusion-related diffusion coefficient D* were estimated using a bi-exponential function to fit the DWI data. DCE MRI was acquired with a temporal resolution of 3-5?s. Maps of the initial area under the gadolinium concentration curve (IAUGC), time to peak (TTP) and maximum slope of increase (MSI) were derived using commercial software. The relationships between the DCE MRI and IVIM DWI measurements were assessed by Spearman's test. To exclude false positive results under multiple testing, the false discovery rate (FDR) procedure was applied. The Mann-Whitney test was used to evaluate the differences between all variables in patients with non-myxoid and myxoid STT. No significant relationship was found between IVIM parameters and any DCE MRI parameters. Higher f and D*f values were found in non-myxoid tumors compared with myxoid tumors (p?=?0.004 and p?=?0.003, respectively). MSI was significantly higher in non-myxoid tumors than in myxoid tumors (p?=?0.029). From the visual assessments of single clinical cases, both f and D*f maps were in satisfactory agreement with DCE maps in the extreme cases of an avascular mass and a highly vascularized mass, whereas, for tumors with slight vascularity or with a highly heterogeneous perfusion pattern, this association was not straightforward. Although IVIM DWI was demonstrated to be feasible in STT, our data did not support evident relationships between perfusion-related IVIM parameters and perfusion measured by DCE MRI. Copyright 2015 John Wiley & Sons, Ltd. PMID:26602061

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

    PubMed

    Kami?ski, Rados?aw; Domaga?a, S?awomir; Jarzembska, Katarzyna N; Hoser, Anna A; Sanjuan-Szklarz, W Fabiola; Gutmann, Matthias J; Makal, Anna; Mali?ska, Maura; B?k, Joanna M; Wo?niak, 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 ?-oxalic acid dihydrate (C2H2O42H2O) 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)? (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?(-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

  20. 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.

  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. 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

  3. 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

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

    SciTech Connect

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

    2009-06-01

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

  5. Chemical interaction of atmospheric mineral dust-derived nanoparticles with natural seawater--EPS and sunlight-mediated changes.

    PubMed

    Kadar, Enik; Cunliffe, Michael; Fisher, Andrew; Stolpe, Bjrn; Lead, Jamie; Shi, Zongbo

    2014-01-15

    Laboratory studies were conducted to investigate the interactions of nanoparticles (NPs) formed via simulated cloud processing of mineral dust with seawater under environmentally relevant conditions. The effect of sunlight and the presence of exopolymeric substances (EPS) were assessed on the: (1) colloidal stability of the nanoparticle aggregates (i.e. size distribution, zeta potential, polydispersity); (2) micromorphology and (3) Fe dissolution from particles. We have demonstrated that: (i) synthetic nano-ferrihydrite has distinct aggregation behaviour from NPs formed from mineral dusts in that the average hydrodynamic diameter remained unaltered upon dispersion in seawater (~1500 nm), whilst all dust derived NPs increased about three fold in aggregate size; (ii) relatively stable and monodisperse aggregates of NPs formed during simulated cloud processing of mineral dust become more polydisperse and unstable in contact with seawater; (iii) EPS forms stable aggregates with both the ferrihydrite and the dust derived NPs whose hydrodynamic diameter remains unchanged in seawater over 24h; (iv) dissolved Fe concentration from NPs, measured here as <3 kDa filter-fraction, is consistently >30% higher in seawater in the presence of EPS and the effect is even more pronounced in the absence of light; (v) micromorphology of nanoparticles from mineral dusts closely resemble that of synthetic ferrihydrite in MQ water, but in seawater with EPS they form less compact aggregates, highly variable in size, possibly due to EPS-mediated steric and electrostatic interactions. The larger scale implications on real systems of the EPS solubilising effect on Fe and other metals with the additional enhancement of colloidal stability of the resulting aggregates are discussed. PMID:24035844

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

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

    PubMed

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

    2015-05-01

    The interaction between anionic algal polysaccharides ((?)-, (?)-, (?)-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 (?)-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 ?-carrageenan was stronger than for other polysaccharides ((?)-, (?)-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

  13. Scientific objectives and derived system requirements of the European Space Agency's Earth Explorer Land-Surface Processes and Interactions Mission

    NASA Astrophysics Data System (ADS)

    Rast, Michael; Berger, Michael; Silvestrin, Pierluigi; Del Bello, Umberto

    1999-12-01

    The Earth Explorer Missions are research/demonstration missions for Earth Observation that are planned for implementation in the frame of the European Space Agency's 'Living Planet' Programme. The program focuses on advancing understanding of different processes that contribute to govern the Earth Systems. One of the four Earth Explorer Missions which was the subject of a Phase A study is the Land-Surface Processes and Interactions Mission (LSPIM). The scientific objectives are the study of land surface processes and their interactions with the atmosphere. It focuses on the measurement of surface characteristics such as albedo, reflectance, bidirectional reflectance distribution function (BRDF) and surface temperature, which are linked to the processes driving bio/geophysical and biochemical variables. To fulfil the mission requirements a hyperspectral imager is proposed as the LSPIM core instrument. The LSPIM imaging spectrometer will provide contiguous spectral coverage in 142 bands within the VIS/NIR/SWIR spectral region with spectral resolution between 10 and 15 nm. Furthermore, TIR observations will be performed by a radiometer in two wavebands. A spatial resolution of 50 m X 50 m with a swath width of 50 km at nadir will be provided. This mission will also have a de- pointing capability for BRDF observations along-track and areal access across-track such that each site of interest can be revisited at 3 days intervals. It is the purpose of this paper to outline the planned spaceborne mission, its scientific objectives and the derived system requirements.

  14. Interactions of histatin 5 and histatin 5-derived peptides with liposome membranes: surface effects, translocation and permeabilization.

    PubMed Central

    Den Hertog, Alice L; Wong Fong Sang, Harro W; Kraayenhof, Ruud; Bolscher, Jan G M; Van't Hof, Wim; Veerman, Enno C I; Nieuw Amerongen, Arie V

    2004-01-01

    A number of cationic antimicrobial peptides, among which are histatin 5 and the derived peptides dhvar4 and dhvar5, enter their target cells and interact with internal organelles. There still are questions about the mechanisms by which antimicrobial peptides translocate across the membrane. We used a liposome model to study membrane binding, translocation and membrane-perturbing capacities of histatin 5, dhvar4 and dhvar5. Despite the differences in amphipathic characters of these peptides, they bound equally well to liposomes, whereas their membrane activities differed remarkably: dhvar4 translocated at the fastest rate, followed by dhvar5, whereas the histatin 5 translocation rate was much lower. The same pattern was seen for the extent of calcein release: highest with dhvar4, less with dhvar5 and almost none with histatin 5. The translocation and disruptive actions of dhvar5 did not seem to be coupled, because translocation occurred on a much longer timescale than calcein release, which ended within a few minutes. We conclude that peptide translocation can occur through peptide-phospholipid interactions, and that this is a possible mechanism by which antimicrobial peptides enter cells. However, the translocation rate was much lower in this model membrane system than that seen in yeast cells. Thus it is likely that, at least for some peptides, additional features promoting the translocation across biological membranes are involved as well. PMID:14733612

  15. NMR characterization of the interaction between the C-terminal domain of interferon-? and heparin-derived oligosaccharides

    PubMed Central

    Vanhaverbeke, Ccile; Simorre, Jean-Pierre; Sadir, Rabia; Gans, Pierre; Lortat-Jacob, Hugues

    2004-01-01

    Interferons are cytokines that play a complex role in the resistance of mammalian hosts to pathogens. IFN? (interferon-?) is secreted by activated T-cells and natural killer cells. IFN? is involved in a wide range of physiological processes, including antiviral activity, immune response, cell proliferation and apoptosis, as well as the stimulation and repression of a variety of genes. IFN? activity is modulated by the binding of its C-terminal domain to HS (heparan sulphate), a glycosaminoglycan found in the extracellular matrix and at the cell surface. In the present study, we analysed the interaction of isolated heparin-derived oligosaccharides with the C-terminal peptide of IFN? by NMR, in aqueous solution. We observed marked changes in the chemical shifts of both peptide and oligosaccharide compared with the free state. Our results provide evidence of a binding through electrostatic interactions between the charged side chains of the protein and the sulphate groups of heparin that does not induce specific conformation of the C-terminal part of IFN?. Our data also indicate that an oligosaccharide size of at least eight residues displays the most efficient binding. PMID:15270718

  16. Determination of pharmacological interactions of uliginosin B, a natural phloroglucinol derivative, with amitriptyline, clonidine and morphine by isobolographic analysis.

    PubMed

    Stolz, Eveline D; Mller, Liz G; Antonio, Camila B; da Costa, Paola F; von Poser, Gilsane L; Nol, Franois; Rates, Stela M K

    2014-10-15

    Uliginosin B is a natural phloroglucinol derivative, obtained from Hypericum species native to South America. Previous studies have shown that uliginosin B presents antidepressant-like and antinociceptive effects. Although its mechanism of action is still not completely elucidated, it is known that it involves the activation of monoaminergic neurotransmission. The aim of the current study was to further investigate the antinociceptive mechanism of action of uliginosin B by combining it with different drugs used for treating pain in clinical practice. The intraperitoneal administration of uliginosin B, morphine, amitriptyline and clonidine, alone or in mixture, produced a dose-dependent antinociceptive effect in the hot-plate assay in mice. The effect of the mixtures of drugs was studied using an adapted isobologram analysis at the effect level of 50% of the maximal effect observed. The analysis showed that the interactions between uliginosin B and morphine was synergistic, while the interactions between uliginosin B and amitriptyline or clonidine were additive. These findings point to uliginosin B as a potential adjuvant for pain pharmacotherapy, especially for opioid analgesia. PMID:25442277

  17. 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 molmol(-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

  18. 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

  19. 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.

  20. Change of the sign of superconducting intraband order parameters induced by interband pair hopping interaction in iron-based high-temperature superconductors

    NASA Astrophysics Data System (ADS)

    Ptok, Andrzej; Crivelli, Dawid; Jerzy Kapcia, Konrad

    2015-04-01

    Iron based superconductors are characterized by the {{s}+/- } gap symmetry, where the gap changes its sign between pockets of the Fermi surface. We discuss another sign change mechanism of the superconducting order parameter (OP)the interband Cooper pairs hopping interaction. In the minimal two-orbital model of iron based superconductors we show that this interaction can lead to a change of the sign of the intraband superconducting OP regardless of its symmetry.

  1. 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.

  2. 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

  3. Structural derivatives of pindolol: relationship between in vivo and in vitro potencies for their interaction with central beta-adrenergic receptors

    SciTech Connect

    Tejani-Butt, S.M.; Brunswick, D.J.

    1987-08-24

    Although (-)-/sup 125/I-iodopindolol (IPIN) can be used to label beta-adrenergic receptors in the central nervous system (CNS) in vivo, use of this ligand for receptor imaging studies in humans may be limited due to its relatively poor penetration into the CNS. A series of derivatives related to pindolol was therefore studied in an effort to determine the factors that might influence the penetration and interaction of these compounds with central beta-adrenergic receptors in vivo. Evaluation of the ability of these derivatives to displace the binding of IPIN in the brain upon systemic administration provides an assessment of whether the derivatives penetrate and interact with central beta-adrenergic receptors in vivo. Multiple regression analyses showed that the most important factor which influences the ability of the pindolol derivatives to penetrate into the brain and interact with beta-adrenergic receptors in vivo is the affinity of the derivatives for binding to beta-adrenergic receptors in vitro. Both lipophilicity and the molecular weights of the derivatives are important secondary factors which influence their in vivo potency. 15 references, 4 figures, 1 table.

  4. Characterisation of the interaction of neuropilin-1 with heparin and a heparan sulfate mimetic library of heparin-derived sugars

    PubMed Central

    Uniewicz, Katarzyna A.; Ori, Alessandro; Ahmed, Yassir A.; Yates, Edwin A.

    2014-01-01

    Background. Neuropilin-1 (NRP-1) is a multidomain membrane protein with soluble isoforms interacting with a complex network of other membrane receptors, their respective ligands and heparan sulfate (HS). It is involved in the development of vasculature, neural patterning, immunological responses and pathological angiogenesis. Methods. We have characterised the binding of a Fc fusion of rat NRP-1 (Fc rNRP-1) and of a soluble isoform, corresponding to the first four extracellular domains of human NRP-1, shNRP-1, using optical biosensor-based binding assays with a library of heparin derivatives. Selective labelling of lysines protected upon heparin binding allowed their identification by mass spectrometry. Results. Fc rNRP-1 bound to heparin with high affinity (2.5 nM) and fast ka (9.8 106 M?1s?1). Unusually, NRP-1 bound both highly sulfated and completely desulfated stretches of heparin and exhibited a complex pattern of preferences for chemically modified heparins possessing one or two sulfate groups, e.g., it bound heparin with just a 6-O sulfate group better than heparin with any two of N-sulfate, 6-O sulfate and 2-O sulfate. Mass-spectrometry based mapping identified that, in addition to the expected the b1 domain, the a1, and c domains and the L2 linker were also involved in the interaction. In contrast, shNRP-1 bound heparin far more weakly. This could only be shown by affinity chromatography and by differential scanning fluorimetry. Discussion. The results suggest that the interaction of NRP-1 with HS is more complex than anticipated and involving a far greater extent of the protein than just the b1b2 domains. NRP-1s preference for binding long saccharide structures suggests it has the potential to bind large segments of HS chains and so organise their local structure. In contrast, the four domain soluble isoform, shNRP-1 binds heparin weakly and so would be expected to diffuse away rapidly from the source cell. PMID:25024924

  5. 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. Sarkisyan, Physica E 28 (2005) 423-430. Yu.N. Demkov, J.D. Meyer, Eur. Phys. J. B 42 (2004) 361-365. P.M. Krassovitskiy, N.Zh. Takibaev, Bull. Russian Acad. Sci. Phys. 70 (2006) 815-818. V.S. Melezhik, J.I. Kim, P. Schmelcher, Phys. Rev. A 76 (2007) 053611-1-15. F.M. Pen'kov, Phys. Rev. A 62 (2000) 044701-1-4. M. Born, X. Huang, Dynamical Theory of Crystal Lattices, The Clarendon Press, Oxford, England, 1954. L.V. Kantorovich, V.I. Krylov, Approximate Methods of Higher Analysis, Wiley, New York, 1964. U. Fano, Colloq. Int. C.N.R.S. 273 (1977) 127;A.F. Starace, G.L. Webster, Phys. Rev. A 19 (1979) 1629-1640. C.V. Clark, K.T. Lu, A.F. Starace, in: H.G. Beyer, H. Kleinpoppen (eds.), Progress in Atomic Spectroscopy, Part C, Plenum, New York, 1984, pp. 247-320. O. Chuluunbaatar, A.A. Gusev, V.L. Derbov, M.S. Kaschiev, L.A. Melnikov, V.V. Serov, S.I. Vinitsky, J. Phys. A 40 (2007) 11485-11524. A.G. Abrashkevich, D.G. Abrashkevich, M.S. Kaschiev, I.V. Puzynin, Comput. Phys. Comm. 85 (1995) 40-64. K.J. Bathe, Finite Element Procedures in Engineering Analysis, Englewood Cliffs, Prentice-Hall, New York, 1982. O. Chuluunbaatar, A.A. Gusev, M.S. Kaschiev, V.A. Kaschieva, A. Amaya-Tapia, S.Y. Larsen, S.I. Vinitsky, J. Phys. B 39 (2006) 243-269. Yu.A. Kuperin, P.B. Kurasov, Yu.B. Melnikov, S.P. Merkuriev, Ann. Phys. 205 (1991) 330-361. O. Chuluunbaatar, A.A. Gusev, V.P. Gerdt, V.A. Rostovtsev, S.I. Vinitsky, A.G. Abrashkevich, M.S. Kaschiev, V.V. Serov, Comput. Phys. Comm. 178 (2008) 301-330. A.G. Abrashkevich, M.S. Kaschiev, S.I. Vinitsky, J. Comp. Phys. 163 (2000) 328-348.

  6. Hepatoma-derived growth factor-related protein-3 interacts with microtubules and promotes neurite outgrowth in mouse cortical neurons.

    PubMed

    El-Tahir, Heba M; Abouzied, Mekky M; Gallitzendoerfer, Rainer; Gieselmann, Volkmar; Franken, Sebastian

    2009-04-24

    Hepatoma-derived growth factor-related proteins (HRP) comprise a family of 6 members, which the biological functions are still largely unclear. Here we show that during embryogenesis HRP-3 is strongly expressed in the developing nervous system. At early stages of development HRP-3 is located in the cytoplasm and neurites of cortical neurons. Upon maturation HRP-3 relocalizes continuously to the nuclei and in the majority of neurons of adult mice it is located exclusively in the nucleus. This redistribution from neurites to nuclei is also found in embryonic cortical neurons maturing in cell culture. We show that HRP-3 is necessary for proper neurite outgrowth in primary cortical neurons. To identify possible mechanisms of how HRP-3 modulate neuritogenesis we isolated HRP-3 interaction partners and demonstrate that it binds tubulin through the N-terminal so called HATH region, which is strongly conserved among members of the HRP family. It promotes tubulin polymerization, stabilizes and bundles microtubules. This activity depends on the extranuclear localization of HRP-3. HRP-3 thus could play an important role during neuronal development by its modulation of the neuronal cytoskeleton. PMID:19237540

  7. Interaction of platelet-derived autotaxin with tumor integrin ?V?3 controls metastasis of breast cancer cells to bone

    PubMed Central

    Leblanc, Raphael; Lee, Sue-Chin; David, Marion; Bordet, Jean-Claude; Norman, Derek D.; Patil, Renukadevi; Miller, Duane; Sahay, Debashish; Ribeiro, Johnny; Clzardin, Philippe; Tigyi, Gabor J.

    2014-01-01

    Autotaxin (ATX), through its lysophospholipase D activity controls physiological levels of lysophosphatidic acid (LPA) in blood. ATX is overexpressed in multiple types of cancers, and together with LPA generated during platelet activation promotes skeletal metastasis of breast cancer. However, the pathophysiological sequelae of regulated interactions between circulating LPA, ATX, and platelets remain undefined in cancer. In this study, we show that ATX is stored in ?-granules of resting human platelets and released upon tumor cell-induced platelet aggregation, leading to the production of LPA. Our in vitro and in vivo experiments using human breast cancer cells that do not express ATX (MDA-MB-231 and MDA-B02) demonstrate that nontumoral ATX controls the early stage of bone colonization by tumor cells. Moreover, expression of a dominant negative integrin ?v?3-?744 or treatment with the anti-human ?v?3 monoclonal antibody LM609, completely abolished binding of ATX to tumor cells, demonstrating the requirement of a fully active integrin ?v?3 in this process. The present results establish a new mechanism for platelet contribution to LPA-dependent metastasis of breast cancer cells, and demonstrate the therapeutic potential of disrupting the binding of nontumor-derived ATX with the tumor cells for the prevention of metastasis. PMID:25277122

  8. Profiling the interaction mechanism of quinoline/quinazoline derivatives as MCHR1 antagonists: an in silico method.

    PubMed

    Wu, Mingwei; Li, Yan; Fu, Xinmei; Wang, Jinghui; Zhang, Shuwei; Yang, Ling

    2014-01-01

    Melanin concentrating hormone receptor 1 (MCHR1), a crucial regulator of energy homeostasis involved in the control of feeding and energy metabolism, is a promising target for treatment of obesity. In the present work, the up-to-date largest set of 181 quinoline/quinazoline derivatives as MCHR1 antagonists was subjected to both ligand- and receptor-based three-dimensional quantitative structure-activity (3D-QSAR) analysis applying comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The optimal predictable CoMSIA model exhibited significant validity with the cross-validated correlation coefficient (Q²) = 0.509, non-cross-validated correlation coefficient (R²(ncv)) = 0.841 and the predicted correlation coefficient (R²(pred)) = 0.745. In addition, docking studies and molecular dynamics (MD) simulations were carried out for further elucidation of the binding modes of MCHR1 antagonists. MD simulations in both water and lipid bilayer systems were performed. We hope that the obtained models and information may help to provide an insight into the interaction mechanism of MCHR1 antagonists and facilitate the design and optimization of novel antagonists as anti-obesity agents. PMID:25257526

  9. Atrazine immobilization on sludge derived biochar and the interactive influence of coexisting Pb(II) or Cr(VI) ions.

    PubMed

    Zhang, Weihua; Zheng, Juan; Zheng, Pingping; Qiu, Rongliang

    2015-09-01

    Sludge derived biochars (SDBCs) may have the potential to simultaneously remove heavy metals and organic contaminants in relation to their various active sorption sites for both metal ions and organic compounds. SDBCs have been proven to provide a considerable capacity for immobilizing Pb(II) and Cr(VI) ions in solution, and in this study their ability to sorb atrazine, in addition to their corresponding interactive influences with coexisting metal ions, is extensively investigated. The results indicate that all atrazine adsorption isotherms fit well with the Freundlich equation, and the greatest value of 16.8 mg g(-1) sorption capacity occurred with SDBCs pyrolyzed at 400C for 2h. The slow sorption kinetics fit well with the Lagergren's 2nd order reaction, and depend upon the initial atrazine concentration, indicating the significance of a site-specific process. The ionic strength-dependence of the atrazine adsorption behavior further consolidates the involvement of the mechanism of the H-bond with hydroxyl groups on SDBC. However, when Pb(II)/Cr(VI) metal ions coexist in solution, they substantially suppress atrazine adsorption, probably because the inner complex between the hydroxyl groups on SDBCs and Pb(II)/Cr(III) ions intrude the weak H-bond with atrazine. As a result, metal adsorption was found to be unaffected by the coexisting atrazine. Therefore, although SDBC is applicable for atrazine removal/immobilization in most of environmentally relevant conditions, a two-step process may be required if heavy metal ions coexist. PMID:25989523

  10. Glycosaminoglycans in human retinoblastoma cells: Heparan sulfate, a modulator of the pigment epithelium-derived factor-receptor interactions

    PubMed Central

    Alberdi, Elena M; Weldon, John E; Becerra, S Patricia

    2003-01-01

    Background Pigment epithelium-derived factor (PEDF) has binding affinity for cell-surface receptors in retinoblastoma cells and for glycosaminoglycans. We investigated the effects of glycosaminoglycans on PEDF-receptor interactions. Results 125I-PEDF formed complexes with protease-resistant components of medium conditioned by human retinoblastoma Y-79 cells. Using specific glycosaminoglycan degrading enzymes in spectrophotometric assays and PEDF-affinity chromatography, we detected heparin and heparan sulfate-like glycosaminoglycans in the Y-79 conditioned media, which had binding affinity for PEDF. The Y-79 conditioned media significantly enhanced the binding of 125I-PEDF to Y-79 cell-surface receptors. However, enzymatic and chemical depletion of sulfated glycosaminoglycans from the Y-79 cell cultures by heparitinase and chlorate treatments decreased the degree of 125I-PEDF binding to cell-surface receptors. Conclusions These data indicate that retinoblastoma cells secrete heparin/heparan sulfate with binding affinity for PEDF, which may be important in efficient cell-surface receptor binding. PMID:12625842

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

    PubMed Central

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

    2009-01-01

    Dr adhesins are expressed on the surface of uropathogenic and diffusely adherent strains of Escherichia coli. The major adhesin subunit (DraE/AfaE) of these organelles mediates attachment of the bacterium to the surface of the host cell and possibly intracellular invasion through its recognition of the complement regulator decay-accelerating factor (DAF) and/or members of the carcinoembryonic antigen (CEA) family. The adhesin subunit of the Dr haemagglutinin, a Dr-family member, additionally binds type IV collagen and is inhibited in all its receptor interactions by the antibiotic chloramphenicol (CLM). In this study, previous structural work is built upon by reporting the X-ray structures of DraE bound to two chloramphenicol derivatives: chloramphenicol succinate (CLS) and bromamphenicol (BRM). The CLS structure demonstrates that acylation of the 3-hydroxyl group of CLM with succinyl does not significantly perturb the mode of binding, while the BRM structure implies that the binding pocket is able to accommodate bulkier substituents on the N-acyl group. It is concluded that modifications of the 3-hydroxyl group would generate a potent Dr haemagglutinin inhibitor that would not cause the toxic side effects that are associated with the normal bacteriostatic activity of CLM. PMID:19465765

  12. Interaction of the lymphocyte-derived Epstein-Barr virus nuclear antigen EBNA-1 with its DNA-binding sites.

    PubMed Central

    Jones, C H; Hayward, S D; Rawlins, D R

    1989-01-01

    The Epstein-Barr virus (EBV) nuclear antigen EBNA-1 plays an integral role in the maintenance of latency in EBV-infected B lymphocytes. EBNA-1 binds to sequences within the plasmid origin of replication (oriP). It is essential for the replication of the latent episomal form of EBV DNA and may also regulate the expression of the EBNA group of latency gene products. We have used sequence-specific DNA-binding assays to purify EBNA-1 away from nonspecific DNA-binding proteins in a B-lymphocyte cell extract. The availability of this eucaryotic protein has allowed an examination of the interaction of EBNA-1 with its specific DNA-binding sites and an evaluation of possible roles for the different binding loci within the EBV genome. DNA filter binding assays and DNase I footprinting experiments showed that the intact Raji EBNA-1 protein recognized the two binding site loci in oriP and the BamHI-Q locus and no other sites in the EBV genome. Competition filter binding experiments with monomer and multimer region I consensus binding sites indicated that cooperative interactions between binding sites have relatively little impact on EBNA-1 binding to region I. An analysis of the binding parameters of the Raji EBNA-1 to the three naturally occurring binding loci revealed that the affinity of EBNA-1 for the three loci differed. The affinity for the sites in region I of oriP was greater than the affinity for the dyad symmetry sites (region II) of oriP, while the physically distant region III locus showed the lowest affinity. This arrangement may provide a mechanism whereby EBNA-1 can lowest affinity. This arrangement may provide a mechanism whereby EBNA-1 can mediate differing regulatory functions through differential binding to its recognition sequence. Images PMID:2535719

  13. Photophysical and photochemical parameters of octakis (benzylthio) phthalocyaninato zinc, aluminium and tin: Red shift index concept in solvent effect on the ground state absorption of zinc phthalocyanine derivatives

    NASA Astrophysics Data System (ADS)

    Akpe, Victor; Brismar, Hjalmar; Nyokong, Tebello; Osadebe, P. O.

    2010-12-01

    This paper addresses the synthesis of octa-substituted benzylthio metallophthalocyanines (OBTMPcs) that contain the central metal ions of Zn 2+, Al 3+ and Sn 4+. The ground state absorption of ZnPc(SR) 8 (OBTZnPc) along with the ZnPc derivatives, well documented in literature were used to study a new concept called the red shift index ( R sI ). The concept is based on the empirical values of R sI of the different complexes in solvent media. Unequivocally, parameters used in this paper show strong correlations that are consistent with the results obtained. For instance, R sI of the complexes tend to increase as the refractive index, n D, and solvent donor, DN, of solvent increases. Photodegradation (photobleaching) quantum yield, ϕ d measurements of these compounds show that they are highly photostable, ϕ d (0.03-0.33 × 10 -5). The triplet quantum yield, ϕ T (0.40-0.53) and the triplet lifetime, τ T (610-810 μs) are within the typical range for metallophthalocyanines in DMSO. The photosensitisation efficiency, SΔ, is relatively high for all the molecules (0.74-0.90).

  14. A Process-based, Climate-Sensitive Model to Derive Methane Emissions from Natural Wetlands: Application to 5 Wetland Sites, Sensitivity to Model Parameters and Climate

    NASA Technical Reports Server (NTRS)

    Walter, Bernadette P.; Heimann, Martin

    1999-01-01

    Methane emissions from natural wetlands constitutes the largest methane source at present and depends highly on the climate. In order to investigate the response of methane emissions from natural wetlands to climate variations, a 1-dimensional process-based climate-sensitive model to derive methane emissions from natural wetlands is developed. In the model the processes leading to methane emission are simulated within a 1-dimensional soil column and the three different transport mechanisms diffusion, plant-mediated transport and ebullition are modeled explicitly. The model forcing consists of daily values of soil temperature, water table and Net Primary Productivity, and at permafrost sites the thaw depth is included. The methane model is tested using observational data obtained at 5 wetland sites located in North America, Europe and Central America, representing a large variety of environmental conditions. It can be shown that in most cases seasonal variations in methane emissions can be explained by the combined effect of changes in soil temperature and the position of the water table. Our results also show that a process-based approach is needed, because there is no simple relationship between these controlling factors and methane emissions that applies to a variety of wetland sites. The sensitivity of the model to the choice of key model parameters is tested and further sensitivity tests are performed to demonstrate how methane emissions from wetlands respond to climate variations.

  15. Tables and graphs of photon-interaction cross sections from 0. 1 keV to 100 MeV derived from the LLL evaluated-nuclear-data library

    SciTech Connect

    Plechaty, E.F.; Cullen, D.E.; Howerton, R.J.

    1981-11-11

    Energy-dependent evaluated photon interaction cross sections and related parameters are presented for elements H through Cf(Z = 1 to 98). Data are given over the energy range from 0.1 keV to 100 MeV. The related parameters include form factors and average energy deposits per collision (with and without fluorescence). Fluorescence information is given for all atomic shells that can emit a photon with a kinetic energy of 0.1 keV or more. In addition, the following macroscopic properties are given: total mean free path and energy deposit per centimeter. This information is derived from the Livermore Evaluated-Nuclear-Data Library (ENDL) as of October 1978.

  16. New insights into the mechanism of interaction between CO2 and polymers from thermodynamic parameters obtained by in situ ATR-FTIR spectroscopy.

    PubMed

    Gabrienko, Anton A; Ewing, Andrew V; Chibiryaev, Andrey M; Agafontsev, Alexander M; Dubkov, Konstantin A; Kazarian, Sergei G

    2016-03-01

    This work reports new physical insights of the thermodynamic parameters and mechanisms of possible interactions occurring in polymers subjected to high-pressure CO2. ATR-FTIR spectroscopy has been used in situ to determine the thermodynamic parameters of the intermolecular interactions between CO2 and different functional groups of the polymers capable of specific interactions with sorbed CO2 molecules. Based on the measured ATR-FTIR spectra of the polymer samples subjected to high-pressure CO2 (30 bar) at different temperatures (300-340 K), it was possible to characterize polymer-polymer and CO2-polymer interactions. Particularly, the enthalpy and entropy of the formation of the specific non-covalent complexes between CO2 and the hydroxy (-OH), carbonyl (C[double bond, length as m-dash]O) and hydroxyimino ([double bond, length as m-dash]N-OH) functional groups of the polymer samples have been measured. Furthermore, the obtained spectroscopic results have provided an opportunity for the structure of these complexes to be proposed. An interesting phenomenon regarding the behavior of CO2/polymer systems has also been observed. It has been found that only for the polyketone, the value of enthalpy was negative indicating an exothermic process during the formation of the CO2-polymer non-covalent complexes. Conversely, for the polyoxime and polyalcohol samples there is a positive enthalpy determined. This is a result of the initial polymer-polymer interactions requiring more energy to break than is released during the formation of the CO2-polymer complex. The effect of increasing temperature to facilitate the breaking of the polymer-polymer interactions has also been observed. Hence, a mechanism for the formation of CO2-polymer complexes was suggested based on these results, which occurs via a two-step process: (1) the breaking of the existing polymer-polymer interactions followed by (2) the formation of new CO2-polymer non-covalent interactions. PMID:26862594

  17. Trends and interactions of physical and bio-geo-chemical features in the Adriatic Sea as derived from satellite observations.

    PubMed

    Barale, Vittorio; Schiller, Christian; Tacchi, Ruggero; Marechal, Cecile

    2005-12-15

    Time series of satellite data, generated by the AVHRR (1981-1999), CZCS (1979-1985) and SeaWiFS (1998-2002), have been used to assess trends and interactions of physical and bio-geo-chemical features in the Adriatic Sea. The images were processed to estimate Sea Surface Temperature (SST) and Chlorophyll-like Pigment Concentration (CPC). Long-term composites and climatologies were derived, using fixed geographical grids and projections. The AVHRR data show an apparent warming trend, when plotting the sequence of seasonal cycles (monthly mean SST, averaged over the whole basin) against time, due to a steady rise of summer values. Considering 3 regions (north, central and south), split into east and west sections, the northern Adriatic shows high SST fluctuations (possibly associated with the cycle of winter cooling and summer warming, typical of the relatively shallow sub-basin), while the southern Adriatic exhibits a lower variability (possibly influenced by the periodic water incoming from, and outflowing to the Ionian Sea). During summer, an east-west gradient prevails, while during winter only a general north-south gradient can be found. The SeaWiFS-derived CPC values, distributions and trends appear to be consistent with the historical CZCS record. Persistent differences in the quantitative assessment of CPC for coastal waters is due to the use of improved algorithms, less influenced by the presence of dissolved organics and suspended sediments in the water column, for the processing of SeaWiFS data. Apparent incongruities of the space and time patterns in the SeaWiFS record with respect to the reference climatology, obtained by CZCS more than a decade before, occur chiefly when considering the spring bloom in the southern Adriatic and the summer development of the north Adriatic front. The comparison of the long-term times series of satellite data shows that there is a high correlation between patterns in the thermal field and in the colour field. This suggests that different surface waters, identified by the SST index, are also traced by different ecological features, identified by the CPC index. Both indices also show a high correlation with the classical cyclonic circulation scheme of the Adriatic Sea, proposing once again an intimate relationship between the water dynamics and its bio-geo-chemistry. PMID:16271746

  18. Derivation of Force field Parameters for SnO2-H2O Surface Systems from Plane-Wave Density Functional Theory Calculations

    SciTech Connect

    Wesolowski, David J; Bandura, Andrei V.; Sofo, Jorge O.; Kubicki, James D.

    2006-01-01

    Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO{sub 2} (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H{sub 2}O present. A classical interatomic force field has been developed to describe bulk SnO{sub 2} and SnO{sub 2}-H{sub 2}O surface interactions. Periodic density functional