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.

    2014-09-01

    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.

  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.

    2014-01-01

    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.

  4. 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.

  5. Deriving Protocol Specifications from Service Specifications Including Parameters

    E-print Network

    von Bochmann, Gregor

    Deriving Protocol Specifications from Service Specifications Including Parameters REINHARD GOTZHEIN and GREGOR VON BOCHMANN University of Montreal The service specification concept has acquired an increasing level of recognition by protocol designers. This architectural concept influences the methodology

  6. Photon Interaction Parameters for Some Borate Glasses

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Saffe, C.

    2011-04-01

    We implemented a Fortran code that determines fundamental parameters of solar type stars from a list of Fe line equivalent widths. The solution should verify three conditions in the standard method: ionization equilibrium, excitation equilibrium and independence between metallicity and equivalent widths. Solar-scaled Kurucz model atmospheres with NEWODF opacities are calculated with an independent program. Parameter files control different details, such as the mixing-length parameter and the overshooting. FUNDPAR derives the uncertainties following two methods: the criterion of Gonzalez & Vanture (1998) and the dispersion using the ?2 function. The code uses the 2009 version of the MOOG program. The results derived with FUNDPAR are in agreement with previous determinations in the literature. The program is freely available from the web.

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  11. Modeling Interactions of Erythromycin Derivatives with Ribosomes.

    PubMed

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

    2015-11-01

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

  12. 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.

  13. 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.

  14. CONFIGURATION INTERACTION ENERGY DERIVATIVES Jack Simons

    E-print Network

    Simons, Jack

    orbitaIs (as given by the MCSCF orbital response of J0rgensen) allows the variation of the CI orbital (ao) parameterization and orthonormalization proeessl allows for effieient treatment are in the moleeular orbital basis. The resulting expressions for geometrieal derivatives of the Hamiltonian eontain ao

  15. 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.

  16. 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.

  17. 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...

  18. 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.

  19. 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

  20. 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.

  1. Characterizing Tissue with Acoustic Parameters Derived from Ultrasound Data

    SciTech Connect

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

    2002-01-23

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

  2. Interactions of Arsenic and the Dissolved Substances Derived from

    E-print Network

    Florida, University of

    Interactions of Arsenic and the Dissolved Substances Derived from Turf Soils Z H A N G R O N G C H for the control of weeds in turf grasses at golf courses in Florida. There are concerns about arsenic (As for arsenic species (arsenite, AsIII and arsenate, AsV), dissolved organic matter, and additional constituents

  3. Structural and interaction parameters of thermosensitive native ?-elastin biohybrid microgel

    NASA Astrophysics Data System (ADS)

    Balaceanu, Andreea; Singh, Smriti; Demco, Dan E.; Möller, Martin

    2014-09-01

    The structural and water interaction parameters for native, ?-elastin biohybrid microgel crosslinked with hydrophilic and hydrophobic crosslinkers are obtained from the volume phase transition temperature behaviour, 1H high-resolution magic-angle sample spinning transverse magnetization relaxation NMR, and modified Flory-Rehner swelling theory. Firstly, considering a homogeneous morphology the number of subchains in the biohybrid microgel, the residual water in deswollen state as a function of crosslink density and the temperature dependence of the Flory biopolymer-water interaction parameters are reported for the biohybrid microgels prepared with hydrophilic (PEG-DGE) and hydrophobic (BS3) crosslinkers. The Flory-Rehner classical approach is subsequently modified taking into account the heterogeneities observed by NMR transverse relaxation measurements. Two differently mobile regions are determined, a hydrophobic domain and a crosslinking domain with relative reduced mobility. For the first time, the influence of chain mobility on the Flory interaction parameter is investigated through a modified Flory state equation. The contributions of amino-acids located in the hydrophobic and crosslinking domains in the polypeptide sequence are separated while analyzing the biopolymer-water interaction.

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

    NASA Technical Reports Server (NTRS)

    Mathur, Sanjay

    2011-01-01

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

  5. 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

  6. Bulk properties of light deformed nuclei derived from a medium-modified meson-exchange interaction

    E-print Network

    F. Gruemmer; B. Q. Chen; Z. Y. Ma; S. Krewald

    1996-09-06

    Deformed Hartree-Fock-Bogoliubov calculations for finite nuclei are carried out. As residual interaction, a Brueckner G-matrix derived from a meson-exchange potential is taken. Phenomenological medium modifications of the meson masses are introduced. The binding energies, radii, and deformation parameters of the Carbon, Oxygen, Neon, and Magnesium isotope chains are found to be in good agreement with the experimental data.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. On consistent kinetic and derivative interactions for gravitons

    NASA Astrophysics Data System (ADS)

    Noller, Johannes

    2015-04-01

    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.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  14. 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.

  15. Deriving physical parameters of unresolved star clusters. IV. The M 33 star cluster system

    NASA Astrophysics Data System (ADS)

    de Meulenaer, P.; Narbutis, D.; Mineikis, T.; Vansevi?ius, V.

    2015-09-01

    Context. When trying to derive the star cluster physical parameters of the M 33 galaxy using broad-band unresolved ground-based photometry, previous studies mainly made use of simple stellar population models, shown in the recent years to be oversimplified. Aims: In this study, we aim to derive the star cluster physical parameters (age, mass, and extinction; metallicity is assumed to be LMC-like for clusters with age below 1 Gyr and left free for older clusters) of this galaxy using models that take stochastic dispersion of cluster integrated colors into account. Methods: We use three recently published M 33 catalogs of cluster optical broad-band photometry in standard UBVRI and in CFHT/MegaCam u?g'r'i'z' photometric systems. We also use near-infrared JHK photometry that we derive from deep 2MASS images. We derive the cluster parameters using a method that takes into account the stochasticity problem, presented in previous papers of this series. Results: The derived differential age distribution of the M 33 cluster population is composed of a two-slope profile indicating that the number of clusters decreases when age gets older. The first slope is interpreted as the evolutionary fading phase of the cluster magnitudes, and the second slope as the cluster disruption. The threshold between these two phases occurs at ~300 Myr, comparable to what is observed in the M 31 galaxy. We also model by use of artificial clusters the ability of the cluster physical parameter derivation method to correctly derive the two-slope profile for different photometric systems tested. Figures 2, 5-8 are available in electronic form at http://www.aanda.org

  16. 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

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

    PubMed

    Gagné, 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?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

  18. Decadal changes in glacier parameters in the Cordillera Blanca, Peru, derived from remote sensing

    E-print Network

    Williams, Mark W.

    Decadal changes in glacier parameters in the Cordillera Blanca, Peru, derived from remote sensing´a Jiro´n Cahuide No. 175 ­ Jesu´s Mari´a, Lima 11, Peru ABSTRACT. We present spatial patterns of glacier fluctuations from the Cordillera Blanca, Peru, (glacier area, terminus elevations, median elevations

  19. 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.

  20. Spectroscopic interaction of a coumarin derivative with bovine serum albumin.

    PubMed

    Sindhu, Rajeev; Tiwari, Anjani K; Mishra, Lokesh C; Husain, M M

    2012-09-01

    The absorption and fluorescence spectra of the 7-diethylamino-4-methyl coumarin (DAMC) in ethanol-water (1:9 v/v) solution at varying pH values were investigated. The interaction between DAMC and bovine serum albumin (BSA) was investigated by fluorescence spectroscopy. The Stern-Volmer quenching constant, the quenching rate constant of the bimolecular reaction (kq), the binding constant, and number of binding sites are mentioned but not calculated in the paper. Moreover, in a preliminary pharmacological study, DAMC not only remarkably increased cellular apoptosis in a concentration-dependent manner but also clearly induced A549 cell cycle arrest. Thus, these coumarin derivatives merit investigation as novel potential antitumor agents with further structural modification to produce an optimal lead compound and elucidate the detailed pharmacological mechanism. PMID:22947088

  1. Fast derivation of soil surface roughness parameters using multi-band SAR imagery and the Integral Equation Model

    E-print Network

    Hamburg,.Universität

    radar cross section (NRCS) of dielectric sur- faces given surface and radar parameters. To derive of this model inversion to derive soil surface rough- ness parameters from synthetic aperture radar (SAR) remote parameters. The radar backscattering of soil surface is measured by the SAR sensors and depends on different

  2. Structural consequences of weak interactions in dispirooxindole derivatives.

    PubMed

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

    2015-11-01

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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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 ?=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

  8. 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

  9. 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.

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

    DOE PAGESBeta

    Stone, Daniel K.; Savannah River Site; 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

  11. Derivative-free optimization of rate parameters of capsid assembly models from bulk in vitro data

    E-print Network

    Xie, Lu; Schwartz, Russell

    2015-01-01

    The assembly of virus capsids from free coat proteins proceeds by a complicated cascade of association and dissociation steps, the great majority of which cannot be directly experimentally observed. This has made capsid assembly a rich field for computational models to attempt to fill the gaps in what is experimentally observable. Nonetheless, accurate simulation predictions depend on accurate models and there are substantial obstacles to model inference for such systems. Here, we describe progress in learning parameters for capsid assembly systems, particularly kinetic rate constants of coat-coat interactions, by computationally fitting simulations to experimental data. We previously developed an approach to learn rate parameters of coat-coat interactions by minimizing the deviation between real and simulated light scattering data monitoring bulk capsid assembly in vitro. This is a difficult data-fitting problem, however, because of the high computational cost of simulating assembly trajectories, the stochas...

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

    NASA Astrophysics Data System (ADS)

    Unal, B.; Askan, A.

    2014-12-01

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

  13. 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

  14. Cloud parameters derived from GOES during the 1987 marine stratocumulus FIRE Intensive Field Observation (IFO) period

    NASA Technical Reports Server (NTRS)

    Young, David F.; Minnis, Patrick; Harrison, Edwin F.

    1990-01-01

    The Geostationary Operational Environmental Satellite (GOES) is well suited for observations of the variations of clouds over many temporal and spatial scales. For this reason, GOES data taken during the Marine Stratocumulus Intensive Field Observations (IFO) (June 29 to July 19, 1987, Kloessel et al.) serve several purposes. One facet of the First ISCCP Regional Experiment (FIRE) is improvement of the understanding of cloud parameter retrievals from satellite-observed radiances. This involves comparisons of coincident satellite cloud parameters and high resolution data taken by various instruments on other platforms during the IFO periods. Another aspect of FIRE is the improvement of both large- and small-scale models of stratocumulus used in general circulation models (GCMs). This may involve, among other studies, linking the small-scale processes observed during the IFO to the variations in large-scale cloud fields observed with the satellites during the IFO and Extended Time Observation (ETO) periods. Preliminary results are presented of an analysis of GOES data covering most of the IFO period. The large scale cloud-field characteristics are derived, then related to a longer period of measurements. Finally, some point measurements taken from the surface are compared to regional scale cloud parameters derived from satellite radiances.

  15. 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.

  16. Cubic interaction parameters for t2g Wannier orbitals

    NASA Astrophysics Data System (ADS)

    Ribic, T.; Assmann, E.; Tóth, 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).

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

    E-print Network

    Peter K. Morse; Eric I. Corwin

    2015-08-24

    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.

  18. 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.

  19. New derivation of Born's law and parameter estimation based on a relative state formulation

    E-print Network

    Fuyuhiko Tanaka

    2009-07-26

    Excluding the concept of probability in quantum mechanics, we derive Born's law from the remaining postulates in quantum mechanics using type method. We also give a way of determining the unknown parameter in a state vector based on an indirect measurement model. While Deutsch adopt a concept of rational decision-maker who introduces probability, we adopt a concept of statistician in our measurement model and clarifies the distinguished feature of quantum measurement. Like many worlds interpretation, our scenario gives a simple solution for problem of measurement.

  20. PPN parameters in gravitational theory with non-minimally derivative coupling

    E-print Network

    Zhu, Yi

    2015-01-01

    The non-minimal coupling of the kinetic term to Einstein's tensor helps the implementation of inflationary models due to the gravitationally enhanced friction. We calculate the parameterized post-Newtonian parameters for the scalar-tensor theory of gravity with non-minimally derivative coupling. We find that under experiment constraint from the orbits of millisecond pulsars in our galaxy, the theory deviates from Einstein's general relativity in the order of $10^{-20}$, and the effect of the non-minimal coupling is negligible if we take the scalar field as dynamical dark energy. Under the assumed conditions, the scalar field is required to be massless.

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

    NASA Technical Reports Server (NTRS)

    Goetz, Alexander F. H.

    2000-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  5. Novel polypyrrole derivatives to enhance conductive polymer-tissue interactions

    E-print Network

    George, Paul M. (Paul Matthew)

    2005-01-01

    Developing materials that interact effectively with surrounding tissue is a major obstacle in sensor and drug delivery research. The body's natural immune response prevents foreign objects from easily integrating with an ...

  6. 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.

  7. Specific Recognition of p53 Tetramers by Peptides Derived from p53 Interacting Proteins

    E-print Network

    Lebendiker, Mario

    Specific Recognition of p53 Tetramers by Peptides Derived from p53 Interacting Proteins Ronen proteins, and in modulating their interactions. p53 is a homotetrameric transcription factor that has, which is a site for numerous protein-protein interactions. Those can either depend on or regulate p53

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

    SciTech Connect

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

    2014-07-28

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

  9. 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

  10. 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.

  11. 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.

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

    PubMed

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

    2013-01-01

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

  13. Some turbulence and diffusion parameter estimates within cooling tower plumes derived from sodar data

    SciTech Connect

    Coulter, R.L.; Underwood, K.H.

    1980-12-01

    Temperature and velocity fluctuations within a cooling tower plume in stable conditions at the Keystone power plant in Pennsylvania have been measured by use of a calibrated sodar. Monostatic and bistatic systems probed the plume at several positions 40 to 300 m downwind of the cooling tower. Comparison of the sodar estimates of the temperature and velocity structure parameters (C/sub T/ /sup 2/ and C/sub V/ /sup 2/) with those derived from measurements taken by aircraft at the same location shows acceptable agreement. Alternate methods of averaging profiles of C/sub T/ /sup 2/ through the plume are used to investigate single and relative dispersion coefficients. Both methods describe a linear increase of plume width with distance from the cooling tower. Combining values of temperature and velocity structure parameters leads to estimates of turbulence kinetic energy dissipation rate e near 0.3 m/sup 2/ s/sup -3/ and temperature fluctuation destruction rate N of 0.01--0.21 K/sup 2/ s/sup -1/. T he decrease in C/sub T//sup 2/ and C/sub V/ /sup 2/ is found to be exponential with horizontal distance from the tower; C/sub T/ /sup 2/ decreases more rapidly than C/sub V/ /sup 2/. Time-lapse photography used simultaneously with the sodar measurements indicates that the thermal turbulence plume is larger than the condensation plume by a factor of 2--5.

  14. Photon collider at TESLA: parameters and interaction region issues

    E-print Network

    Valery Telnov

    2001-01-04

    Photon colliders (gamma-gamma, gamma-e) are based on backward Compton scattering of laser light off the high energy electrons of linear colliders. Recent study has shown that the gamma-gamma luminosity in the high energy peak can reach 0.3--0.5 L (e+e-). Typical cross sections of interesting processes in gamma-gamma collisions are higher than those in e+e- collisions by about one order of magnitude, so the number of events in gamma-gamma collisions will be more than that in e+e- collisions. In this paper possible parameters of a photon collider at TESLA and a laser scheme are briefly discussed.

  15. 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

  16. Constraining the Symmetry Parameters of the Nuclear Interaction

    NASA Astrophysics Data System (ADS)

    Lattimer, James M.; Lim, Yeunhwan

    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 Sv 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 ? star, is in the narrow window 10.7 km

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

    NASA Astrophysics Data System (ADS)

    Gençy?lmaz, Olcay; Atay, Ferhunde; Akyüz, ?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.

  18. Parameter Evaluation of a Simple Mean-Field Model of Social Interaction

    E-print Network

    Ignacio Gallo; Adriano Barra; Pierluigi Contucci

    2008-11-20

    The aim of this work is to implement a statistical mechanics theory of social interaction, generalizing econometric discrete choice models. A class of simple mean field discrete models is introduced and discussed both from the theoretical and phenomenological point of view. We propose a parameter evaluation procedure and test it by fitting our model against three families of data coming from different cases: the estimated interaction parameters are found to have similar positive values establishing a quantitative confirmation of the peer imitation behavior found in social psychology. Moreover all the values of the interaction parameters belong to the phase transition regime suggesting its possible role in the study of social systems.

  19. Parameter Evaluation of a Simple Mean-Field Model of Social Interaction

    E-print Network

    Gallo, Ignacio; Contucci, Pierluigi

    2008-01-01

    The aim of this work is to implement a statistical mechanics theory of social interaction, generalizing econometric discrete choice models. A class of simple mean field discrete models is introduced and discussed both from the theoretical and phenomenological point of view. We propose a parameter evaluation procedure and test it by fitting our model against three families of data coming from different cases: the estimated interaction parameters are found to have similar positive values establishing a quantitative confirmation of the peer imitation behavior found in social psychology. Moreover all the values of the interaction parameters belong to the phase transition regime suggesting its possible role in the study of social systems.

  20. 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.

  1. A New Approach to Empirical Intermolecular and Conformational Potential Energy Functions. I. Description of Model and Derivation of Parameters

    PubMed Central

    Shipman, Lester L.; Burgess, Antony W.; Scheraga, Harold A.

    1975-01-01

    An empirical potential energy function based on the interactions of the electrons and nuclei in molecules has been developed and tested. The potential energy of interaction is approximated by the sum of the coulombic interactions between all point charge centers (electrons and nuclei), an exponential repulsion to represent electron-electron overlap repulsion, and an R-6 (R = distance) attraction to simulate dispersion and other attractive energies between the heavy atom fragments of the molecules. The parameters of the potential energy function have been determined from experimental gas-phase and crystal data. The results indicate that both intramolecular and intermolecular interaction energies can be treated with the same set of parameters. In comparison to other empirical interaction potentials now in use, there are fewer independent parameters, there is no need for intrinsic torsional potentials to obtain the correct rotational barriers, and there is no need for special hydrogen bonding functions to account for the directionality and energetics of hydrogen bonding. PMID:16592221

  2. 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 ...

  3. 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.

  4. Pharmacokinetic interaction between verapamil and methylxanthine derivatives in mice.

    PubMed

    Wyska, Elzbieta

    2010-01-01

    The aim of this study was to assess the impact of a P-glycoprotein and CYP3A inhibitor, verapamil on the pharmacokinetics of two methylxanthines, pentoxifylline and lisofylline in male CD-1 mice. To differentiate the effects of verapamil, both methylxanthines were also given to male CF-1 mdr1a (-/-) and mdr1a (+/+) mice. CD-1 mice received a single dose (50 mg/kg) of pentoxifylline or lisofylline intravenously, whereas mutant animals were given the same dose of both compounds intravenously and orally. Blood and tissue samples were collected at different time points following drug administration and concentrations of pentoxifylline and lisofylline were measured by a chiral HPLC method. Verapamil significantly increased concentrations of both methylxanthines in murine serum and tissues. In contrast to lisofylline, pentoxifylline concentrations were also significantly higher in mutant mice 30 min following intravenous administration. Due to the fact that pentoxifylline is not a good P-glycoprotein substrate, a possible mechanism of this interaction might be that in the presence of verapamil, pentoxifylline elimination is inhibited by its metabolites that are normally eliminated through P-glycoprotein-mediated transport. This hypothesis was supported by the outcomes of pharmacokinetic analysis. In conclusion, the interaction between verapamil and pentoxifylline is, at least partially, P-glycoprotein-mediated, whereas alterations in lisofylline pharmacokinetics are caused by inhibition of drug metabolising enzymes. PMID:20201780

  5. 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.

  6. INCORPORATING WITHIN-HOUSEHOLD INTERACTIONS INTO A MODE CHOICE MODEL USING A GENETIC ALGORITHM FOR PARAMETER

    E-print Network

    Toronto, University of

    INCORPORATING WITHIN-HOUSEHOLD INTERACTIONS INTO A MODE CHOICE MODEL USING A GENETIC ALGORITHM is used in parallel to perform the necessary calculations and a genetic algorithm is used for parameter and a genetic algorithm is used for parameter estimation. The next section of this paper discusses some

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

    We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS3D project. We study trends between our dynamically derived IMF normalization ?dyn ? (M/L)stars/(M/L)Salp and absorption line strengths, and interpret these via single stellar population-equivalent ages, abundance ratios (measured as [?/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 ?dyn at a given population parameter. As a result, we find weak ?dyn-[?/Fe] and ?dyn -Age correlations and no significant ?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.

  8. 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.

  9. 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; Krajnovi?, 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 ?{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 [?/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 ?{sub dyn} at a given population parameter. As a result, we find weak ?{sub dyn}-[?/Fe] and ?{sub dyn} –Age correlations and no significant ?{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.

  10. 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.

  11. 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 ?–? 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  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. Inter- and intramolecular CF···c?o interactions on aliphatic and cyclohexane carbonyl derivatives.

    PubMed

    Cormanich, Rodrigo A; Rittner, Roberto; O'Hagan, David; Bühl, 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 F···C?O interactions were stabilizing by about 1 kcal mol(-1) for various carbonyl containing functional groups. Intramolecular CF···C?O interactions were also detected in aliphatic and fluorinated cyclohexane carbonyl derivatives. However, the stabilization provided by intramolecular CF···C?O interactions was not enough to govern the conformational preferences of compounds 2-4. © 2015 Wiley Periodicals, Inc. PMID:25903504

  18. 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.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  1. 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.

  2. 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…

  3. Deriving the static interaction between electric dipoles via the quantum gauge transformation

    E-print Network

    Makoto Morinaga

    2013-02-14

    Gauge transformation leaves the electric and the magnetic fields unchanged as long as the gauge function is treated classically. In this paper we consider the gauge transformation commonly used to obtain the electric dipole interaction Hamiltonian in a system of dipoles and the electromagnetic field (Goeppert-Mayer transformation) and treat the vector potential that appear in the gauge function as an operator. While it modifies the electric field, the static interaction between the dipoles is derived.

  4. Kinetic Theory of Turbulence Modeling: Smallness Parameter, Scaling and Microscopic Derivation of Smagorinsky Model

    E-print Network

    Santosh Ansumali; Iliya V. Karlin; Sauro Succi

    2004-02-06

    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.

  5. 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.

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

    PubMed

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

    2014-11-20

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

  7. Characterization of the Flory-Huggins interaction parameter of polymer thermodynamics

    NASA Astrophysics Data System (ADS)

    Russell, Travis H.; Edwards, Brian J.; Khomami, Bamin

    2014-12-01

    Flory-Huggins theory is the main basis of polymer solution and blend thermodynamics. A key piece of this theory is a parameter quantifying the enthalpic interactions between the components; however, experiments have revealed that this parameter is not composition independent, as originally assumed. This composition dependence has been attributed by some theorists to experimental error; others have tried to explain it based on several competing hypotheses. Here, we use atomistic simulations of isotopic blends based on realistic potentials to study this parameter without making any prior hypotheses. Simulations reveal a composition dependence of this parameter that compares well with experimental data, and serve to verify theoretical relationships between the various forms of this parameter.

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

    EPA Science Inventory

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

  9. Systematic study of rapidity dispersion parameter in high energy nucleus-nucleus interactions

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, Swarnapratim; Haiduc, Maria; Neagu, Alina Tania; Firu, Elena

    2014-03-01

    A systematic study of rapidity dispersion parameter as a quantitative measure of clustering of particles has been carried out in the interactions of 16O, 28Si and 32S projectiles at 4.5 A GeV/c with heavy (AgBr) and light (CNO) groups of targets present in the nuclear emulsion. For all the interactions, the total ensemble of events has been divided into four overlapping multiplicity classes depending on the number of shower particles. For all the interactions and for each multiplicity class, the rapidity dispersion parameter values indicate the occurrence of clusterization during the multiparticle production at Dubna energy. The measured rapidity dispersion parameter values are found to decrease with the increase of average multiplicity for all the interactions. The dependence of rapidity dispersion parameter on the average multiplicity can be successfully described by a relation D(?) = a + b + c2. The experimental results have been compared with the results obtained from the analysis of Monte Carlo simulated (MC-RAND) events. MC-RAND events show weaker clusterization among the pions in comparison to the experimental data.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  11. 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.

  12. Role of deceleration parameter and interacting dark energy in singularity avoidance

    NASA Astrophysics Data System (ADS)

    Abdussattar; Prajapati, S. R.

    2011-02-01

    A class of non-singular bouncing FRW models are obtained by constraining the deceleration parameter in the presence of an interacting dark energy represented by a time-varying cosmological constant. The models being geometrically closed, initially accelerate for a certain period of time and decelerate thereafter and are also free from the entropy and cosmological constant problems. Taking a constant of integration equal to zero one particular model is discussed in some detail and the variation of different cosmological parameters are shown graphically for specific values of the parameters of the model. For some specific choice of the parameters of the model the ever expanding models of Ozer & Taha and Abdel-Rahman and the decelerating models of Berman and also the Einstein de-Sitter model may be obtained as special cases of this particular model.

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

    NASA Astrophysics Data System (ADS)

    Fischer, Andrea

    2015-04-01

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

  14. 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

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

    E-print Network

    Boeche, C

    2015-01-01

    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=2,000-20,000). Methods: After the astrophysical calibration of the oscillator strengths of 4643 absorption lines covering the wavelength ranges 5212-6860\\AA\\ and 8400-8924\\AA, 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 s...

  16. 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

  17. Comparison of Two Optimization Methods to Derive Energy Parameters for Protein Folding: Perceptron and Z Score

    E-print Network

    Mirny, Leonid

    methods are of similar quality and fairly closely related. This finding indicates that standard, naturally energy parameters from known native protein conformations and corresponding sets of decoys. One is based by a the sequence of amino acids, by S the conformation (represented by its contact map,1 and by w the set of energy

  18. Comparison of two optimization methods to derive energy parameters for protein folding

    E-print Network

    Domany, Eytan

    and fairly closely related. This finding indicates that standard, naturally occuring sets of decoys parameters from known native protein conformations and corresponding sets of decoys. One is based on finding; S; w) = N X i!j S ij w(a i ; a j ) ; (1) where we denoted by a the sequence of amino acids

  19. 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...

  20. 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, ?, ?=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 (?) 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.

  1. Comparison of Transport Parameters derived from Time-Lapse Electrical Resistivity Tomography, TDR and Effluent Break Through Curves

    NASA Astrophysics Data System (ADS)

    Koestel, J.; Kemna, A.; Javaux, M.; Vanderborght, J.; Binley, A.; Vereecken, H.

    2007-05-01

    During the recent years it was shown that time-lapse electrical resistivity tomography (ERT) has potential to image subsurface solute transport processes. In this study we captured the spatio-temporal evolution of an inert salt tracer plume by means of time-lapse ERT in an unsaturated undisturbed soil column (height: 1.4 m, diameter: 1.16 m). The experiment was performed two-fold for 2 different steady state flow conditions, respectively, corresponding to approximately 15 % and 55 % of saturation. The ERT data were inverted with a three dimensional, smoothness-constrained inversion algorithm based on finite-element modelling. Identical error parameters were used for all ERT inversions and experiments. The image time series provides spatially resolved break-through curves (BTCs). Simultaneously, the BTCs in the outflow were measured and local BTCs within the monolith were measured with TDR. Following a stream tube approach, effective transport parameters were obtained by fitting the convective-dispersive equation to all available break-through curves. However, due to the non-uniqueness of the ERT inversion, the parameters derived from time lapse ERT might not be robust. Therefore, we appraised their robustness by comparing them with parameters derived from effluent and TDR measured BTCs. For all break through experiments, the mean ERT derived effective velocities at the TDR positions matched the ones found by TDR with a mean deviation of app. 5 %. The ERT derived dispersivities exceeded the ones found by TDR by a factor of two or more for the upper soil layers. For the deeper soil layers where the electrical contrasts were smoothed by dispersion, ERT and TDR derived effective dispersivities converged. For the four experiments, the effective velocity which was obtained from the effluent BTC matched the mean of the velocities derived from the bottommost ERT voxels with accuracy of 2.5 % to 5.5 %. The dispersivities of the effluent BTCs could be predicted from the variance of the ERT voxel velocities and the mean ERT voxel dispersivities with an accordance of 2.5 % to 23.5 %. The results confirm that smoothness constraint time lapse ERT images can be interpreted quantitatively up to a certain degree. We expect that a greater accuracy could be achieved if time-lapse information was incorporated into the inversion algorithm or a hydro-geophysical joint inversion approach was used.

  2. 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.

  3. 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.

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

    SciTech Connect

    Ohya, Satoshi

    2014-12-15

    We study non-Abelian geometric phase in N=2 supersymmetric quantum mechanics for a free particle on a circle with two point-like interactions at antipodal points. We show that non-Abelian Berry’s connection is that of SU(2) magnetic monopole discovered by Moody, Shapere and Wilczek in the context of adiabatic decoupling limit of diatomic molecule. - Highlights: • Supersymmetric quantum mechanics is an ideal playground for studying geometric phase. • We determine the parameter space of supersymmetric point-like interactions. • Berry’s connection is given by a Wu–Yang-like magnetic monopole in SU(2) Yang–Mills.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    Several geometrical models (e.g., cone and flux rope models) have been suggested to infer three-dimensional parameters of CMEs using multi-view observations (STEREO/SECCHI) and single-view observations (SOHO/LASCO). To prepare for when only single view observations are available, we have made a test whether the cone model parameters from single-view observations are consistent with those from multi-view ones. For this test, we select 35 CMEs which are identified as CMEs, whose angular widths are larger than 180 degrees, by one spacecraft and as limb CMEs by the other ones. For this we use SOHO/LASCO and STEREO/SECCHI data during the period from 2010 December to 2011 July when two spacecraft were separated by 90±10 degrees. In this study, we compare the 3-D parameters of these CMEs from three different methods: (1) a triangulation method using STEREO/SECCHI and SOHO/LASCO data, (2) a Graduated Cylindrical Shell (GCS) flux rope model using STEREO/SECCHI data, and (3) an ice cream cone model using SOHO/LASCO data. The parameters used for comparison are radial velocities, angular widths and source location (angle ? 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.

  6. Pharmacokinetic drug interactions of morphine, codeine, and their derivatives: theory and clinical reality, part I.

    PubMed

    Armstrong, Scott C; Cozza, Kelly L

    2003-01-01

    Pharmacokinetic drug-drug interactions with morphine, hydromorphone, and oxymorphone are reviewed in this column. Morphine is a naturally occurring opiate that is metabolized chiefly through glucuronidation by uridine diphosphate glucuronosyl transferase (UGT) enzymes in the liver. These enzymes produce an active analgesic metabolite and a potentially toxic metabolite. In vivo drug-drug interaction studies with morphine are few, but they do suggest that inhibition or induction of UGT enzymes could alter morphine and its metabolite levels. These interactions could change analgesic efficacy. Hydromorphone and oxymorphone, close synthetic derivatives of morphine, are also metabolized primarily by UGT enzymes. Hydromorphone may have a toxic metabolite similar to morphine. In vivo drug-drug interaction studies with hydromorphone and oxymorphone have not been done, so it is difficult to make conclusions with these drugs. PMID:12618536

  7. Study on the interaction between gelatin and polyurethanes derived from fatty acids.

    PubMed

    González-Paz, R J; Lligadas, G; Ronda, J C; Galià, M; Ferreira, A M; Boccafoschi, F; Ciardelli, G; Cádiz, V

    2013-04-01

    In this study, gelatin was blended to proprietary noncytotoxic polyurethanes (PU) derived from vegetable oils with different weight ratios, as material for the preparation of novel biomedical products. The PU/gelatin blends were characterized for their morphology through scanning electron microscopy. Mechanical and thermal properties, chemical interactions between components, degradation behavior, surface properties, cell adhesion, and bioactivity were investigated as a function of the protein content. Higher blend miscibility was observed for the amorphous PUs, derived from oleic acid. Properties of PU/gelatin films were strongly influenced by the concentration of gelatin in the films. Gelatin enhanced the hydrophilicity, bioactivity, and cell adhesion of PUs. PMID:22965488

  8. Resonance Parameters and Uncertainties Derived from Epithermal Neutron Capture and Transmission Measurements of Natural Molybdenum

    E-print Network

    Danon, Yaron

    Measurements of Natural Molybdenum G. Leinweber,* D. P. Barry, J. A. Burke, and N. J. Drindak Bechtel Marine was used to explore neutron interactions with molybdenum in the energy region from 10 eV to 2 keV. Neutron of elemental molybdenum metal samples ranging from 0.051 mm (0.002 in.) to 6.35 mm (0.250 in.) were measured

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    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)4] layers to form a solid of formula unit T(ImD)2[Ni(CN)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)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 ?-? interaction was detected.

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

    NASA Astrophysics Data System (ADS)

    Peikert, Benjamin; Schaumann, Gabriele Ellen

    2014-05-01

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

  11. Nonparametric Estimation of Derivative Functions with Data-Driven Optimally Selected Smoothing Parameters 

    E-print Network

    Yao, Shuang

    2014-07-30

    denotes an alternative local polynomial estimator. Hence, our objective function is based on CVLP (h) = 1 n n? j=1 [ ?ˆLL(xj)? ?ˆLP (xj) ]2 M(xj). (2.5) Our candidates for ?ˆLP (·) are from the set of local polynomial estimators, local- constant (LC...(x). Ideally, we would like to choose the smoothing parameter h to minimize the estimation mean squared error E{[?ˆLL(x)? ?(x)]2}, or the sample analogue of it: CV (h) def = 1 n n? j=1 [?ˆLL(xj)? ?(xj)] 2M(xj), (2.2) where M(·) is a weight function with bounded...

  12. 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

  13. 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 ?sol 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 (?sol H°) and transfer (?tr 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.

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

    PubMed Central

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

    2015-01-01

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

  15. 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

  16. 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.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Moeser, D.; Stähli, M.; Jonas, T.

    2015-07-01

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

  19. Physical parameters of the near-surface of Mars derived from SHARAD radar reflectivity: Statistical approach

    NASA Astrophysics Data System (ADS)

    Grima, Cyril; Kofman, Wlodek; Herique, Alain; Seu, Roberto

    Onboard sounding radars are relatively new instruments in planetary exploration. This method is ground penetrating and then well suited to the search for buried water ice on Mars. Their capacity to resolve glacial structures down to kilometers depth has already provided precious informations related to Martian glaciers. Sounding radars are also relevant tools to determine the physical parameters of the near-surface from reflectivity measurements. Whereas common observation instruments do not exceed few millimeters, radar reflectivity probes the first de-cameters of the surface (depending on the bandwidth). Because radar reflectivity contains information on both the surface geometry and geologic composition, a main issue is to apply an efficient method to separate those components. The SHAllow RADar (SHARAD/ASI) is an instrument onboard the NASA's Mars Reconnais-sance Orbiter (MRO). The routine science observations that started in November 2006 is still ongoing. SHARAD provides remote sensing observations of most of the Martian surface at a 20 MHz frequency (10 MHz bandwidth). The along-track foot print range is between 0.3 and 1 km, while the typical footprint radius (Fresnel zone) is 1.5 km. SHARAD reflectivity depends on the first 5-10 meters of the surface, according to the dielectric constant of the sounded material. In terrestrial SAR (synthetic aperture radar) imagery, numerous statistical methods were exten-sively studied because of their abilities to classify remote terrains. Here we present applications of such methods based on SAR statistics to extract the physical parameters embedded in the SHARAD reflected signal of the near-surface. Preliminary results are reported over different key regions of Mars -especially glacial and periglacial units -in order to illustrate the limits and the possibilities of this approach.

  20. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-09-01

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

  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. 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

  7. Deriving Definitive Parameters for the Long Period Cepheid S Vulpeculae (Abstract)

    NASA Astrophysics Data System (ADS)

    Turner, D. G.

    2013-12-01

    (Abstract only) The long-period variable S Vul is now recognized to be a classical Cepheid, following a period a century ago when its status was less well established. Its pulsation period of 68.5 days makes S Vul the longest period Cepheid recognized in the Galaxy. Possible membership in an OB association was considered briefly thirty years ago, until it was discovered to be surrounded by a sparse cluster of faint stars designated as Turner 1. Membership of S Vul in the cluster was considered unlikely in the original photometric study of Turner 1 because of contradictory implications regarding the reddening and distance of S Vul with that of cluster stars, but a recent revisiting of the data supplemented by APASS observations indicates that the cluster and Cepheid are indeed related. The implications for the implied parameters of S Vul, its reddening, distance, age, and evolutionary mass, are discussed in light of our refined knowledge of the cluster in which the Cepheid resides.

  8. 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

  9. 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

  10. Parameter-optimized model of cardiovascular-rotary blood pump interactions.

    PubMed

    Lim, Einly; Dokos, Socrates; Cloherty, Shaun L; Salamonsen, Robert F; Mason, David G; Reizes, John A; Lovell, Nigel H

    2010-02-01

    A lumped parameter model of human cardiovascular-implantable rotary blood pump (iRBP) interaction has been developed based on experimental data recorded in two healthy pigs with the iRBP in situ. The model includes descriptions of the left and right heart, direct ventricular interaction through the septum and pericardium, the systemic and pulmonary circulations, as well as the iRBP. A subset of parameters was optimized in a least squares sense to faithfully reproduce the experimental measurements (pressures, flows and pump variables). Our fitted model compares favorably with our experimental measurements at a range of pump operating points. Furthermore, we have also suggested the importance of various model features, such as the curvilinearity of the end systolic pressure-volume relationship, the Starling resistance, the suction resistance, the effect of respiration, as well as the influence of the pump inflow and outflow cannulae. Alterations of model parameters were done to investigate the circulatory response to rotary blood pump assistance under heart failure conditions. The present model provides a valuable tool for experiment designs, as well as a platform to aid in the development and evaluation of robust physiological pump control algorithms. PMID:19770086

  11. 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}).

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  13. 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

  14. 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; ?ahin, 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.

  15. 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 1–4 are 4-bromo dipicolinic acid esters substituted with methyl, ethyl, propyl, and benzyl groups, respectively. The main structure-directing motif within 1–3 is a pairwise O···H 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 O···H interaction in 5, where the dominant structure-directing motifs are ?-based interactions. However, the pairwise O···H 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

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

    E-print Network

    Yu-Feng Li; Ye-Ling Zhou

    2015-03-20

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  18. 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

  19. 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 ?l in UV spectroscopic study, while the concentration of DNA in gel electrophoresis remained constant at 10 ?l. 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

  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 ? 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.

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

    PubMed Central

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

    2015-01-01

    It has now become increasingly clear that a complete atomic description of how biomacromolecules recognize each other requires knowledge not only of the structures of the complexes but also of how kinetics and thermodynamics drive the binding process. In particular, such knowledge is lacking for protein–glycosaminoglycan (GAG) complexes. Isothermal titration calorimetry (ITC) is the only technique that can provide various thermodynamic parameters—enthalpy, entropy, free energy (binding constant), and stoichiometry—from a single experiment. Here we describe different factors that must be taken into consideration in carrying out ITC titrations to obtain meaningful thermodynamic data of protein–GAG interactions. PMID:25325962

  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. Running of Oscillation Parameters in Matter with Flavor-Diagonal Non-Standard Interactions of the Neutrino

    E-print Network

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

    2015-10-10

    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 $\\theta_{12}$ and $\\theta_{13}$, while the flavor-diagonal NSI's only affect $\\theta_{23}$. The CP-violating phase $\\delta$ 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 numu to numu 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 $\\theta_{23}$ and the sign of the NSI parameter for a given choice of mass hierarchy in a simple manner.

  4. 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 ? 12 and ? 13, while the flavor-diagonal NSI's only affect ? 23. The CP-violating phase ? 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 ? ? ? ? ? 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 ? 23 and the sign of the NSI parameter for a given choice of mass hierarchy in a simple manner.

  5. Cytotoxic and DNA-topoisomerase effects of lapachol amine derivatives and interactions with DNA.

    PubMed

    Esteves-Souza, A; Figueiredo, D V; Esteves, A; Câmara, C A; Vargas, M D; Pinto, A C; Echevarria, A

    2007-10-01

    The cytotoxic activity of amino (3a-e), aza-1-antraquinone (4a-e) lapachol derivatives against Ehrlich carcinoma and human K562 leukemia cells was investigated. Cell viability was determined using MTT assay, after 48 (Ehrlich) or 96 h (K562) of culture, and vincristine (for K562 leukemia) and quercetin (for Ehrlich carcinoma) were used as positive controls. The results showed dose-dependent growth-inhibiting activities and that the amino derivatives were active against the assayed cells, whereas the 4a-e derivatives were not. The allylamine derivative 3a was the most active against Ehrlich carcinoma, with IC50 = 16.94 +/- 1.25 microM, and against K562 leukemia, with IC50 = 14.11 +/- 1.39 microM. The analogous lawsone derivative, 5a, was also active against Ehrlich carcinoma (IC50 = 23.89 +/- 2.3 microM), although the 5d and 5e derivatives showed lower activity. The interaction between 3a-d and calf thymus DNA was investigated by fluorimetric titration and the results showed a hyperchromic effect indicating binding to DNA as presented of ethidium bromide, used as positive control. The inhibitory action on DNA-topoisomerase II-a was also evaluated by a relaxation assay of supercoiled DNA plasmid, and the etoposide (200 microM) was used as positive control. Significant inhibitory activities were observed for 3a-d at 200 microM and a partial inhibitory action was observed for lapachol and methoxylapachol. PMID:17713652

  6. Assessment of solid-state interactions of naproxen with amorphous cyclodextrin derivatives by DSC.

    PubMed

    Bettinetti, G P; Sorrenti, M; Rossi, S; Ferrari, F; Mura, P; Faucci, M T

    2002-11-01

    A microcalorimetric method based on differential scanning calorimetry (DSC) of drug-additive binary systems to assess kneading-induced interactions was applied to naproxen (NAP) in combinations with amorphous hydroxypropyl beta-cyclodextrin (HPbetaCd), beta-cyclodextrin sulfobutyl ether, sodium salt ((SBE)(7m)-betaCd), acetyl beta-cyclodextrin (AcbetaCd) and acetyl gamma-cyclodextrin (AcgammaCd). Modifications of thermal parameters of NAP in DSC curves of physical mixtures indicate heating-induced interactions which resulted in a broadening of the NAP melting endotherm in the combinations with HPbetaCd, AcbetaCd and AcgammaCd. The effect of kneading on the interaction was particularly pronounced for the NAP-HPbetaCd and NAP-(SBE)(7m)-betaCd systems, which show a similar drug-to-carrier interaction ratio (1:2 by weight) as that of the other systems. Drug-to-carrier ratios, calculated considering the amount of NAP which recrystallizes from the melted mixtures equivalent to NAP not bound to the carrier, show a distinctly lower affinity in solid-state of the drug for the anionically charged (SBE)(7m)-betaCd with respect to other neutral carriers. The similar affinity of NAP for AcbetaCd and AcgammaCd demonstrates that the geometry of the cavity, which is a determinant factor for the inclusion complexation in liquid state, does not influence the interaction process in solid-state. PMID:12408907

  7. Theoretical studies on the interaction of fluorene derivatives with nucleic acids

    NASA Astrophysics Data System (ADS)

    Sawaryn, Andrzej; Bradaczek, Hans

    The results of empirical and semitheoretical potential function calculations have shown that fluorene derivatives with established carcinogenic activity can intercalate, in the Lerman sense, between the complementary pairs of cytidylyl-guanosine. The interaction energy is strongly dependent on the ionization state of the compounds studied. The optimized intercalation position depends on the position of substitution on the fluorene ring and to a lesser extent on the nature of the side chain. The intercalation effect explains the different biological activity of 2- and 4-substituted isomers of acetylaminofluorene.

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

    PubMed

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

    2015-08-24

    The halogen bond, similar to the hydrogen bond, is an important noncovalent interaction and plays important roles in diverse chemistry-related fields. Herein, bromine- and iodine-based halogen-bonding interactions between two benzene derivatives (C6 F5 Br and C6 F5 I) and dimethyl sulfoxide (DMSO) are investigated by using IR and NMR spectroscopy and ab initio calculations. The results are compared with those of interactions between C6 F5 Cl/C6 F5 H and DMSO. First, the interaction energy of the hydrogen bond is stronger than those of bromine- and chlorine-based halogen bonds, but weaker than iodine-based halogen bond. Second, attractive energies depend on 1/r(n) , in which n is between three and four for both hydrogen and halogen bonds, whereas all repulsive energies are found to depend on 1/r(8.5) . Third, the directionality of halogen bonds is greater than that of the hydrogen bond. The bromine- and iodine-based halogen bonds are strict in this regard and the chlorine-based halogen bond only slightly deviates from 180°. The directional order is iodine-based halogen bond>bromine-based halogen bond>chlorine-based halogen bond>hydrogen bond. Fourth, upon the formation of hydrogen and halogen bonds, charge transfers from DMSO to the hydrogen- and halogen-bond donors. The CH3 group contributes positively to stabilization of the complexes. PMID:26118800

  9. 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.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

    Ohlsson, Tommy; Zhang, He; Zhou, Shun

    2014-01-01

    Precision measurements of leptonic mixing parameters and the determination of the neutrino mass hierarchy are the primary goals of the forthcoming medium-baseline reactor antineutrino experiments, such as JUNO and RENO-50. In this work, we investigate the impact of nonstandard neutrino interactions (NSIs) on the measurements of {sin2 ?12,?m212} and {sin2 ?13,?m312}, and on the sensitivity to the neutrino mass hierarchy, at the medium-baseline reactor experiments by assuming a typical experimental setup. It turns out that the true mixing parameter sin2 ?12 can be excluded at a more than 3? level if the NSI parameter ? or ? is as large as 2% in the most optimistic case. However, the discovery reach of NSI effects has been found to be small, and depends crucially on the CP-violating phases. Finally, we show that NSI effects could enhance or reduce the discrimination power of the JUNO and RENO-50 experiments between the normal and inverted neutrino mass hierarchies.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  14. Structural and solubility parameter correlations of gelation abilities for dihydroxylated derivatives of long-chain, naturally occurring fatty acids.

    PubMed

    Zhang, Mohan; Selvakumar, Sermadurai; Zhang, Xinran; Sibi, Mukund P; Weiss, Richard G

    2015-06-01

    Creating structure-property correlations at different distance scales is one of the important challenges to the rational design of molecular gelators. Here, a series of dihydroxylated derivatives of long-chain fatty acids, derived from three naturally occurring molecules-oleic, erucic and ricinoleic acids-are investigated as gelators of a wide variety of liquids. Conclusions about what constitutes a more (or less!) efficient gelator are based upon analyses of a variety of thermal, structural, molecular modeling, and rheological results. Correlations between the manner of molecular packing in the neat solid or gel states of the gelators and Hansen solubility data from the liquids leads to the conclusion that diol stereochemistry, the number of carbon atoms separating the two hydroxyl groups, and the length of the alkanoic chains are the most important structural parameters controlling efficiency of gel formation for these gelators. Some of the diol gelators are as efficient or even more efficient than the well-known, excellent gelator, (R)-12-hydroxystearic acid; others are much worse. The ability to form extensive intermolecular H-bonding networks along the alkyl chains appears to play a key role in promoting fiber growth and, thus, gelation. In toto, the results demonstrate how the efficiency of gelation can be modulated by very small structural changes and also suggest how other structural modifications may be exploited to create efficient gelators. PMID:25926104

  15. 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

  16. Microscopic analysis of quadrupole collective motion in Cr-Fe nuclei: I. Renormalization of collective states and interacting-boson-model parameters

    E-print Network

    H. Nakada; T. Otsuka

    1996-12-03

    We present a new method by which wavefunctions with simple structure are renormalized so as to contain more complicated structure. This method, called $H^n$-cooling method, is applied to the study of the quadrupole collective motion of $^{56}$Fe, $^{54}$Cr, $^{58}$Fe and $^{56}$Cr. The shell-model wavefunctions of lowest-lying states of these nuclei are well treated by this method. By using the wavefunctions obtained via the $H^n$-cooling method, IBM-2 parameters are derived from a realistic shell-model hamiltonian and transition operators. The Majorana interaction becomes sizably repulsive, primarily as an effect of the renormalization. The bosonic E2 effective-charges are enhanced due to the renormalization, while a quenching occurs in the M1 and M3 parameters for proton bosons. It is shown that the $\\chi$ parameters take similar values in the hamiltonian and in the E2 operator.

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

    SciTech Connect

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

    2014-11-01

    Given the fantastic experimental effort, it is important to thoroughly explore the signature space of inflationary models. The fact that higher derivative operators do not renormalize lower derivative ones allows us to find a large class of technically natural single-clock inflationary models where, in the context of the Effective Field Theory of Inflation, the leading interactions have many derivatives. We systematically explore the 3-point function induced by these models and their overlap with the standard equilateral and orthogonal templates. We find that in order to satisfactorily cover the signature space of these models, two new additional templates need to be included. We then perform the optimal analysis of the WMAP 9-year data for the resulting four templates, finding that the overall significance of a non-zero signal is between 2–2.5?, depending on the choice of parameter space, partially driven by the preference for nonzero f{sub NL}{sup orth} in WMAP9.

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

    PubMed

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

    2015-03-01

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

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

    PubMed

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

    2015-12-01

    During tissue injury and wound healing process, there are dynamic reciprocal interactions among cells, extracellular matrix (ECM), and mediating molecules which are crucial for functional tissue repair. Nitric oxide (NO) is one of the key mediating molecules that can positively regulate various biological activities involved in wound healing. Various ECM components serve as binding sites for cells and mediating molecules, and the interactions further stimulate cellular activities. Human mesenchymal stem cells (hMSCs) can migrate to the wound site and contribute to tissue regeneration through differentiation and paracrine signaling. The objective of this work was to investigate the regulatory effect of NO on hMSCs in an interactive ECM-rich microenvironment. In order to mimic the in vivo stromal environment in wound site, a cell-derived ECM scaffold that was able to release NO within the range of in vivo wound fluid NO level was fabricated. Results showed that the micro-molar level of NO released from the ECM scaffold had an inhibitory effect on cellular activities of hMSCs. The NO impaired cell growth, altered cell morphology, disrupted the F-actin organization, also decreased the expression of focal adhesion related molecules integrin ?5 and paxillin. These results may contribute to the elucidation of how NO acts on hMSCs in wound healing process. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 103A: 3807-3814, 2015. PMID:26074441

  20. alpha(2A)-adrenergic receptor derived peptide adsorbates: a G-protein interaction study.

    PubMed

    Vahlberg, Cecilia; Petoral, Rodrigo M; Lindell, Carina; Broo, Klas; Uvdal, Kajsa

    2006-08-15

    The affinity of alpha(2A)-adrenergic receptor (alpha(2A)-AR) derived peptide adsorbates for the functional bovine brain G-protein is studied in the search for the minimum sequence recognition. Three short peptides (GPR-i2c, GPR-i3n, and GPR-i3c) are designed to mimic the second and third intracellular loops of the receptor. X-ray photoelectron spectroscopy is used to study the chemical composition of the peptides and the binding strength to the surfaces. Chemisorption of the peptides to the gold substrates is observed. Infrared spectroscopy is used to study the characteristic absorption bands of the peptides. The presence of peptides on the surfaces is verified by prominent amide I and amide II bands. The interaction between the peptides and the G-protein is studied with surface plasmon resonance. It is shown that GPR-i3n has the highest affinity for the G-protein. Equilibrium analysis of the binding shows that the G-protein keeps its native conformation when interacting with GPR-i3c, but during the interaction with GPR-i2c and GPR-i3n the conformation of G-protein is changed, leading to the formation of aggregates and/or multilayers. PMID:16893224

  1. Complexes between dihydrogen and amine, phosphine, and arsine derivatives. Hydrogen bond versus pnictogen interaction.

    PubMed

    Grabowski, S?awomir J; Alkorta, Ibon; Elguero, José

    2013-04-18

    A theoretical study of the complexes between dihydrogen, H2, and a series of amine, phosphine, and arsine derivatives (ZH3 and ZH2X, with Z = N, P, or As and X = F, Cl, CN, or CH3) has been carried out using ab initio methods (MP2/aug-cc-pVTZ). Three energetic minima configurations have been characterized for each case with the H2 molecule in the proximity of the pnictogen atom (Z). In configuration A, the ?-electrons of H2 interact with ?-hole region of the pnictogen atom generated by the of X-Z bond. These complexes can be ascribed as pnictogen bonded. In configuration C, the lone electron pair of Z acts as the Lewis base, and H2 plays the role of the Lewis acid. Finally, configuration B presents a variety of noncovalent interactions depending on the binary complex considered. The atoms-in-molecules theory (AIM), natural bond orbitals (NBO) method as well as the density functional theory-symmetry adapted perturbation theory (DFT-SAPT) approach were used in this study to deepen the nature of the interactions considered. PMID:23514567

  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. Claridge et al.: Model based inversion for deriving maps of histological parameters characteristic of cancer 1 Abstract--A model-based inversion method was used to

    E-print Network

    Claridge, Ela

    Claridge et al.: Model based inversion for deriving maps of histological parameters characteristic of histological parameters from multispectral images of the colon and to examine their potential.04. Validation on ex vivo images demonstrated that parametric maps show gross correspondence with histological

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  6. 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.

  7. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    PubMed Central

    Warner, Daniel A.; Shine, Richard

    2011-01-01

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

  11. 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

  12. 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.

  13. 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

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

    PubMed

    Weber, Jeffrey K; Pande, Vijay S

    2013-02-28

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

  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 Vam3–Syk interaction. Our studies may be helpful in the structural optimization of Vam3, and also aid the design of novel Syk inhibitors in the future. PMID:25257535

  16. An electrochemical study into the interaction between complement-derived peptides and DOPC mono- and bilayers.

    PubMed

    Ringstad, Lovisa; Protopapa, Elisabeth; Lindholm-Sethson, Britta; Schmidtchen, Artur; Nelson, Andrew; Malmsten, Martin

    2008-01-01

    Electrochemical methods employing the hanging mercury drop electrode were used to study the interaction between variants of the complement-derived antimicrobial peptide CNY21 (CNYITELRRQH ARASHLGLAR) and dioleoyl phosphatidylcholine (DOPC) monolayers. Capacitance potential and impedance measurements showed that the CNY21 analogues investigated interact with DOPC monolayers coating the mercury drop. Increasing the peptide hydrophobicity by substituting the two histidine residues with leucine resulted in a deeper peptide penetration into the hydrophobic region of the DOPC monolayer, indicated by an increase in the dielectric constant of the lipid monolayer (Deltaepsilon = 2.0 after 15 min interaction). Increasing the peptide net charge from +3 to +5 by replacing the histidines by lysines, on the other hand, arrests the peptide in the lipid head group region. Reduction of electroactive ions (Tl+, Pb2+, Cd2+, and Eu3+) at the monolayer-coated electrode was employed to further characterize the types of defects induced by the peptides. All peptides studied permeabilize the monolayer to Tl+ to an appreciable extent, but this effect is more pronounced for the more hydrophobic peptide (CNY21L), which also allows penetration of larger ions and ions of higher valency. The results for the various ions indicate that charge repulsion rather than ion size is the determining factor for cation penetration through peptide-induced defects in the DOPC monolayer. The effects obtained for monolayers were compared to results obtained with bilayers from liposome leakage and circular dichroism studies for unilamellar DOPC vesicles, and in situ ellipsometry for supported DOPC bilayers. Trends in peptide-induced liposome leakage were similar to peptide effects on electrochemical impedance and permeability of electroactive ions for the monolayer system, demonstrating that formation of transmembrane pores alone does not constitute the mechanism of action for the peptides investigated. Instead, our results point to the importance of local packing defects in the lipid membrane in close proximity to the adsorbed peptide molecules. PMID:18052298

  17. CJX1, an amlodipine derivative, interacts with ATPase of human P-glycoprotein.

    PubMed

    Ji, Bian-Sheng; He, Ling

    2009-10-01

    Our aim has been to elucidate the possible mechanism of CJX1, an amlodipine derivative, in the modulation of P-gp function by determining its effect on P-gp ATPase activity. Basal P-gp ATPase activity was increased by CJX1 with half-maximal activity concentration (Km) of 8.6+/-1.4 microM. Kinetic analysis indicated a non-competitive inhibition of Verapamil (Ver)-stimulated P-gp ATPase activity by CJX1 and competitive inhibition of CJX1-stimulated P-gp ATPase activity by tetrandrine (Tet). The effect of CsA on CJX1-stimulated and Ver-stimulated P-gp ATPase activity was non-competitive and competitive inhibition, respectively. These findings implying that CJX1 and Tet can bind P-gp either on overlapping sites or distinct but interacting sites, while CJX1 and Ver as well as CsA can bind P-gp on separated sites in K562/DOX cells. Furthermore, the combined effect of CJX1 and Ver has been evaluated isobolographically in numerous fixed-ratio combinations of 1:1, 1:2, 1:4, 1:8, 1:10 in K562/DOX cells. The results show that mixtures of both drugs at these fixed-ratios exerted synergistic interactions, indicating that when the two reverses that bind P-gp on separated sites are combined, each can contribute to the overall interaction with P-gp, leading to the greater effect than that by either agent alone. PMID:19589390

  18. 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.

  19. 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).

  20. Resolving CP violation by standard and nonstandard interactions and parameter degeneracy in neutrino oscillations

    NASA Astrophysics Data System (ADS)

    Gago, A. M.; Minakata, H.; Nunokawa, H.; Uchinami, S.; Zukanovich Funchal, R.

    2010-01-01

    In neutrino oscillation with non-standard interactions (NSI) the system is enriched with CP violation caused by phases due to NSI in addition to the standard lepton Kobayashi-Maskawa phase ?. In this paper we show that it is possible to disentangle the two CP violating effects by measurement of muon neutrino appearance by a near-far two detector setting in neutrino factory experiments. Prior to the quantitative analysis we investigate in detail the various features of the neutrino oscillations with NSI, but under the assumption that only one of the NSI elements, ? e? or ? e?, is present. They include synergy between the near and the far detectors, the characteristic differences between the ? e? and ? e? systems, and in particular, the parameter degeneracy. Finally, we use a concrete setting with the muon energy of 50GeV and magnetized iron detectors at two baselines, one at L = 3000 km and the other at L = 7000 km, each having a fiducial mass of 50 kton to study the discovery potential of NSI and its CP violation effects. We demonstrate, by assuming 4 × 1021 useful muon decays for both polarities, that one can identify nonstandard CP violation down to |? e?| ? a few × 10-3, and |? e?| ? 10-2 at 3? CL for ?13 down to sin2 2?13 = 10-4 in most of the region of ?. The impact of the existence of NSI on the measurement of ? and the mass hierarchy is also worked out.

  1. Structural connectivity and ionic transport in molten ZnCl 2: Optimization of chlorine interaction parameters

    NASA Astrophysics Data System (ADS)

    Ruberto, R.; Pastore, G.; Tosi, M. P.

    2010-02-01

    We report molecular-dynamics simulations of pseudoclassical models of liquid ZnCl 2 near its standard freezing point (sfp) and in thermodynamic states at higher temperature and pressure. Our calculations are firstly aimed at investigating the model sensitivity of the results for the temperature-dependent self-diffusion coefficients of the two species and for the structural connectivity of the liquid as defined in terms of corner-sharing versus edge-sharing ZnCl 4 tetrahedra. Data from coherent neutron scattering experiments near the sfp and from ionic diffusivity measurements along the standard-pressure isobar guide us to a “best” choice of the model parameters describing the electric polarizability and the van der Waals interaction coefficient of the chlorine ions. This choice also provides a consistent picture of the behaviour of the liquid under pressure: with increasing pressure the Zn ions are progressively squeezed from fourfold into sixfold coordination sites, in correspondence to crystal structures built on these two coordination states. The proposed “best” interionic force law is further tested by comparing its predictions with existing first-principles calculations on the structure of the molecular dimer Zn 2Cl 4 and with new first-principles calculations on distorted configurations of the ZnCl 2 monomer as created by extensive bond stretching or bond bending.

  2. Baseline tissue Doppler imaging-derived echocardiographic parameters and left ventricle reverse remodelling following cardiac resynchronization therapy introduction

    PubMed Central

    Wili?ski, Jerzy; Czarnecka, Danuta; Wojciechowska, Wiktoria; Kloch-Bade?ek, Ma?gorzata; Jastrz?bski, Marek; Bacior, Bogumi?a; Sondej, Tomasz; Kusiak, Aleksander

    2011-01-01

    Introduction The aim of the study was to assess the relation of baseline mechanical dyssynchrony with the left ventricular end-systolic volume (LVESV) decrease following cardiac resynchronization (CRT) therapy introduction. Material and methods Sixty consecutive patients (aged 66.3 ± 8.7 years; 57 men) with chronic heart failure (71.7% of ischaemic and 28.3% of non-ischaemic origin) and current indications for CRT were assessed before and 3 months after biventricular heart stimulator implantation. Longitudinal movements of twelve segments of the left ventricle (LV) (6 basal and 6 midlevel) and two segments of the right ventricle (RV) were analysed using tissue Doppler imaging (TDI) techniques with time from onset of Q wave in ECG to peak systolic velocity in colour-coded TDI (TTDI), time to peak strain (Tstrain) and time to peak strain rate (Tstrain rate). Minimal and maximal time differences within LV and between LV and RV walls were calculated. Results In the study group LVEF and 6-min walk test distance increased, while NYHA class, NT-proBNP level, left ventricular end-diastolic volume and LVESV decreased. Significant correlations between the magnitude of LVESV reduction with maximal time differences between Tstrain of 12 LV segments (r=0.34, p = 0.017) and time differences between TTDI basal LV-RV segments (r = –0.29, p=0.041) were found. Conclusions Only a few TDI-derived parameters such as maximal time differences between Tstrain of 12 LV segments and TTDI difference of LV-RV basal segments can be useful to predict the magnitude of left ventricle reverse remodelling after CRT introduction. PMID:22291826

  3. 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.

  4. 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

  5. Interaction of cinnamic acid derivatives with ?-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 ?-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 ?-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 ?-CD with CAs determined by experimental observations. PMID:26471667

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. Interactions of acyclic and cyclic bis-phenanthridinium derivatives with ss-and ds-polynucleotidesq,qq

    E-print Network

    Cudic, Predrag

    Interactions of acyclic and cyclic bis-phenanthridinium derivatives with ss- and ds and the cyclic analogue 3 bind to ss-RNA by bis-intercalation. Due to it's shorter linker 1 exhibits mono-polynucleotides by non-intercalative mode. Comparing the ss-/ds-polynucleotide selectivity obtained for 3 and previously

  11. Self-Assembly and Lipid Interactions of Diacylglycerol Lactone Derivatives Studied at the Air/Water Interface

    E-print Network

    Jelinek, Raz

    Self-Assembly and Lipid Interactions of Diacylglycerol Lactone Derivatives Studied at the Air for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer

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

    PubMed

    Borgonovo, Emanuele

    2010-03-01

    In risk analysis problems, the decision-making process is supported by the utilization of quantitative models. Assessing the relevance of interactions is an essential information in the interpretation of model results. By such knowledge, analysts and decisionmakers are able to understand whether risk is apportioned by individual factor contributions or by their joint action. However, models are oftentimes large, requiring a high number of input parameters, and complex, with individual model runs being time consuming. Computational complexity leads analysts to utilize one-parameter-at-a-time sensitivity methods, which prevent one from assessing interactions. In this work, we illustrate a methodology to quantify interactions in probabilistic safety assessment (PSA) models by varying one parameter at a time. The method is based on a property of the functional ANOVA decomposition of a finite change that allows to exactly determine the relevance of factors when considered individually or together with their interactions with all other factors. A set of test cases illustrates the technique. We apply the methodology to the analysis of the core damage frequency of the large loss of coolant accident of a nuclear reactor. Numerical results reveal the nonadditive model structure, allow to quantify the relevance of interactions, and to identify the direction of change (increase or decrease in risk) implied by individual factor variations and by their cooperation. PMID:20199656

  13. 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.

  14. 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

  15. 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.

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

    E-print Network

    Bochsler, P.

    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. ...

  17. The double Caldeira-Leggett model: Derivation and solutions of the master equations, reservoir-induced interactions and decoherence

    E-print Network

    A. Cacheffo; M. H. Y. Moussa; M. A. de Ponte

    2009-03-25

    In this paper we analyze the double Caldeira-Leggett model: the path integral approach to two interacting dissipative harmonic oscillators. Assuming a general form of the interaction between the oscillators, we consider two different situations: i) when each oscillator is coupled to its own reservoir, and ii) when both oscillators are coupled to a common reservoir. After deriving and solving the master equation for each case, we analyze the decoherence process of particular entanglements in the positional space of both oscillators. To analyze the decoherence mechanism we have derived a general decay function for the off-diagonal peaks of the density matrix, which applies both to a common and separate reservoirs. We have also identified the expected interaction between the two dissipative oscillators induced by their common reservoir. Such reservoir-induced interaction, which gives rise to interesting collective damping effects, such as the emergence of relaxation- and decoherence-free subspaces, is shown to be blurred by the high-temperature regime considered in this study. However, we find that different interactions between the dissipative oscillators, described by rotating or counter-rotating terms, result in different decay rates for the interference terms of the density matrix.

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

    SciTech Connect

    Shcherbina, Natalia S.; Perminova, Irina V.; Kalmykov, Stephan N.; Kovalenko, Anton N.; Novikov, Alexander P.; Haire, Richard {Dick} G

    2007-01-01

    Actinides in their higher valence states (e.g., MO{sub 2}{sup +} and MO{sub 2}{sup 2+}, where M can be Np, Pu, etc) possess a higher potential for migration and in turn pose a substantial environmental threat. To minimize this potential for migration, reducing them to lower oxidation states (e.g., their tetravalent state) can be an attractive and efficient remedial process. These lower oxidation states are often much less soluble in natural aqueous media and are, therefore, less mobile in the environment. The research presented here focuses on assessing the performance of quinonoid-enriched humic derivatives with regards to complexing and/or reducing Np(V) present in solution. These 'designer' humics are essentially derived reducing agents that can serve as reactive components of a novel humic-based remediation technology. The derivatives are obtained by incorporating different quinonoid-moieties into leonardite humic acids. Five quinonoid-derivatives are tested in this work and all five prove more effective as reducing agents for selected actinides than the parent leonardite humic acid, and the hydroquinone derivatives are better than the catechol derivatives. The reduction kinetics and the Np(V) species formed with the different derivatives are studied via a batch mode using near-infrared (NIR)-spectroscopy. Np(V) reduction by the humic derivatives under anoxic conditions at 293 K and at pH 4.7 obeys first-order kinetics. Rate constants range from 1.70 x 10{sup -6} (parent humic acid) to 1.06 x 10{sup -5} sec{sup -1} (derivative with maximum hydroquinone content). Stability constants for Np(V)-humic complexes calculated from spectroscopic data produce corresponding Log{beta} values of 2.3 for parent humic acid and values ranging from 2.5 to 3.2 at pH 4.7 and from 3.3 to 3.7 at pH 7.4 for humic derivatives. Maximum constants are observed for hydroquinone-enriched derivatives. It is concluded that among the humic derivatives tested, the hydroquinone-enriched ones are the most useful for addressing remedial needs of actinide-contaminated aquifers.

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

    PubMed

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

    2007-10-15

    Actinides in their higher valence states (e.g., MO2+ and MO2(2+), where M can be Np, Pu, etc) possess a higher potential for migration and in turn pose a substantial environmental threat. To minimize this potential for migration, reducing them to lower oxidation states (e.g., their tetravalent state) can be an attractive and efficient remedial process. These lower oxidation states are often much less soluble in natural aqueous media and are, therefore, less mobile in the environment. The research presented here focuses on assessing the performance of quinonoid-enriched humic derivatives with regardsto complexing and/ or reducing Np(V) present in solution. These "designer" humics are essentially derived reducing agents that can serve as reactive components of a novel humic-based remediation technology. The derivatives are obtained by incorporating different quinonoid-moieties into leonardite humic acids. Five quinonoid-derivatives are tested in this work and all five prove more effective as reducing agents for selected actinides than the parent leonardite humic acid, and the hydroquinone derivatives are better than the catechol derivatives. The reduction kinetics and the Np(V) species formed with the different derivatives are studied via a batch mode using near-infrared (NIR)-spectroscopy. Np(V) reduction by the humic derivatives under anoxic conditions at 293 K and at pH 4.7 obeys first-order kinetics. Rate constants range from 1.70 x 10(-6) (parent humic acid) to 1.06 x 10(-5) sec(-1) (derivative with maximum hydroquinone content). Stability constants for Np(V)-humic complexes calculated from spectroscopic data produce corresponding Logbeta values of 2.3 for parent humic acid and values ranging from 2.5 to 3.2 at pH 4.7 and from 3.3 to 3.7 at pH 7.4 for humic derivatives. Maximum constants are observed for hydroquinone-enriched derivatives. It is concluded that among the humic derivatives tested, the hydroquinone-enriched ones are the most useful for addressing remedial needs of actinide-contaminated aquifers. PMID:17993141

  20. Order parameters and hysteresis behavior of a ferromagnetic Blume-Capel thin film: The role of the crystal field interactions

    NASA Astrophysics Data System (ADS)

    Yüksel, Yusuf

    2014-03-01

    As a complementary work of a recent study (Physica B 433 (2014) 96), ferromagnetic thin films in simple cubic lattice structure described by a spin-1 Blume-Capel Hamiltonian have been considered within the framework of effective-field theory (EFT). Thermal variations of bulk and surface order parameters (i.e. magnetization and quadrupolar moments), as well as hysteresis loops in the presence of modified surface interactions, and crystal fields have been examined. We have found that depending on the type of the phase transition (i.e. ordinary or extraordinary), bulk and surface order parameters may exhibit fairly non-monotonous and quite exotic profiles. Regarding the bulk and surface hysteresis loops, at a fixed set of system parameters, both the bulk and surface hysteresis loops exhibit the same coercivity whereas remanence of a bulk (surface) loop is greater than that of a surface (bulk) loop in ordinary (extraordinary) case.

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

    PubMed Central

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

    2013-01-01

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

  2. Page 1 of 32 Derivation of an interaction/regulation network describing

    E-print Network

    Lu?trek, Mitja

    transferred interaction and regulation links between genes/proteins from mouse to human on the basis mapping; Phylogenetic profiling; Co-expression; Gene Ontology; RNA interference; Stem cell #12;Page 3. They are supplemented by protein-DNA interactions describing gene regulation by the control of transcription. Describing

  3. 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

  4. 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, ...

  5. 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

  6. 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.

  7. 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

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

    PubMed

    Eriksson, Anders; Jacobi, Martin Nilsson; Nyström, Johan; Tunstrøm, Kolbjørn

    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

  9. Protein conjugated with aldehydes derived from lipid peroxidation as an independent parameter of the carbonyl stress in the kidney damage

    PubMed Central

    2011-01-01

    Background One of the well-defined and characterized protein modifications usually produced by oxidation is carbonylation, an irreversible non-enzymatic modification of proteins. However, carbonyl groups can be introduced into proteins by non-oxidative mechanisms. Reactive carbonyl compounds have been observed to have increased in patients with renal failure. In the present work we have described a procedure designed as aldehyde capture to calculate the protein carbonyl stress derived solely from lipid peroxidation. Methods Acrolein-albumin adduct was prepared as standard at alkaline pH. Rat liver microsomal membranes and serum samples from patients with diabetic nephropathy were subjected to the aldehyde capture procedure and aldol-protein formation. Before alkalinization and incubation, samples were precipitated and redisolved in 6M guanidine. The absorbances of the samples were read with a spectrophotometer at 266 nm against a blank of guanidine. Results Evidence showed abundance of unsaturated aldehydes derived from lipid peroxidation in rat liver microsomal membranes and in the serum of diabetic patients with advanced chronic kidney disease. Carbonyl protein and aldol-proteins resulted higher in the diabetic nephropathy patients (p < 0.004 and p < 0.0001 respectively). Conclusion The aldehyde-protein adduct represents a non oxidative component of carbonyl stress, independent of the direct amino acid oxidation and could constitute a practical and novelty strategy to measure the carbonyl stress derived solely from lipid peroxidation and particularly in diabetic nephropathy patients. In addition, we are in a position to propose an alternative explanation of why alkalinization of urine attenuates rhabdomyolysis-induced renal dysfunction. PMID:22059738

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

    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 Pöschl, 2005). We expect that the presented model framework will serve as a useful tool and basis for experimental and theoretical studies investigating and describing atmospheric aerosol and cloud surface chemistry and gas-particle interactions. In particular, it is meant to support the planning and design of laboratory experiments for the elucidation and determination of kinetic parameters; the establishment, evaluation, and quality assurance of comprehensive and self-consistent collections of rate parameters; and the development of detailed master mechanisms for process models and the derivation of simplified but yet realistic parameterizations for atmospheric and climate models.

  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.

    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.

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

    SciTech Connect

    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 VEGF???-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.

  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. 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

  16. Self-Assembled Fullerene-Derivative Monolayers on a Gold Substrate Using Phenanthroline-Au Interactions

    E-print Network

    Tao, Nongjian

    Self-Assembled Fullerene-Derivative Monolayers on a Gold Substrate Using Phenanthroline of the final product, phenanthrolyl[60]fullerene, compound 1, in a 43% isolated yield. Spontaneous self in the formation of a secondary layer of fullerene moieties. Since the fullerene diameter is approximately 1.0 nm

  17. Virus-host interactions in persistently FMDV-infected cells derived from bovine pharynx

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foot-and-mouth disease virus (FMDV) produces a disease in cattle characterized by vesicular lesions and a persistent infection with asymptomatic low-level production of virus. Here we describe the establishment of a persistently infected primary cell culture derived from bovine pharynx tissue (PBPT)...

  18. 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.

  19. Experimental and theoretical NMR studies of interaction between phenylalanine derivative and egg yolk lecithin.

    PubMed

    Wa??sa, Roksana; Ptak, Tomasz; Siod?ak, Dawid; Kupka, Teobald; Broda, Ma?gorzata A

    2014-06-01

    The interaction of phenylalanine diamide (Ac-Phe-NHMe) with egg yolk lecithin (EYL) in chloroform was studied by (1)H and (13)C NMR. Six complexes EYL-Ac-Phe-NHMe, stabilized by N-H···O or/and C-H···O hydrogen bonds, were optimized at M06-2X/6-31G(d,p) level. The assignment of EYL and Ac-Phe-NHMe NMR signals was supported using GIAO (gauge including atomic orbital) NMR calculations at VSXC and B3LYP level of theory combined with STO-3Gmag basis set. Results of our study indicate that the interaction of peptides with lecithin occurs mainly in the polar 'head' of the lecithin. Additionally, the most probable lecithin site of H-bond interaction with Ac-Phe-NHMe is the negatively charged oxygen in phosphate group that acts as proton acceptor. PMID:24639342

  20. Derivative expansion for the boundary interaction terms in the Casimir effect: generalized $?$-potentials

    E-print Network

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

    2009-08-12

    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

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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

  6. Higher-derivative gauge interactions of Bagger-Lambert-Gustavsson theory in N=1 superspace

    SciTech Connect

    Ketov, Sergei V.; Kobayashi, Shutaro

    2011-02-15

    We study the structure of the gauge sector of the Bagger-Lambert-Gustavsson theory in the form proposed by van Raamsdonk, adapted to three dimensions, N=1 superspace. By using the novel Higgs mechanism proposed by Mukhi and Papageorgakis, we derive the manifestly N=1 supersymmetric higher-order terms (beyond the supersymmetric Yang-Mills action) that follow from the Bagger-Lambert-Gustavsson theory in its expansion with respect to the inverse gauge coupling constant squared. We find that all those terms have at least one anticommutator of the super-Yang-Mills field strength superfields as a factor, and thus are reducible to the supersymmetric Yang-Mills terms with the higher (spacetime) derivatives.

  7. 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.

  8. 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…

  9. Dynamic calibration of higher eigenmode parameters of a cantilever in atomic force microscopy by using tip–surface 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 tip–surface force reconstruction technique and does not require any prior knowledge of the eigenmode shape or the particular form of the tip–surface interaction. The calibration method proposed requires a single-point force measurement by using a multimodal drive and its accuracy is independent of the unknown physical amplitude of a higher eigenmode. PMID:25383301

  10. 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.

  11. Derivation of the nonlinearity parameter B/A of saturated, unconsolidated marine sediments via a statistical approach

    NASA Astrophysics Data System (ADS)

    Lee, H.; Noh, E.; Ohm, W.-S.; Kwon, O.-C.

    2015-10-01

    Marine sediments are known to exhibit the nonlinearity parameter B/A that is much greater than that of homogeneous fluids and solids. The enormous value of B/A is particularly sensitive to the state of grain contacts. Although there exists a large body of literature that deals with the B/A of marine sediments, few studies have addressed how the random nature of grain contacts affects B/A. Here, we develop a model for the B/A of saturated, unconsolidated marine sediments, which accounts for random grain contacts. The number of contacts per grain and the distribution of contact stress between grains are treated statistically. The quadratic nonlinearity of the equivalent suspension of grains and the interstitial fluid is then combined with the nonlinearity arising from the random Hertzian contacts to produce the effective B/A of marine sediments.

  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 ([?/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. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

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

    PubMed

    Friedrich, Péter; Vella, Michael; Gulyás, Attila I; Freund, Tamás F; Káli, Szabolcs

    2014-01-01

    The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool. PMID:25071540

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

    PubMed Central

    Friedrich, Péter; Vella, Michael; Gulyás, Attila I.; Freund, Tamás F.; Káli, Szabolcs

    2014-01-01

    The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool. PMID:25071540

  18. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

  20. 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.

  1. 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.

  2. A robotic crawler exploiting directional frictional interactions: experiments, numerics, and derivation of a reduced model

    E-print Network

    Giovanni Noselli; Antonio DeSimone

    2014-08-26

    We present experimental and numerical results for a model crawler which is able to extract net positional changes from reciprocal shape changes, i.e. 'breathing-like' deformations, thanks to directional, frictional interactions with a textured solid substrate, mediated by flexible inclined feet. We also present a simple reduced model that captures the essential features of the kinematics and energetics of the gait, and compare its predictions with the results from experiments and from numerical simulations.

  3. 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.

  4. 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

  5. Interaction of carbonic anhydrase isozymes I, II, and IX with some pyridine and phenol hydrazinecarbothioamide derivatives.

    PubMed

    I??k, Semra; Vullo, Daniela; Durdagi, Serdar; Ekinci, Deniz; ?entürk, Murat; Çetin, Ahmet; ?entürk, Esra; Supuran, Claudiu T

    2015-12-01

    A series of hydrazinecarbothioamide derivatives incorporating ethyl, phenyl, tolyl, benzyl, and allyl moieties were prepared and tested as possible inhibitors of three members of the pH regulatory enzyme family, carbonic anhydrase (CA; EC 4.2.1.1). The inhibitory and activatory potencies of the compounds against the cytosolic human isoforms hCA I and hCA II and the transmembrane, tumor-associated hCA IX were analyzed by a hydrase assay with CO2 as substrate, and the inhibition constants (KI) were calculated. Most compounds investigated here exhibited nanomolar or low micromolar inhibition constants against the three isoenzymes. KI values were in the range of 34.1-871nM for hCA I and compounds 5-10 showed interesting activation of the hCA II with KA value of 0.81-12.5?M. Compounds 11-16 exhibited moderate inhibition effects on hCA IX in the range of 0.317-1.245?M but they were less effective for hCA II. Tested compounds were also investigated using in silico applications at the binding pockets of these three targets. The different mechanisms of inhibition by these tested compounds as compared to sulfonamides, and their diverse inhibition profile for these mammalian isozymes, makes this class of derivatives of great interest for the design of novel CA inhibitors. PMID:26520662

  6. Derivation of physiological inhalation rates in children, adults, and elderly based on nighttime and daytime respiratory parameters.

    PubMed

    Brochu, Pierre; Brodeur, Jules; Krishnan, Kannan

    2011-02-01

    The methodology developed in our previous studies ( Brochu et al. 2006a-c ) for the determination of physiological daily inhalation rates was improved by integrating into the calculation process, both nighttime and daytime respiratory parameters, namely oxygen uptake factors (H) and ventilatory equivalents (VQ). H values during fasting (0.2057±0.0018 L of O2/kcal; mean±SD) and postprandial phases (0.2059±0.0019 L of O2/kcal) as well as VQ values for subjects at rest (27.4±4.8 to 32.2±3.1, unitless) and during the aggregate daytime activities (29.9±4.2 to 33.7±7.2) were determined and combined with published doubly labeled water measurements for the calculation of daily inhalation rates in normal-weight males and females aged 0.22-96 years (n=1235). Depending upon the unit value chosen, the highest 99th percentiles for inhalation data were found in males aged 35 to <45 years (35.40 m3/day), 2.6 to <6 months (1.138 m3/kg-day), and 10 to <16.5 years (22.29 m3/m2-day). Means and percentiles expressed in m3/kg-day as well as in m3/m2-day suggest generally higher intakes of air pollutants in children than in adults and in males than in females (in g/kg-day or g/m2-day) for identical exposure concentrations and conditions. For instance, means in boys aged 2.6 to <6 months of 10.99±3.50 m3/m2-day and 0.572±0.191 m3/kg-day are 1.3- and 2.5-folds higher, respectively, than those in adult males 65?96 years old (8.42±2.13 m3/m2-day, 0.225±0.059 m3/kg-day). PMID:21299435

  7. Twenty-Two Years of Combined GPS Daily Coordinate Time Series and Derived Parameters: Implications for ITRF

    NASA Astrophysics Data System (ADS)

    Bock, Y.; Kedar, S.; Moore, A. W.; Fang, P.; Liu, Z.; Owen, S. E.; Squibb, M. B.

    2014-12-01

    The NASA-funded "Solid Earth Science ESDR System (SESES)" MEaSUREs project publishes long-term Earth Science Data Records (ESDRs), the result of a combined solution of independent daily JPL (GIPSY-OASIS software) and SIO (GAMIT software) GPS analyses, using a common source of metadata from the SOPAC database. The project has now produced up to twenty-two years of consistent, calibrated and validated ESDR products for over 3200 GPS stations from Western North America, other plate boundaries, and global networks made available through the GPS Explorer data portal and NASA's CDDIS archive. The combined solution of daily coordinate time series uses SOPAC h-files and JPL STACOV files as input to the st_filter software. The combined time series are then fit with the analyze_tseri software for daily positions/displacements, secular velocities, coseismic and postseismic displacements, as well as annual and semi-annual signatures and non-coseismic offsets due primarily to equipment (antenna) changes. Published uncertainties for the estimated parameters take into account temporal noise in the daily coordinate time series. The resulting residual coordinate time series with typical daily RMS values of 1.5-4.0 mm in the horizontal and 4.0-8.0 mm in the vertical can then can be mined for other signals such as transient deformation associated with earthquake tremor and slip (ETS) and hydrological effects. As part of this process we have catalogued and characterized coseismic displacements due to more than 80 earthquakes affecting over hundreds of regional and global stations, as well as significant postseismic deformation for the larger events. The larger events can affect stations 1000's of km from the earthquake epicenters and thus significantly affect the positions of stations used in defining the reference frame. We discuss the implications and contributions of our ongoing analysis to the long-term maintenance of the international terrestrial reference frame.

  8. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  10. 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.

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

    PubMed

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

    2014-04-01

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

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

    PubMed

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Mennickent, R. E.; Djuraševi?, G.; Cabezas, M.; Cséki, A.; Rosales, J. G.; Niemczura, E.; Araya, I.; Curé, 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.

  14. 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

  15. Guest-host interaction of C60 adsorbed on an ordered layer of phthalocyanine derivatives

    NASA Astrophysics Data System (ADS)

    Samuely, Tomas; Stoehr, Meike; Wintjes, Nikolai; Jung, Thomas A.; Haas, Marco; Liu, Shi-Xia; Decurtins, Silvio

    2008-03-01

    Symmetrically substituted phthalocyanines (Pcs) with eight peripheral di-(tert-butyl)phenoxy (DTPO) groups self-organize on noble metal substrates. The rotational degrees of freedom, specific for the DTPO substituents, allow a bowl-like conformation of the Pc derivatives and thus, hosting of the C60 molecules in two clearly distinguishable binding sites. Moreover, controlled manipulation of the C60 by the STM tip enables switching from one site to the other. Since Pcs are well-known electron donors and C60 molecules are good acceptors, it can be conceived as a system with two morphologically different donor-acceptor complexes, individually addressable by an STM tip. Preliminary STS analysis shows vast differences in the electronic properties. Exploration of such a system is of great interest because of its similarity to fundamental biological processes (photosynthesis, respiration), as well as its potential for application in energy storage, conversion, nanoelectronics, etc.

  16. 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.

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

    PubMed

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

    2016-01-01

    The LCC-CdTe quantum dots (QDs) hybrid was fabricated by mixing the N-lauryl-N, O-carboxymethyl chitosan (LCC) micelle with water-soluble CdTe QDs in an aqueous solution via hydrophobic forces and the electronic attraction. The structures of LCC and LCC-CdTe QDs hybrid were determined by differential scanning calorimetry (DSC), Fourier transform infrared (FT-IR) spectroscopy and transmission electron microscopy (TEM). The results showed that the lauryl and carboxymethyl were successfully grafted to chitosan oligosaccharide (CSO), and a number of CdTe QDs were encapsulated by LCC micelle to form a core/shell structure. The tested results of the fluorescent characteristics of LCC, CdTe QDs and LCC-CdTe QDs hybrid showed that there were some obvious fluorescent interactions between LCC and CdTe QDs. Meanwhile, with the change in LCC space structure, the fluorescent interactions between LCC and QDs showed different fluorescent characteristics. The QDs fluorescent (FL) intensity increased first and then decreased to almost quenching, while LCC FL intensity decreased continually. PMID:26232578

  19. 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.

  20. Model membrane interaction and DNA-binding of antimicrobial peptide Lasioglossin II derived from bee venom.

    PubMed

    Bandyopadhyay, Susmita; Lee, Meryl; Sivaraman, J; Chatterjee, Chiradip

    2013-01-01

    Lasioglossins, a new family of antimicrobial peptide, have been shown to have strong antimicrobial activity with low haemo-lytic and mast cell degranulation activity, and exhibit cytotoxic activity against various cancer cells in vitro. In order to understand the active conformation of these pentadecapeptides in membranes, we have studied the interaction of Lasioglossin II (LL-II), one of the members of Lasioglossins family with membrane mimetic micelle Dodecylphosphocholine (DPC) by fluorescence, Circular Dichroism (CD) and two dimensional (2D) (1)H NMR spectroscopy. Fluorescence experiments provide evidence of interaction of the N-terminal tryptophan residue of LL-II with the hydrophobic core of DPC micelle. CD results show an extended chain conformation of LL-II in water which is converted to a partial helical conformation in the presence of DPC micelle. Moreover we have determined the first three-dimensional NMR structure of LL-II bound to DPC micelle with rmsd of 0.36Å. The solution structure of LL-II shows hydrophobic and hydrophilic core formation in peptide pointing towards different direction in the presence of DPC. This amphipathic structure may allow this peptide to penetrate deeply into the interfacial region of negatively charged membranes and leading to local membrane destabilization. Further we have elucidated the DNA binding ability of LL-II by agarose gel retardation and fluorescence quenching experiments. PMID:23159628

  1. Secretion Modification Region-Derived Peptide Disrupts HIV-1 Nef's Interaction with Mortalin and Blocks Virus and Nef Exosome Release

    PubMed Central

    Shelton, Martin N.; Huang, Ming-Bo; Ali, Syed A.; Powell, Michael D.

    2012-01-01

    Nef is secreted from infected cells in exosomes and is found in abundance in the sera of HIV-infected individuals. Secreted exosomal Nef (exNef) induces apoptosis in uninfected CD4+ T cells and may be a key component of HIV pathogenesis. The exosomal pathway has been implicated in HIV-1 virus release, suggesting a possible link between these two viral processes. However, the underlying mechanisms and cellular components of exNef secretion have not been elucidated. We have previously described a Nef motif, the secretion modification region (SMR; amino acids 66 to 70), that is required for exNef secretion. In silico modeling data suggest that this motif can form a putative binding pocket. We hypothesized that the Nef SMR binds a cellular protein involved in protein trafficking and that inhibition of this interaction would abrogate exNef secretion. By using tandem mass spectrometry and coimmunoprecipitation with a novel SMR-based peptide (SMRwt) that blocks exNef secretion and HIV-1 virus release, we identified mortalin as an SMR-specific cellular protein. A second set of coimmunoprecipitation experiments with full-length Nef confirmed that mortalin interacts with Nef via Nef's SMR motif and that this interaction is disrupted by the SMRwt peptide. Overexpression and microRNA knockdown of mortalin revealed a positive correlation between exNef secretion levels and mortalin protein expression. Using antibody inhibition we demonstrated that the Nef/mortalin interaction is necessary for exNef secretion. Taken together, this work constitutes a significant step in understanding the underlying mechanism of exNef secretion, identifies a novel host-pathogen interaction, and introduces an HIV-derived peptide with antiviral properties. PMID:22013042

  2. 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

  3. 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

  4. 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

  5. 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

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

    PubMed

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

    2014-01-01

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

  7. 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; Jó?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-H···C(?), C,N(?)···C,N(?) and H···H types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment. PMID:22101546

  8. 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

  9. 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 ?-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

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

    PubMed

    Sternberg, Eleanore D; Lefèvre, Thierry; Li, James; de Castillejo, Carlos Lopez Fernandez; Li, Hui; Hunter, Mark D; de Roode, Jacobus C

    2012-11-01

    Organisms can protect themselves against parasite-induced fitness costs through resistance or tolerance. Resistance includes mechanisms that prevent infection or limit parasite growth while tolerance alleviates the fitness costs from parasitism without limiting infection. Although tolerance and resistance affect host-parasite coevolution in fundamentally different ways, tolerance has often been ignored in animal-parasite systems. Where it has been studied, tolerance has been assumed to be a genetic mechanism, unaffected by the host environment. Here we studied the effects of host ecology on tolerance and resistance to infection by rearing monarch butterflies on 12 different species of milkweed food plants and infecting them with a naturally occurring protozoan parasite. Our results show that monarch butterflies experience different levels of tolerance to parasitism depending on the species of milkweed that they feed on, with some species providing over twofold greater tolerance than other milkweed species. Resistance was also affected by milkweed species, but there was no relationship between milkweed-conferred resistance and tolerance. Chemical analysis suggests that infected monarchs obtain highest fitness when reared on milkweeds with an intermediate concentration, diversity, and polarity of toxic secondary plant chemicals known as cardenolides. Our results demonstrate that environmental factors-such as interacting species in ecological food webs-are important drivers of disease tolerance. PMID:23106703

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

    PubMed Central

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

    2012-01-01

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

  12. Running of Neutrino Oscillation Parameters in Matter with Flavor-Diagonal Non-Standard Interactions of the Neutrino

    E-print Network

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

    2015-01-01

    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 $\\theta_{12}$ and $\\theta_{13}$, while the flavor-diagonal NSI's only affect $\\theta_{23}$. The CP-violating phase $\\delta$ 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 numu to numu channel, which can probed in future atmospheric neutrino experiments, if the NSI's are of the order of their curren...

  13. 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

  14. 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

  15. 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

  16. 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 ?H and ?S 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.

  17. 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, 310K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ?H and ?S 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

  18. 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

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

    PubMed

    Kadar, Enikö; Cunliffe, Michael; Fisher, Andrew; Stolpe, Björn; 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

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

    PubMed

    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 Ca(2+) 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

  1. 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.

  2. 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.

  3. 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.

  4. Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions.

    PubMed

    Chaudhari, Rajan; Heim, Andrew J; Li, Zhijun

    2015-05-01

    Evidenced by the three-rounds of G-protein coupled receptors (GPCR) Dock competitions, improving homology modeling methods of helical transmembrane proteins including the GPCRs, based on templates of low sequence identity, remains an eminent challenge. Current approaches addressing this challenge adopt the philosophy of "modeling first, refinement next". In the present work, we developed an alternative modeling approach through the novel application of available multiple templates. First, conserved inter-residue interactions are derived from each additional template through conservation analysis of each template-target pairwise alignment. Then, these interactions are converted into distance restraints and incorporated in the homology modeling process. This approach was applied to modeling of the human ?2 adrenergic receptor using the bovin rhodopsin and the human protease-activated receptor 1 as templates and improved model quality was demonstrated compared to the homology model generated by standard single-template and multiple-template methods. This method of "refined restraints first, modeling next", provides a fast and complementary way to the current modeling approaches. It allows rational identification and implementation of additional conserved distance restraints extracted from multiple templates and/or experimental data, and has the potential to be applicable to modeling of all helical transmembrane proteins. PMID:25503850

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

    NASA Astrophysics Data System (ADS)

    Pöschl, 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 Pöschl, 2007). We expect that the presented model framework will serve as a useful tool and basis for experimental and theoretical studies investigating and describing atmospheric aerosol and cloud surface chemistry and gas-particle interactions. It shall help to end the "Babylonian confusion" that seems to inhibit scientific progress in the understanding of heterogeneous chemical reactions and other multiphase processes in aerosols and clouds. In particular, it shall support the planning and design of laboratory experiments for the elucidation and determination of fundamental kinetic parameters; the establishment, evaluation, and quality assurance of comprehensive and self-consistent collections of rate parameters; and the development of detailed master mechanisms for process models and derivation of simplified but yet realistic parameterizations for atmospheric and climate models.

  6. 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.

  7. Interactions between bufadienolides derived from toad venom and verapamil in langendorff-perfused guinea-pig hearts.

    PubMed

    Ma, Hongyue; Zhou, Jing; Shang, Erxin; Zhang, Junfeng; Lu, Wenjuan; Zhan, Zhen; Qian, Dawei; Duan, Jinao; Fan, Xinsheng

    2013-02-01

    Drug toxicity may occur due to dangerous drug combination. We aimed to investigate the influence of verapamil (a P-gp inhibitor)--bufadienolides interaction on cardiotoxicity and bufadienolide uptake by the isolated heart. The study was performed in Langendorff isolated perfused guinea-pig hearts by bufadienolides infusion in the absence and presence of verapamil (250, 500ng/ml). Arrhythmia parameters were evaluated by ECG and the content of bufadienolides in heart were measured by ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS). In the present of verapamil, the wide QRS duration and lightly rapid heart rate (HR) were markedly reduced in the early stage of bufadienolide intoxication. However, the ECG changes characterized by prolonged P-R interval, and slow heart rate and low QRS amplitude in the late stage of bufadienolide intoxication were significantly enhanced. Furthermore, the contents of a variety of bufadienolide compounds in the verapamil+bufadienolide group were significantly higher when cardiac arrest occurred. Although verapamil reduced the bufadienolide-induced ventricular arrhythmias, verapamil worsened heart block and lethal bradycardia of bufadienolides partly via increasing the uptake of bufadienolides in heart tissue, which could compromise the protective effects of verapamil against bufadienolide intoxication. These results suggested that the verapamil may produce dangerous interactions with drugs containing bufadienolides. PMID:22921427

  8. 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 se

  9. The modified extended Hansen method to determine partial solubility parameters of drugs containing a single hydrogen bonding group and their sodium derivatives: benzoic acid/Na and ibuprofen/Na.

    PubMed

    Bustamante, P; Pena, M A; Barra, J

    2000-01-20

    Sodium salts are often used in drug formulation but their partial solubility parameters are not available. Sodium alters the physical properties of the drug and the knowledge of these parameters would help to predict adhesion properties that cannot be estimated using the solubility parameters of the parent acid. This work tests the applicability of the modified extended Hansen method to determine partial solubility parameters of sodium salts of acidic drugs containing a single hydrogen bonding group (ibuprofen, sodium ibuprofen, benzoic acid and sodium benzoate). The method uses a regression analysis of the logarithm of the experimental mole fraction solubility of the drug against the partial solubility parameters of the solvents, using models with three and four parameters. The solubility of the drugs was determined in a set of solvents representative of several chemical classes, ranging from low to high solubility parameter values. The best results were obtained with the four parameter model for the acidic drugs and with the three parameter model for the sodium derivatives. The four parameter model includes both a Lewis-acid and a Lewis-base term. Since the Lewis acid properties of the sodium derivatives are blocked by sodium, the three parameter model is recommended for these kind of compounds. Comparison of the parameters obtained shows that sodium greatly changes the polar parameters whereas the dispersion parameter is not much affected. Consequently the total solubility parameters of the salts are larger than for the parent acids in good agreement with the larger hydrophilicity expected from the introduction of sodium. The results indicate that the modified extended Hansen method can be applied to determine the partial solubility parameters of acidic drugs and their sodium salts. PMID:10601690

  10. 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).

  11. 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

  12. A simultaneous study of ionospheric parameters derived from FORMOSAT-3/COSMIC, GRACE, and CHAMP missions over middle, low, and equatorial latitudes: Comparison with ionosonde data

    NASA Astrophysics Data System (ADS)

    Habarulema, John Bosco; Katamzi, Zama Thobeka; Yizengaw, Endawoke

    2014-09-01

    Accurate ionospheric modeling efforts are partly restricted by lack of enough reliable ground-based data and the inability to validate the existing space-based data. In this article, we present a first time comprehensive reliability and validation check of ionospheric data derived using the GPS Radio Occultation (RO) Technique (from three separate missions: FORMOSAT-3/COSMIC, GRACE, and CHAMP) by comparing RO data with ionosonde data for low-latitude, equatorial, and midlatitude stations, simultaneously. This paper discusses two main objectives: (a) Determination of the appropriate spatial resolutions for effective RO and ionosonde data comparisons and (b) Estimating the accuracy of the ionospheric parameters derived from RO missions with respect to ionosonde data within the African sector. For the first time, ionospheric parameters retrieved from RO data have been compared (in details) to ionosonde data over the African sector, specifically for the South African midlatitude stations Grahamstown, GR13L (33.3°S, 26.5°E), and Madimbo, MU12K (22.4°S, 30.9°E). For the equatorial and low-latitude regions, data for Fortaleza FZA0M (3.8°S, 38°W), Brazil, and Ascension Islands AS00Q (7.9°S, 14.4°W) was analyzed. A simple but important method to determine the latitudinal and longitudinal range to be used in comparison with ionosonde data has been established. Based on statistical analysis, it is found that 4.5°×4.5°, 3°×3°, and 4°×4° are the approximate suitable spatial resolutions in both latitude and longitude spaces over an ionosonde station for effective comparisons for midlatitude, low-latitude, and equatorial regions, respectively. Appropriate spatial coverage for effective comparisons vary with region and therefore a constant assumption should not be applied on regional/global basis especially if the studies/investigations or modeling extends from middle to low/equatorial latitude zones. For the three latitude regions, COSMIC overestimates the maximum height of the F2 layer (hmF2) and underestimates the maximum electron densities. These results provide a step-by-step basis and motivation for the usage of RO data in ionospheric modeling (especially for models which give average conditions) and characterisation over regions that do not have sufficient ground-based instruments/data.

  13. 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.

  14. 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 b1–b2 domains. NRP-1’s 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

  15. 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

  16. Profiling the Interaction Mechanism of Quinoline/Quinazoline Derivatives as MCHR1 Antagonists: An in Silico Method

    PubMed Central

    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 (R2ncv) = 0.841 and the predicted correlation coefficient (R2pred) = 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

  17. 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 400°C 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

  18. 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.

  19. 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.

  20. Interactive effects of elevated CO2 concentration and irrigation on photosynthetic parameters and yield of maize in Northeast China.

    PubMed

    Meng, Fanchao; Zhang, Jiahua; Yao, Fengmei; Hao, Cui

    2014-01-01

    Maize is one of the major cultivated crops of China, having a central role in ensuring the food security of the country. There has been a significant increase in studies of maize under interactive effects of elevated CO2 concentration ([CO2]) and other factors, yet the interactive effects of elevated [CO2] and increasing precipitation on maize has remained unclear. In this study, a manipulative experiment in Jinzhou, Liaoning province, Northeast China was performed so as to obtain reliable results concerning the later effects. The Open Top Chambers (OTCs) experiment was designed to control contrasting [CO2] i.e., 390, 450 and 550 µmol·mol(-1), and the experiment with 15% increasing precipitation levels was also set based on the average monthly precipitation of 5-9 month from 1981 to 2010 and controlled by irrigation. Thus, six treatments, i.e. C550W+15%, C550W0, C450W+15%, C450W0, C390W+15% and C390W0 were included in this study. The results showed that the irrigation under elevated [CO2] levels increased the leaf net photosynthetic rate (Pn) and intercellular CO2 concentration (Ci) of maize. Similarly, the stomatal conductance (Gs) and transpiration rate (Tr) decreased with elevated [CO2], but irrigation have a positive effect on increased of them at each [CO2] level, resulting in the water use efficiency (WUE) higher in natural precipitation treatment than irrigation treatment at elevated [CO2] levels. Irradiance-response parameters, e.g., maximum net photosynthetic rate (Pnmax) and light saturation points (LSP) were increased under elevated [CO2] and irrigation, and dark respiration (Rd) was increased as well. The growth characteristics, e.g., plant height, leaf area and aboveground biomass were enhanced, resulting in an improved of yield and ear characteristics except axle diameter. The study concluded by reporting that, future elevated [CO2] may favor to maize when coupled with increasing amount of precipitation in Northeast China. PMID:24848097

  1. Wh-Questions in Child L2 French: Derivational Complexity and Its Interactions with L1 Properties, Length of Exposure, Age of Exposure, and the Input

    ERIC Educational Resources Information Center

    Prévost, Philippe; Strik, Nelleke; Tuller, Laurie

    2014-01-01

    This study investigates how derivational complexity interacts with first language (L1) properties, second language (L2) input, age of first exposure to the target language, and length of exposure in child L2 acquisition. We compared elicited production of "wh"-questions in French in two groups of 15 participants each, one with L1 English…

  2. Magma-derived gas influx and water-rock interactions in the volcanic aquifer of Mt. Vesuvius, Italy

    NASA Astrophysics Data System (ADS)

    Federico, C.; Aiuppa, A.; Allard, P.; Bellomo, S.; Jean-Baptiste, P.; Parello, F.; Valenza, M.

    2002-03-01

    We report in this paper a systematic investigation of the chemical and isotopic composition of groundwaters flowing in the volcanic aquifer of Mt. Vesuvius during its current phase of dormancy, including the first data on dissolved helium isotope composition and tritium content. The relevant results on dissolved He and C presented in this paper reveal that an extensive interaction between rising magmatic volatiles and groundwaters currently takes place at Vesuvius. Vesuvius groundwaters are dilute (mean TDS ˜ 2800 mg/L) hypothermal fluids ( mean T = 17.7°C) with a prevalent alkaline-bicarbonate composition. Calcium-bicarbonate groundwaters normally occur on the surrounding Campanian Plain, likely recharged from the Apennines. ?D and ? 18O data evidence an essentially meteoric origin of Vesuvius groundwaters, the contribution from either Tyrrhenian seawater or 18O-enriched thermal water appearing to be small or negligible. However, the dissolution of CO 2-rich gases at depth promotes acid alteration and isochemical leaching of the permeable volcanic rocks, which explains the generally low pH and high total carbon content of waters. Attainment of chemical equilibrium between the rock and the weathering solutions is prevented by commonly low temperature (10 to 28°C) and acid-reducing conditions. The chemical and isotope (C and He) composition of dissolved gases highlights the magmatic origin of the gas phase feeding the aquifer. We show that although the pristine magmatic composition may vary upon gas ascent because of either dilution by a soil-atmospheric component or fractionation processes during interaction with the aquifer, both 13C/ 12C and 3He/ 4He measurements indicate the contribution of a magmatic component with a ? 13C ˜ 0‰ and R/R a of ˜2.7, which is consistent with data from Vesuvius fumaroles and phenocryst melt inclusions in olivine phenocrysts. A main control of tectonics on gas ascent is revealed by data presented in this paper. For example, two areas of high CO 2 release and enhanced rock leaching are recognized on the western (Torre del Greco) and southwestern (Torre Annunziata-Pompeii) flanks of Vesuvius, where important NE-SW and NW-SE tectonic structures are recognized. In contrast, waters flowing through the northern sector of the volcano are generally colder, less saline, and CO 2 depleted, despite in some cases containing significant concentrations of magma-derived helium. The remarkable differences among the various sectors of the volcano are reconciled in a geochemical interpretative model, which is consistent with recent structural and geophysical evidences on the structure of Somma-Vesuvius volcanic complex.

  3. Comparison of anomalies and trends of OLR as observed by CERES and computed from geophysical parameters derived from analysis of AIRS/AMSU data

    NASA Astrophysics Data System (ADS)

    Susskind, J.; Molnar, G. I.

    2009-12-01

    Anomalies and trends of OLR serve as important indicators of climate change. Several satellite based instruments currently provide information related to OLR. CERES, on board the EOS Aqua and Terra satellites, contains broad band radiometers that measure total flux and short-wave flux, from which OLR is determined. AIRS is a high spectral resolution IR sounder on EOS Aqua that measures IR radiances covering most of the spectral interval 650 cm-1 to 2670 cm-1. These observations enable the determination of detailed information about atmospheric temperature, moisture, and ozone profiles, as well as surface skin temperatures and cloud parameters. The AIRS OLR product is the total flux over the spectral interval 2 cm-1 to2750 cm-1 computed for the surface and atmospheric state determined from AIRS observations. We compared spatial anomalies and trends of OLR, over the seven year period September 2002 through August 2009, as observed by CERES and computed using Version 5 AIRS products. These two sets of OLR anomalies and trends, obtained in very different ways, agree with each other almost perfectly in essentially every detail. This important finding shows that a very stable high spectral infra-red sounder such as AIRS corroborates the anomalies and trends of OLR obtained from CERES. More significantly, anomalies and trends of the individual geophysical parameters derived from AIRS explain the detailed causes of the anomalies and trends of CERES OLR. Both sets of results show that global mean OLR has been decreasing at a rate of 0.12 W/m2/yr over the seven year time period under study. Both also confirm that the primary cause of this is due to changes in the tropics, in which OLR has been decreasing at a rate of 0.27 W/m2/yr. AIRS products show that the decrease of tropical OLR is a result of increasing tropical atmospheric water vapor and cloud cover over the time period studied, which in turn is responding to a very strong El Nino/ La Nina cycle. Equatorial ocean temperatures between 160E and 120W cooled considerably during this time period, with corresponding local decreases in mid-tropospheric humidity and cloud cover, resulting in increases in local OLR. This was more than compensated by substantial increases in water vapor and cloud cover elsewhere in the tropics, resulting in a net decrease in tropical OLR.

  4. Comparison of Anomalies and Trends of OLR as Observed by CERES and Computed from Geophysical Parameters Derived from Analysis of AIRS/AMSU Data

    NASA Technical Reports Server (NTRS)

    Susskind, Joel; Molnar, Gyula I.

    2009-01-01

    Anomalies and trends of outgoing longwave radiation (OLR) serve as important indicators of climate change. Several satellite based instruments currently provide information related to OLR. CERES, on board the EOS Aqua and Terra satellites, contains broad band radiometers that measure total flux and short-wave flux, from which OLR is determined. AIRS is a high spectral resolution IR sounder on EOS Aqua that measures IR radiances covering most of the spectral interval 650 cm-1 to 2670 cm-1. These observations enable the determination of detailed information about atmospheric temperature, moisture, and ozone profiles, as well as surface skin temperatures and cloud parameters. The AIRS OLR product is the total flux over the spectral interval 2 cm-1 to2750 cm-1 computed for the surface and atmospheric state determined from AIRS observations. We compared spatial anomalies and trends of OLR, over the seven year period September 2002 through August 2009, as observed by CERES and computed using Version 5 AIRS products. These two sets of OLR anomalies and trends, obtained in very different ways, agree with each other almost perfectly in essentially every detail. This important finding shows that a very stable high spectral infra-red sounder such as AIRS corroborates the anomalies and trends of OLR obtained from CERES. More significantly, anomalies and trends of the individual geophysical parameters derived from AIRS explain the detailed causes of the anomalies and trends of CERES OLR. Both sets of results show that global mean OLR has been decreasing at a rate of 0.12 W/m2/yr over the seven year time period under study. Both also confirm that the primary cause of this is due to changes in the tropics, in which OLR has been decreasing at a rate of 0.27 W/m2/yr. AIRS products show that the decrease of tropical OLR is a result of increasing tropical atmospheric water vapor and cloud cover over the time period studied, which in turn is responding to a very strong E1 Nino/ La Nina cycle. Equatorial ocean temperatures between 160E and 120W cooled considerably during this time period, with corresponding local decreases in mid-tropospheric humidity and cloud cover, resulting in increases in local OLR. This was more than compensated by substantial increases in water vapor and cloud cover elsewhere in the tropics, resulting in a net decrease in tropical OLR.

  5. Structure of Ca2+ -Bound S100A4 and Its Interaction With Peptides Derived from Nonmuscle Myosin-IIA

    SciTech Connect

    Malashkevich,V.; Varney, K.; Garrett, S.; Wilder, P.; Knight, D.; Charpentier, T.; Ramagopal, U.; Almo, S.; Weber, D.; Bresnick, A.

    2008-01-01

    S100A4, also known as mts1, is a member of the S100 family of Ca2+-binding proteins that is directly involved in tumor invasion and metastasis via interactions with specific protein targets, including nonmuscle myosin-IIA (MIIA). Human S100A4 binds two Ca2+ ions with the typical EF-hand exhibiting an affinity that is nearly 1 order of magnitude tighter than that of the pseudo-EF-hand. To examine how Ca2+ modifies the overall organization and structure of the protein, we determined the 1.7 Angstroms crystal structure of the human Ca2+-S100A4. Ca2+ binding induces a large reorientation of helix 3 in the typical EF-hand. This reorganization exposes a hydrophobic cleft that is comprised of residues from the hinge region, helix 3, and helix 4, which afford specific target recognition and binding. The Ca2+-dependent conformational change is required for S100A4 to bind peptide sequences derived from the C-terminal portion of the MIIA rod with submicromolar affinity. In addition, the level of binding of Ca2+ to both EF-hands increases by 1 order of magnitude in the presence of MIIA. NMR spectroscopy studies demonstrate that following titration with a MIIA peptide, the largest chemical shift perturbations and exchange broadening effects occur for residues in the hydrophobic pocket of Ca2+-S100A4. Most of these residues are not exposed in apo-S100A4 and explain the Ca2+ dependence of formation of the S100A4-MIIA complex. These studies provide the foundation for understanding S100A4 target recognition and may support the development of reagents that interfere with S100A4 function.

  6. Distinct functions of macrophage-derived and cancer cell-derived cathepsin Z combine to promote tumor malignancy via interactions with the extracellular matrix

    PubMed Central

    Akkari, Leila; Gocheva, Vasilena; Kester, Jemila C.; Hunter, Karen E.; Quick, Marsha L.; Sevenich, Lisa; Wang, Hao-Wei; Peters, Christoph; Tang, Laura H.; Klimstra, David S.; Reinheckel, Thomas

    2014-01-01

    During the process of tumor progression, cancer cells can produce the requisite growth- and invasion-promoting factors and can also rely on noncancerous cells in the tumor microenvironment as an alternative, cell-extrinsic source. However, whether the cellular source influences the function of such tumor-promoting factors remains an open question. Here, we examined the roles of the cathepsin Z (CtsZ) protease, which is provided by both cancer cells and macrophages in pancreatic neuroendocrine tumors in humans and mice. We found that tumor proliferation was exclusively regulated by cancer cell-intrinsic functions of CtsZ, whereas tumor invasion required contributions from both macrophages and cancer cells. Interestingly, several of the tumor-promoting functions of CtsZ were not dependent on its described catalytic activity but instead were mediated via the Arg–Gly–Asp (RGD) motif in the enzyme prodomain, which regulated interactions with integrins and the extracellular matrix. Together, these results underscore the complexity of interactions within the tumor microenvironment and indicate that cellular source can indeed impact molecular function. PMID:25274726

  7. Peptides derived from human galectin-3 N-terminal tail interact with its carbohydrate recognition domain in a phosphorylation-dependent manner

    SciTech Connect

    Berbís, M. Álvaro; André, Sabine; Cañada, F. Javier; Pipkorn, Rüdiger; Ippel, Hans; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 ; Mayo, Kevin H.; Kübler, Dieter; Gabius, Hans-Joachim; Jiménez-Barbero, Jesús

    2014-01-03

    Highlights: •Galectin-3 is composed of a carbohydrate recognition domain and an N-terminal tail. •Synthetic peptides derived from the tail are shown to interact with the CRD. •This interaction is modulated by Ser- and Tyr-phosphorylation of the peptides. -- Abstract: Galectin-3 (Gal-3) is a multi-functional effector protein that functions in the cytoplasm and the nucleus, as well as extracellularly following non-classical secretion. Structurally, Gal-3 is unique among galectins with its carbohydrate recognition domain (CRD) attached to a rather long N-terminal tail composed mostly of collagen-like repeats (nine in the human protein) and terminating in a short non-collagenous terminal peptide sequence unique in this lectin family and not yet fully explored. Although several Ser and Tyr sites within the N-terminal tail can be phosphorylated, the physiological significance of this post-translational modification remains unclear. Here, we used a series of synthetic (phospho)peptides derived from the tail to assess phosphorylation-mediated interactions with {sup 15}N-labeled Gal-3 CRD. HSQC-derived chemical shift perturbations revealed selective interactions at the backface of the CRD that were attenuated by phosphorylation of Tyr 107 and Tyr 118, while phosphorylation of Ser 6 and Ser 12 was essential. Controls with sequence scrambling underscored inherent specificity. Our studies shed light on how phosphorylation of the N-terminal tail may impact on Gal-3 function and prompt further studies using phosphorylated full-length protein.

  8. Interaction between Marine-Derived n-3 Long Chain Polyunsaturated Fatty Acids and Uric Acid on Glucose Metabolism and Risk of Type 2 Diabetes Mellitus: A Case-Control Study

    PubMed Central

    Li, Kelei; Wu, Kejian; Zhao, Yimin; Huang, Tao; Lou, Dajun; Yu, Xiaomei; Li, Duo

    2015-01-01

    The present case-control study explored the interaction between marine-derived n-3 long chain polyunsaturated fatty acids (n-3 LC PUFAs) and uric acid (UA) on glucose metabolism and risk of type 2 diabetes mellitus (T2DM). Two hundred and eleven healthy subjects in control group and 268 T2DM subjects in case group were included. Plasma phospholipid (PL) fatty acids and biochemical parameters were detected by standard methods. Plasma PL C22:6n-3 was significantly lower in case group than in control group, and was negatively correlated with fasting glucose (r = ?0.177, p < 0.001). Higher plasma PL C22:6n-3 was associated with lower risk of T2DM, and the OR was 0.32 (95% confidence interval (CI), 0.12 to 0.80; p = 0.016) for per unit increase of C22:6n-3. UA was significantly lower in case group than in control group. UA was positively correlated with fasting glucose in healthy subjects, but this correlation became negative in T2DM subjects. A significant interaction was observed between C22:6n-3 and UA on fasting glucose (p for interaction = 0.005): the lowering effect of C22:6n-3 was only significant in subjects with a lower level of UA. In conclusion, C22:6n-3 interacts with UA to modulate glucose metabolism. PMID:26343686

  9. Interaction of inflammatory and anti-inflammatory responses in microglia by Staphylococcus aureus-derived lipoteichoic acid

    SciTech Connect

    Huang, Bor-Ren; Tsai, Cheng-Fang; Lin, Hsiao-Yun; Tseng, Wen-Pei; Huang, Shiang-Suo; Wu, Chi-Rei; Lin, Chingju; Yeh, Wei-Lan; Lu, Dah-Yuu

    2013-05-15

    We investigated the interaction between proinflammatory and inflammatory responses caused by Staphylococcus aureus-derived lipoteichoic acid (LTA) in primary cultured microglial cells and BV-2 microglia. LTA induced inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) protein levels increase in a concentration- and time-dependent manner. Meanwhile, LTA also increased nitric oxide (NO) and PGE{sub 2} production in microglia. Administration of TLR2 antagonist effectively inhibited LTA-induced NO, iNOS, and COX-2 expression. Moreover, treatment of cells with LTA caused a time-dependent activation of ERK, p38, JNK, as well as AKT. We also found that LTA-induced iNOS and COX-2 up-regulation were attenuated by p38, JNK, and PI3-kinase inhibitors. On the other hand, LTA-enhanced HO-1 expression was attenuated by p38 and PI3-kinase inhibitors. Treatment of cells with NF-?B and AP-1 inhibitors antagonized LTA-induced iNOS and COX-2 expression. However, only NF-?B inhibitors reduced LTA-induced HO-1 expression in microglia. Furthermore, stimulation of cells with LTA also activated I?B? phosphorylation, p65 phosphorylation at Ser{sup 536}, and c-Jun phosphorylation. Moreover, LTA-induced increases of ?B-DNA and AP-1-DNA binding activity were inhibited by p38, JNK, and PI3-kinase inhibitors. HO-1 activator CoPP IX dramatically reversed LTA-induced iNOS expression. Our results provided mechanisms linking LTA and inflammation/anti-inflammation, and indicated that LTA plays a regulatory role in microglia activation. - Highlights: • LTA causes an increase in iNOS, COX-2, and HO-1 expression in microglia. • LTA induces iNOS and COX-2 expression through TLR-2/NF-?B and AP-1 pathways. • HO-1 expression is regulated through p38, JNK, PI3K/AKT and AP-1 pathways. • Induced HO-1 reduces LTA-induced iNOS expression. • LTA plays a regulatory role on inflammatory/anti-inflammatory responses.

  10. Integrating effective drought index (EDI) and remote sensing derived parameters for agricultural drought assessment and prediction in Bundelkhand region of India

    NASA Astrophysics Data System (ADS)

    Padhee, S. K.; Nikam, B. R.; Aggarwal, S. P.; Garg, V.

    2014-11-01

    Drought is an extreme condition due to moisture deficiency and has adverse effect on society. Agricultural drought occurs when restraining soil moisture produces serious crop stress and affects the crop productivity. The soil moisture regime of rain-fed agriculture and irrigated agriculture behaves differently on both temporal and spatial scale, which means the impact of meteorologically and/or hydrological induced agriculture drought will be different in rain-fed and irrigated areas. However, there is a lack of agricultural drought assessment system in Indian conditions, which considers irrigated and rain-fed agriculture spheres as separate entities. On the other hand recent advancements in the field of earth observation through different satellite based remote sensing have provided researchers a continuous monitoring of soil moisture, land surface temperature and vegetation indices at global scale, which can aid in agricultural drought assessment/monitoring. Keeping this in mind, the present study has been envisaged with the objective to develop agricultural drought assessment and prediction technique by spatially and temporally assimilating effective drought index (EDI) with remote sensing derived parameters. The proposed technique takes in to account the difference in response of rain-fed and irrigated agricultural system towards agricultural drought in the Bundelkhand region (The study area). The key idea was to achieve the goal by utilizing the integrated scenarios from meteorological observations and soil moisture distribution. EDI condition maps were prepared from daily precipitation data recorded by Indian Meteorological Department (IMD), distributed within the study area. With the aid of frequent MODIS products viz. vegetation indices (VIs), and land surface temperature (LST), the coarse resolution soil moisture product from European Space Agency (ESA) were downscaled using linking model based on Triangle method to a finer resolution soil moisture product. EDI and spatially downscaled soil moisture products were later used with MODIS 16 days NDVI product as key elements to assess and predict agricultural drought in irrigated and rain-fed agricultural systems in Bundelkhand region of India. Meteorological drought, soil moisture deficiency and NDVI degradation were inhabited for each and every pixel of the image in GIS environment, for agricultural impact assessment at a 16 day temporal scale for Rabi seasons (October-April) between years 2000 to 2009. Based on the statistical analysis, good correlations were found among the parameters EDI and soil moisture anomaly; NDVI anomaly and soil moisture anomaly lagged to 16 days and these results were exploited for the development of a linear prediction model. The predictive capability of the developed model was validated on the basis of spatial distribution of predicted NDVI which was compared with MODIS NDVI product in the beginning of preceding Rabi season (Oct-Dec of 2010).The predictions of the model were based on future meteorological data (year 2010) and were found to be yielding good results. The developed model have good predictive capability based on future meteorological data (rainfall data) availability, which enhances its utility in analyzing future Agricultural conditions if meteorological data is available.

  11. Five binary supramolecular organic salts constructed from 2-aminoheterocyclic compounds and carboxylic acid derivatives through strong and weak non-covalent interactions

    NASA Astrophysics Data System (ADS)

    Jin, Shouwen; Zhang, Wenbiao; Liu, Li; Wang, Daqi; He, Haidong; Shi, Tao; Lin, Feng

    2011-04-01

    Studies concentrating on hydrogen bonding between the base of 2-aminoheterocyclic compounds 5,7-dimethyl-1,8-naphthyridine-2-amine, 4-phenylthiazol-2-amine, and carboxylic acid derivatives have led to an increased understanding of the role 2-aminoheterocyclic compounds have in binding with carboxylic acid derivatives. Here anhydrous and hydrous multicomponent adducts of 2-aminoheterocyclic compounds such as 5,7-dimethyl-1,8-naphthyridine-2-amine, and 4-phenylthiazol-2-amine have been prepared with 2-chloronicotinic acid, p-hydroxy benzoic acid, maleic acid, and phthalic acid. The five crystalline forms reported are organic salts of which the crystals and complexes were characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. All supramolecular architectures of salts 1- 5 are stabilized by N sbnd H···O hydrogen bonds as well as other non-covalent interactions. These weak interactions combined, all the complexes displayed 3D structure.

  12. Comprehensive Two-Dimensional Hydrophilic Interaction Chromatography (HILIC) × Reversed-Phase Liquid Chromatography Coupled to High-Resolution Mass Spectrometry (RP-LC-UV-MS) Analysis of Anthocyanins and Derived Pigments in Red Wine.

    PubMed

    Willemse, Chandré M; Stander, Maria A; Vestner, Jochen; Tredoux, Andreas G J; de Villiers, André

    2015-12-15

    Changes in anthocyanin chemistry represent some of the most important transformations involved in red wine aging. However, accurate analysis of the derived pigments, as required to study the evolution of anthocyanins and tannins during aging, is hampered by their extreme structural diversity, low levels, and the fact that many of these compounds have identical mass spectral characteristics. In this context, chromatographic separation is critical. In this contribution, the application of online hydrophilic interaction chromatography (HILIC) × reversed-phase liquid chromatography (RP-LC) separation coupled to high-resolution mass spectrometry (MS) is described for the detailed characterization of anthocyanins and their derived pigments in aged red wine. A systematic approach was followed for the optimization of HILIC × RP-LC separation parameters using a capillary liquid chromatography (LC) system in the first dimension and an ultrahigh-pressure LC system in the second dimension to ensure maximum sensitivity and performance. Ninety four (94) anthocyanin-derived pigments were tentatively identified in one- and six-year-old Pinotage wines using accurate mass and fragmentation information obtained using quadrupole-time-of-flight mass spectrometry (Q-TOF-MS). Online HILIC × RP-LC-MS was found to offer high-resolution separation, because of the combination of two different separation modes, while the structured elution order observed improved the certainty in compound identification. Therefore, this approach shows promise for the detailed elucidation of the chemical alteration of anthocyanins during wine aging. PMID:26554292

  13. Interactions between potential anti-tumour 2,5-bis(1-aziridinyl)-1,4-benzoquinone derivatives and glutathione: reductive activation, conjugation and DNA damage.

    PubMed

    Lusthof, K J; de Mol, N J; Janssen, L H; Prins, B; Verboom, W; Reinhoudt, D N

    1990-08-01

    The interaction between glutathione and potential anti-tumour 3,6-disubstituted 2,5-bis(1-aziridinyl)-1,4-benzoquinone (BABQ) derivatives has been studied using u.v. spectrophotometry and h.p.l.c. The formation of BABQ-glutathione adducts was demonstrated in vitro for the BABQ parent compound (TW13), triaziquone (2,3,5-tris(1-aziridinyl)-1,4-benzoquinone) and for BABQ derivatives containing halogen substituents. The clinically-used BABQ derivative diaziquone (AZQ; 2,5-bis(1-aziridinyl)-3,6-bis(ethoxycarbonylamino)-1,4-benzoquinon e) did not react with glutathione. TW13 and triaziquone markedly inactivated bacteriophage M13-DNA in the presence of glutathione. This inactivation is probably produced by reductive activation of the BABQ derivative to a DNA-alkylating semiquinone radical. However, formation of bulky glutathione adducts decreases reactivity to DNA. Halogen-substituted BABQ derivatives react rapidly with glutathione to form adducts. This appeared to prevent DNA alkylation by these compounds. Comparison of these results with in vivo and in vitro activity against tumour models (L1210) suggests that in vivo halogen-substituted BABQ derivatives are efficiently inactivated by glutathione conjugation. The differences between the halogen-substituted BABQ derivatives on the one hand and TW13 and triaziquone on the other hand are probably caused by a difference in reaction mechanism with glutathione. From the viewpoint of drug design, halogen-substituted BABQ derivatives are expected to be inactive anti-tumour agents, in spite of high reactivity and activity in tumour models in vitro. PMID:2205226

  14. Fibrates and their newly synthesized glycinate or glycinate-methylester derivatives: comparison of the interactions with liver cytochrome P450 dependent monooxygenase- and oxidase-functions in vitro.

    PubMed

    Lupp, Amelie; Karge, Elke; Hopf, Heiner; Machts, Heike; Oelschläger, Herbert; Fleck, Christian

    2003-06-01

    Different fibrates (bezafibrate, ciprofibrate, clofibrate, fenofibrate, gemfibrozil) were investigated in comparison with their newly synthesized glycinate and glycinate-methylester derivatives. Interactions with the cytochrome P450 (CYP) system were studied by assessing binding to CYP and effects on CYP mediated monooxygenase functions in rat liver 9000 g supernatants, as measured by six model reactions for different CYP isoforms (ethoxyresorufin O-deethylation, ethoxycoumarin O-deethylation, pentoxyresorufin O-depentylation, p-nitrophenol-hydroxylation, ethylmorphine N-demethylation, lauric acid 11- or 12-hydroxylation). Possible prooxidant or antioxidant properties were investigated by the stimulated lipid peroxidation, hydrogen peroxide production, and lucigenin and luminol amplified chemiluminescence using rat liver microsomes. Additionally, the influence on luminol amplified rat whole blood chemiluminescence was examined. All substances tested displayed binding to CYP. Effects on the monooxygenase model reactions were in general more distinct with the glycinates than with the parent compounds and most pronounced with the glycinate-methylester derivatives. The slightest effects on all model reactions were seen with clofibrate and its derivatives. On the whole, low antioxidative rather than prooxidative effects were observed. In general and with most model reactions, the antioxidative capacity of the glycinate and glycinate-methylester derivatives slightly exceeded that of the respective parent compounds. Summarizing the results it can be concluded that with respect to possible interactions with the CYP system in vivo and thus with the biotransformation of other concomitantly administered compounds no advantages of the glycinate or glycinate methylester derivatives over their parent fibrates are to be expected. Only the antioxidative capacity of the derivatives was somewhat higher than that of the parent substances, though most probably only of minor therapeutical relevance. PMID:12877356

  15. The Suramin Derivative NF449 Interacts with the 5-fold Vertex of the Enterovirus A71 Capsid to Prevent Virus Attachment to PSGL-1 and Heparan Sulfate

    PubMed Central

    Nishimura, Yorihiro; McLaughlin, Noel P.; Pan, Jieyan; Goldstein, Sara; Hafenstein, Susan; Shimizu, Hiroyuki; Winkler, Jeffrey D.; Bergelson, Jeffrey M.

    2015-01-01

    NF449, a sulfated compound derived from the antiparasitic drug suramin, was previously reported to inhibit infection by enterovirus A71 (EV-A71). In the current work, we found that NF449 inhibits virus attachment to target cells, and specifically blocks virus interaction with two identified receptors—the P-selectin ligand, PSGL-1, and heparan sulfate glycosaminoglycan—with no effect on virus binding to a third receptor, the scavenger receptor SCARB2. We also examined a number of commercially available suramin analogues, and newly synthesized derivatives of NF449; among these, NF110 and NM16, like NF449, inhibited virus attachment at submicromolar concentrations. PSGL-1 and heparan sulfate, but not SCARB2, are both sulfated molecules, and their interaction with EV-A71 is thought to involve positively charged capsid residues, including a conserved lysine at VP1-244, near the icosahedral 5-fold vertex. We found that mutation of VP1-244 resulted in resistance to NF449, suggesting that this residue is involved in NF449 interaction with the virus capsid. Consistent with this idea, NF449 and NF110 prevented virus interaction with monoclonal antibody MA28-7, which specifically recognizes an epitope overlapping VP1-244 at the 5-fold vertex. Based on these observations we propose that NF449 and related compounds compete with sulfated receptor molecules for a binding site at the 5-fold vertex of the EV-A71 capsid. PMID:26430888

  16. Journal of Theoretical Biology 246 (2007) 660680 A 3D interactive method for estimating body segmental parameters

    E-print Network

    Toronto, University of

    2007-01-01

    segmental parameters in animals: Application to the turning and running performance of Tyrannosaurus rex, centers of mass, and moments of inertia for an adult Tyrannosaurus rex, with measurements taken directly Elsevier Ltd. All rights reserved. Keywords: B-spline; Mass; Inertia; Tyrannosaurus; Model 1. Introduction

  17. What is there in the black box of dark energy: variable cosmological parameters or multiple (interacting) components?

    E-print Network

    Javier Grande; Joan Sola; Hrvoje Stefancic

    2007-01-08

    The coincidence problems and other dynamical features of dark energy are studied in cosmological models with variable cosmological parameters and in models with the composite dark energy. It is found that many of the problems usually considered to be cosmological coincidences can be explained or significantly alleviated in the aforementioned models.

  18. Variationality with second derivatives, relativistic uniform acceleration, and the 'spin'-curvature interaction in two-dimensional space-time

    E-print Network

    Matsyuk, Roman

    2015-01-01

    A variational formulation for the geodesic circles in two-dimensional Riemannian manifold is discovered. Some relations with the uniform relativistic acceleration and the one-dimensional 'spin'-curvature interaction is investigated.

  19. A Toll-Like Receptor-4-Interacting Surfactant Protein-A-Derived Peptide Suppresses Tumor Necrosis Factor-? Release from Mouse JAWS II Dendritic CellsS?

    PubMed Central

    Brown, Kevin; King, Catherine; Awasthi, Vibhudutta; Bondugula, Rajkumar

    2011-01-01

    Surfactant protein-A (SP-A) and Toll-like receptor-4 (TLR4) proteins are recognized as pathogen-recognition receptors. An exaggerated activation of TLR4 induces inflammatory response, whereas SP-A protein down-regulates inflammation. We hypothesized that SP-A–TLR4 interaction may lead to inhibition of inflammation. In this study, we investigated interaction between native baboon lung SP-A and baboon and human TLR4-MD2 proteins by coimmunoprecipitation/immunoblotting and microwell-based methods. The interaction between SP-A and TLR4-MD2 proteins was then analyzed using a bioinformatics approach. In the in silico model of SP-A–TLR4–MD2 complex, we identified potential binding regions and amino acids at the interface of SP-A-TLR4. Using this information, we synthesized a library of human SP-A-derived peptides that contained interacting amino acids. Next, we tested whether the TLR4-interacting SP-A peptides would suppress inflammatory cytokines. The peptides were screened for any changes in the tumor necrosis factor-? (TNF-?) response against lipopolysaccharide (LPS) stimuli in the mouse JAWS II dendritic cell line. Different approaches used in this study suggested binding between SP-A and TLR4-MD2 proteins. In cells pretreated with peptides, three of seven peptides increased TNF-? production against LPS. However, two of these peptides (SPA4: GDFRYSDGTPVNYTNWYRGE and SPA5: YVGLTEGPSPGDFRYSDFTP) decreased the TNF-? production in LPS-challenged JAWS II dendritic cells; SPA4 peptide showed more pronounced inhibitory effect than SPA5 peptide. In conclusion, we identify a human SP-A-derived peptide (SPA4 peptide) that interacts with TLR4-MD2 protein and inhibits the LPS-stimulated release of TNF-? in JAWS II dendritic cells. PMID:21159752

  20. Brain-Derived Neurotrophic Factor/FK506-Binding Protein 5 Genotype by Childhood Trauma Interactions Do Not Impact on Hippocampal Volume and Cognitive Performance

    PubMed Central

    Hernaus, Dennis; van Winkel, Ruud; Gronenschild, Ed; Habets, Petra; Kenis, Gunter; Marcelis, Machteld; van Os, Jim; Myin-Germeys, Inez; Collip, Dina

    2014-01-01

    In the development of psychotic symptoms, environmental and genetic factors may both play a role. The reported association between childhood trauma and psychotic symptoms could therefore be moderated by single nucleotide polymorphisms (SNPs) associated with the stress response, such as FK506-binding protein 5 (FKBP5) and brain-derived neurotrophic factor (BDNF). Recent studies investigating childhood trauma by SNP interactions have inconsistently found the hippocampus to be a potential target underlying these interactions. Therefore, more detailed modelling of these effects, using appropriate covariates, is required. We examined whether BDNF/FKBP5 and childhood trauma interactions affected two proxies of hippocampal integrity: (i) hippocampal volume and (ii) cognitive performance on a block design (BD) and delayed auditory verbal task (AVLT). We also investigated whether the putative interaction was different for patients with a psychotic disorder (n?=?89) compared to their non-psychotic siblings (n?=?95), in order to elicit possible group-specific protective/vulnerability effects. SNPs were rs9296158, rs4713916, rs992105, rs3800373 (FKBP5) and rs6265 (BDNF). In the combined sample, no BDNF/FKBP5 by childhood trauma interactions were apparent for either outcome, and BDNF/FKBP5 by childhood trauma interactions were not different for patients and siblings. The omission of drug use and alcohol consumption sometimes yielded false positives, greatly affected explained error and influenced p-values. The consistent absence of any significant BDNF/FKBP5 by childhood trauma interactions on assessments of hippocampal integrity suggests that the effect of these interactions on psychotic symptoms is not mediated by hippocampal integrity. The importance of appropriate statistical designs and inclusion of relevant covariates should be carefully considered. PMID:24658422

  1. Inverse modeling for seawater intrusion in coastal aquifers: Insights about parameter sensitivities, variances, correlations and estimation procedures derived from the Henry problem

    USGS Publications Warehouse

    Sanz, E.; Voss, C.I.

    2006-01-01

    Inverse modeling studies employing data collected from the classic Henry seawater intrusion problem give insight into several important aspects of inverse modeling of seawater intrusion problems and effective measurement strategies for estimation of parameters for seawater intrusion. Despite the simplicity of the Henry problem, it embodies the behavior of a typical seawater intrusion situation in a single aquifer. Data collected from the numerical problem solution are employed without added noise in order to focus on the aspects of inverse modeling strategies dictated by the physics of variable-density flow and solute transport during seawater intrusion. Covariances of model parameters that can be estimated are strongly dependent on the physics. The insights gained from this type of analysis may be directly applied to field problems in the presence of data errors, using standard inverse modeling approaches to deal with uncertainty in data. Covariance analysis of the Henry problem indicates that in order to generally reduce variance of parameter estimates, the ideal places to measure pressure are as far away from the coast as possible, at any depth, and the ideal places to measure concentration are near the bottom of the aquifer between the center of the transition zone and its inland fringe. These observations are located in and near high-sensitivity regions of system parameters, which may be identified in a sensitivity analysis with respect to several parameters. However, both the form of error distribution in the observations and the observation weights impact the spatial sensitivity distributions, and different choices for error distributions or weights can result in significantly different regions of high sensitivity. Thus, in order to design effective sampling networks, the error form and weights must be carefully considered. For the Henry problem, permeability and freshwater inflow can be estimated with low estimation variance from only pressure or only concentration observations. Permeability, freshwater inflow, solute molecular diffusivity, and porosity can be estimated with roughly equivalent confidence using observations of only the logarithm of concentration. Furthermore, covariance analysis allows a logical reduction of the number of estimated parameters for ill-posed inverse seawater intrusion problems. Ill-posed problems may exhibit poor estimation convergence, have a non-unique solution, have multiple minima, or require excessive computational effort, and the condition often occurs when estimating too many or co-dependent parameters. For the Henry problem, such analysis allows selection of the two parameters that control system physics from among all possible system parameters. ?? 2005 Elsevier Ltd. All rights reserved.

  2. 3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information-rich hydropathic interaction environments described by maps.

    PubMed

    Ahmed, Mostafa H; Koparde, Vishal N; Safo, Martin K; Neel Scarsdale, J; Kellogg, Glen E

    2015-06-01

    Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low-resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (?-? stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone-dependent (?, ?) bins, a map similarity metric based on the correlation coefficient was applied to each map-map pair to build matrices suitable for clustering with k-means. The first bin (-200° ? ??interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single ?(1)/?(2) rotamer. The last environment has weak or no interactions with the tyrosine ring and its ?(1)/?(2) rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. PMID:25900573

  3. D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75

    SciTech Connect

    Du Li; Zhao Yaxue; Chen, Jing; Yang Liumeng; Zheng Yongtang; Tang Yun Shen Xu Jiang Hualiang

    2008-10-10

    Integration of viral-DNA into host chromosome mediated by the viral protein HIV-1 integrase (IN) is an essential step in the HIV-1 life cycle. In this process, Lens epithelium-derived growth factor (LEDGF/p75) is discovered to function as a cellular co-factor for integration. Since LEDGF/p75 plays an important role in HIV integration, disruption of the LEDGF/p75 interaction with IN has provided a special interest for anti-HIV agent discovery. In this work, we reported that a benzoic acid derivative, 4-[(5-bromo-4-{l_brace}[2,4-dioxo-3-(2-oxo-2-phenylethyl) -1,3-thiazolidin-5-ylidene]methyl{r_brace}-2-ethoxyphenoxy)methyl]benzoic acid (D77) could potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution thus exhibiting antiretroviral activity. Molecular docking with site-directed mutagenesis analysis and surface plasmon resonance (SPR) binding assays has clarified possible binding mode of D77 against HIV-1 integrase. As the firstly discovered small molecular compound targeting HIV-1 integrase interaction with LEDGF/p75, D77 might supply useful structural information for further anti-HIV agent discovery.

  4. D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75.

    PubMed

    Du, Li; Zhao, Yaxue; Chen, Jing; Yang, Liumeng; Zheng, Yongtang; Tang, Yun; Shen, Xu; Jiang, Hualiang

    2008-10-10

    Integration of viral-DNA into host chromosome mediated by the viral protein HIV-1 integrase (IN) is an essential step in the HIV-1 life cycle. In this process, Lens epithelium-derived growth factor (LEDGF/p75) is discovered to function as a cellular co-factor for integration. Since LEDGF/p75 plays an important role in HIV integration, disruption of the LEDGF/p75 interaction with IN has provided a special interest for anti-HIV agent discovery. In this work, we reported that a benzoic acid derivative, 4-[(5-bromo-4-{[2,4-dioxo-3-(2-oxo-2-phenylethyl)-1,3-thiazolidin-5-ylidene]methyl}-2-ethoxyphenoxy)methyl]benzoic acid (D77) could potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution thus exhibiting antiretroviral activity. Molecular docking with site-directed mutagenesis analysis and surface plasmon resonance (SPR) binding assays has clarified possible binding mode of D77 against HIV-1 integrase. As the firstly discovered small molecular compound targeting HIV-1 integrase interaction with LEDGF/p75, D77 might supply useful structural information for further anti-HIV agent discovery. PMID:18691555

  5. {alpha}-decay and fusion phenomena in heavy ion collisions using nucleon-nucleon interactions derived from relativistic mean-field theory

    SciTech Connect

    Singh, BirBikram; Sahu, B. B.; Patra, S. K.

    2011-06-15

    Nucleus-nucleus potentials are determined in the framework of the double-folding model for a new microscopic nucleon-nucleon (NN) interaction relativistic mean field-3-Yukawa (R3Y) derived from the popular relativistic mean-field theory Lagrangian, and the results are compared for the use of Michigan-3-Yukawa (M3Y) effective NN interactions. The double-folding potentials so obtained are further taken up in the context of the preformed cluster model (PCM) of Gupta and collaborators and the barrier penetration model to study respectively the ground-state (g.s.) {alpha}-decay and low-energy fusion reactions. In this paper, using PCM, we deduce empirically the {alpha} preformation probability P{sub 0}{sup {alpha}(emp)} from experimental data on a few g.s. {alpha} decays in the trans-lead region. For fusion reactions, two projectile-target systems {sup 12}C+{sup 208}Pb and {sup 16}O+{sup 208}Pb are selected for calculating the barrier energies as well positions, fusion cross sections ({sigma}{sub fus}), and fusion barrier distribution [D(E{sub c.m.})]. The barrier energies and positions change for the R3Y NN interactions in comparison with those of the M3Y NN interactions. We find that in the {alpha}-decay studies the values of P{sub 0}{sup {alpha}(emp)}(R3Y) are similar to those of P{sub 0}{sup {alpha}(emp)}(M3Y). Further, both NN interactions give similar {sigma}{sub fus} values using the Wong formula specifically when the R3Y NN interaction calculated {sigma}{sub fus} values are reduced by 1.5 times, and the results are in agreement with the experimental data for both the systems, especially for the higher energies. Results for D(E{sub c.m.}) are also quite similar for both choices of NN interaction.

  6. Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

    SciTech Connect

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-04-07

    Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retained in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.

  7. Tumour cell-derived extracellular vesicles interact with mesenchymal stem cells to modulate the microenvironment and enhance cholangiocarcinoma growth.

    PubMed

    Haga, Hiroaki; Yan, Irene K; Takahashi, Kenji; Wood, Joseph; Zubair, Abba; Patel, Tushar

    2015-01-01

    The contributions of mesenchymal stem cells (MSCs) to tumour growth and stroma formation are poorly understood. Tumour cells can transfer genetic information and modulate cell signalling in other cells through the release of extracellular vesicles (EVs). We examined the contribution of EV-mediated inter-cellular signalling between bone marrow MSCs and tumour cells in human cholangiocarcinoma, highly desmoplastic cancers that are characterized by tumour cells closely intertwined within a dense fibrous stroma. Exposure of MSCs to tumour cell-derived EVs enhanced MSC migratory capability and expression of alpha-smooth muscle actin mRNA, in addition to mRNA expression and release of CXCL-1, CCL2 and IL-6. Conditioned media from MSCs exposed to tumour cell-derived EVs increased STAT-3 phosphorylation and proliferation in tumour cells. These effects were completely blocked by anti-IL-6R antibody. In conclusion, tumour cell-derived EVs can contribute to the generation of tumour stroma through fibroblastic differentiation of MSCs, and can also selectively modulate the cellular release of soluble factors such as IL-6 by MSCs that can, in turn, alter tumour cell proliferation. Thus, malignant cells can "educate" MSCs to induce local microenvironmental changes that enhance tumour cell growth. PMID:25557794

  8. Application of "hydrogen bonding interaction" in new drug development: design, synthesis, antiviral activity, and SARs of thiourea derivatives.

    PubMed

    Lu, Aidang; Wang, Ziwen; Zhou, Zhenghong; Chen, Jianxin; Wang, Qingmin

    2015-02-11

    A series of simple thiourea derivatives were designed based on the structure of natural product harmine and lead compound and synthesized from amines in one step. The antiviral activity of these thiourea derivatives was evaluated. Most of them exhibited significantly higher anti-TMV activity than commercial plant virucides ribavirin, harmine, and lead compound. The hydrogen bond was found to be important but not the more the better. The optimal compound (R,R)-20 showed the best anti-TMV activity in vitro and in vivo (in vitro activity, 75%/500 ?g/mL and 39%/100 ?g/mL; inactivation activity, 71%/500 ?g/mL and 35%/100 ?g/mL; curative activity, 73%/500 ?g/mL and 37%/100 ?g/mL; protection activity, 69%/500 ?g/mL and 33%/100 ?g/mL), which is significantly higher than that of Ningnanmycin. The systematic study provides strong evidence that these simple thiourea derivatives could become potential TMV inhibitors. PMID:25619875

  9. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

    PubMed Central

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice C.; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-01-01

    Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities. PMID:24778628

  10. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions.

    PubMed

    Cole, Jessica K; Hutchison, Janine R; Renslow, Ryan S; Kim, Young-Mo; Chrisler, William B; Engelmann, Heather E; Dohnalkova, Alice C; Hu, Dehong; Metz, Thomas O; Fredrickson, Jim K; Lindemann, Stephen R

    2014-01-01

    Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities. PMID:24778628

  11. Polyethylene glycol derivatives of base and sequence specific DNA ligands: DNA interaction and application for base specific separation of DNA fragments by gel electrophoresis.

    PubMed Central

    Müller, W; Hattesohl, I; Schuetz, H J; Meyer, G

    1981-01-01

    Various base pair specific DNA ligands comprising a phenyl phenazinium dye, a triphenylmethan dye and Hoechst 33258 were covalently bound to polyethylene glycol (PEG) via ester or ether bonds. The DNA interactions of the PEG derivatives formed were shown to exhibit the same base pair specificity as the parent compounds. Since the PEG chains thus bound to the DNA could be expected to increase drastically the frictional coefficient of the DNA, the PEG derivatives were used for base specific DNA separations in agarose and polyacrylamide gel electrophoresis. The procedures, which do not require any special techniques, are described in detail. The resolution observed in agarose gels allows one to separate equally sized DNA fragments differing as little as 1% in base composition at mean travel distances of about 10 cm. Examples of gels showing the base compositional heterogeneity of restriction fragments obtained from lambda DNA, E. coli DNA and calf thymus DNA are given. Images PMID:6259622

  12. Experimental study of sharp and blunt nose streamwise corners at Mach 20. [hypersonic shock-boundary layer interaction parameters

    NASA Technical Reports Server (NTRS)

    Watson, R. D.

    1974-01-01

    Extensive heat transfer and pressure distribution data and oil flow studies on sharp and blunt-nose streamwise corners at Mach 20 in helium are presented. The far corner boundary layers on the wedge surfaces forming the corners are laminar for most test conditions. Analysis of the data indicates that the corner flow field geometry can be described in terms of the inviscid shock pattern on the two dimensional surfaces forming the corner. Parameters used to correlate blunt shock growth can be used to correlate features of the flow field observed in oil flow photographs in addition to the measured pressure and heat transfer distributions on the models. The flow field structure is described from available experimental data. Regions of the flow in which the structure still is not known are discussed.

  13. Spectroscopic study on the interaction of A?42 with di(picolyl)amine derivatives and the toxicity to SH-S5Y5 cells.

    PubMed

    Kong, Meng-Yun; Chen, Qiu-Yun; Yao, Ling; Wang, Yin-Bing

    2015-03-01

    In order to confirm the neurotoxicity of bifunctional chelators containing hydrophobic groups and metal chelating moiety, the interaction of di(picolyl)amine (dpa) derivatives toward A?42 peptide was investigated. Fluorescence titration reveals that a hydrophobic chelator (such as BODIPY) shows high binding affinity to amyloid A?42. Circular dichroism (CD) spectra confirm that the hydrophobic bifunctional chelator can decrease ?-helix fraction and increase the ?-sheet fraction of amyloid A?42. In particular, experimental results indicate that a bifunctional chelator can assemble with Cu(II)-A?42 forming chelator-Cu(II)-A?42 nanospheres, which are toxic to SH-S5Y5 cells. The hydrophobic interaction between the chelator and the amyloid peptide (A?42) has great contribution to the formation of neurotoxic chelator-Cu(II)-A?42 nanospheres. This work gives a general guide to the development of low cytotoxic inhibitors of A?42 aggregation. PMID:25498817

  14. Spectroscopic study on the interaction of A?42 with di(picolyl)amine derivatives and the toxicity to SH-S5Y5 cells

    NASA Astrophysics Data System (ADS)

    Kong, Meng-Yun; Chen, Qiu-Yun; Yao, Ling; Wang, Yin-Bing

    2015-03-01

    In order to confirm the neurotoxicity of bifunctional chelators containing hydrophobic groups and metal chelating moiety, the interaction of di(picolyl)amine (dpa) derivatives toward A?42 peptide was investigated. Fluorescence titration reveals that a hydrophobic chelator (such as BODIPY) shows high binding affinity to amyloid A?42. Circular dichroism (CD) spectra confirm that the hydrophobic bifunctional chelator can decrease ?-helix fraction and increase the ?-sheet fraction of amyloid A?42. In particular, experimental results indicate that a bifunctional chelator can assemble with Cu(II)-A?42 forming chelator-Cu(II)-A?42 nanospheres, which are toxic to SH-S5Y5 cells. The hydrophobic interaction between the chelator and the amyloid peptide (A?42) has great contribution to the formation of neurotoxic chelator-Cu(II)-A?42 nanospheres. This work gives a general guide to the development of low cytotoxic inhibitors of A?42 aggregation.

  15. Interaction between paliperidone extended release and TS-1®, an oral anticancer drug containing a 5-fluorouracil derivative, in a schizophrenic patient

    PubMed Central

    Yasui-Furukori, Norio; Hashimoto, Kojiro; Kubo, Kazutoshi; Tomita, Tetsu

    2013-01-01

    Until now there has been no information available on drug interaction between paliperidone and TS-1®, an oral anticancer drug containing a 5-fluorouracil derivative. The patient in the case presented here was a 39-year-old man with a 15-year history of schizophrenia. The patient’s usual treatment of 2 mg/day of risperidone was changed to 3 mg/day of paliperidone extended release. He experienced worsening psychotic symptoms after switching from risperidone to paliperidone while he was also receiving TS-1. Retrospective analyses showed plasma concentration of paliperidone was consistently lower during the treatment with TS-1 than without TS-1. This case suggests there is drug interaction between paliperidone extended-release tablets and TS-1. PMID:23487437

  16. Study on the inclusion interactions of beta-cyclodextrin and its derivative with dyes by spectrofluorimetry and its analytical application.

    PubMed

    Zhu, Xiashi; Sun, Jing; Wu, Jun

    2007-04-15

    The inclusion interactions of beta-cyclodextrin (beta-CD) and hydroxypropyl-beta-cyclodextrin (HP-beta-CD) with dyes were developed by spectrofluorimetry, and the inclusion constants of inclusion complexes were determined by direct fluorescence technique. The main factors (the host molecule, the guest molecule, and the pH) for the inclusion interaction were discussed in detail. At the same time, the inclusion interaction of HP-beta-CD and vitamin B(6) (VB(6)) was investigated with the competitive fluorescence inclusion method and the inclusion constant of HP-beta-CD and vitamin B(6) (VB(6)) was obtained by indirect fluorescence technique. On the basis of the linear relationship between the change of fluorescence intensity (DeltaF) and the concentration of VB(6), a competitive fluorescence inclusion method was used to the determination of VB(6). The method has been successfully applied to the analysis of VB(6) in synthetic samples, tablets and injections with satisfactory results. PMID:19071608

  17. Interaction of iron-copper mixed metal oxide oxygen carriers with simulated synthesis gas derived from steam gasification of coal

    SciTech Connect

    Siriwardane, Ranjani V.; Ksepko, Ewelina; Tian, Hanging

    2013-01-01

    The objective of this work was to prepare supported bimetallic Fe–Cu oxygen carriers and to evaluate their performance for the chemical-looping combustion (CLC) process with simulated synthesis gas derived from steam gasification of coal/air. Ten-cycle CLC tests were conducted with Fe–Cu oxygen carriers in an atmospheric thermogravimetric analyzer utilizing simulated synthesis gas derived from the steam gasification of Polish Janina coal and Illinois #6 coal as fuel. The effect of temperature on reaction rates, chemical stability, and oxygen transport capacity were determined. Fractional reduction, fractional oxidation, and global rates of reactions were calculated from the thermogravimetric analysis (TGA) data. The supports greatly affected reaction performance. Data showed that reaction rates and oxygen capacities were stable during the 10-cycle TGA tests for most Fe–Cu/support oxygen carriers. Bimetallic Fe–Cu/support oxygen carriers showed higher reduction rates than Fe-support oxygen carriers. The carriers containing higher Cu content showed better stabilities and better reduction rates. An increase in temperature from 800 °C to 900 °C did not have a significant effect on either the oxygen capacity or the reduction rates with synthesis gas derived from Janina coal. Oxidation reaction was significantly faster than reduction reaction for all supported Fe–Cu oxygen carriers. Carriers with higher Cu content had lower oxidation rates. Ten-cycle TGA data indicated that these oxygen carriers had stable performances at 800–900 °C and might be successfully used up to 900 °C for coal CLC reaction in the presence of steam.

  18. Identification of polyproline II regions derived from the proline-rich nuclear receptor coactivators PNRC and PNRC2: new insights for ER? coactivator interactions.

    PubMed

    Byrne, C; Miclet, E; Broutin, I; Gallo, D; Pelekanou, V; Kampa, M; Castanas, E; Leclercq, G; Jacquot, Y

    2013-10-01

    Protein-protein interactions are crucial for signal transductions required for cell differentiation and proliferation. Their modulation is therefore key to the development of therapeutic alternatives, particularly in the context of cancer. According to literature data, the polyproline-rich nuclear receptor coactivators PNRC and PNRC2 interact with estrogen receptor (ER?) through their PxxP SH3-binding motifs. In a search to identify the molecular features governing this interaction, we explored using electronic circular dichroism (ECD) spectroscopy and molecular dynamics (MD) calculations, the capacity of a range of putative biologically active peptides derived from these proteins and containing this PxxP motif(s) to form polyproline II (PPII) domains. An additional more exhaustive structural study on a lead PPII peptide was also performed using 2D nuclear magnetic resonance (NMR) spectroscopy. With the exception of one of all the investigated peptides (PNRC-D), binding assays failed to detect any affinity for Grb2 SH3 domains, suggesting that PPII motifs issued from Grb2 antagonists have a binding mode distinct from those derived from Grb2 agonists. Instead, the peptides revealed a competitive binding ability against a synthetic peptide (ER?17p) with a putative PPII-cognate domain located within a coregulator recruitment region of ER? (AF-2 site). Our work, which constitutes the first structure-related interaction study concerning PNRC and PNRC2, supports not only the existence of PxxP-induced PPII sequences in these coregulators, but also confirms the presence of a PPII recognition site in the AF-2 of the steroid receptor ER?, a region important for transcription regulation. PMID:23925889

  19. Simultaneous eigenstates of the number-difference operator and a bilinear interaction Hamiltonian derived by solving a complex differential equation

    E-print Network

    Hong-yi Fan; Wei-bo Gao

    2005-12-08

    As a continuum work of Bhaumik et al who derived the common eigenvector of the number-difference operator Q and pair-annihilation operator ab (J. Phys. A9 (1976) 1507) we search for the simultaneous eigenvector of Q and (ab-a^{+}b^{+}) by setting up a complex differential equation in the bipartite entangled state representation. The differential equation is then solved in terms of the two-variable Hermite polynomials and the formal hypergeometric functions. The work is also an addendum to Mod. Phys. Lett. A 9 (1994) 1291 by Fan and Klauder, in which the common eigenkets of Q and pair creators are discussed.

  20. Environmental factors differently affect human and rat IAPP: conformational preferences and membrane interactions of IAPP17-29 peptide derivatives.

    PubMed

    Pappalardo, Giuseppe; Milardi, Danilo; Magrì, Antonio; Attanasio, Francesco; Impellizzeri, Giuseppe; La Rosa, Carmelo; Grasso, Domenico; Rizzarelli, Enrico

    2007-01-01

    Interest in the 37-residue human islet amyloid polypeptide (hIAPP) is related to its ability to form amyloid deposits in patients affected by type II diabetes. Attempts to unravel the molecular features of this disease have indicated several regions of this polypeptide to be responsible for either the ability to form insoluble fibrils or the abnormal interaction with membranes. To extend these studies to peptides that enclose His18, whose ionization state is believed to play a key role in the aggregation of hIAPP, we report on the synthesis of two peptides, hIAPP17-29 and rIAPP17-29, encompassing the 17-29 sequences of human and rat IAPP, respectively, as well as on their conformational features in water and in several membrane-mimicking environments as revealed by circular dichroism (CD) and 2D-NMR studies. hIAPP17-29 adopts a beta-sheet structure in water and its solubility increases at low pH. Anionic sodium dodecyl sulfate (SDS) micelles promoted the formation of an alpha-helical structure in the peptide chain, which was poorly influenced by pH variations. rIAPP17-29 was soluble and unstructured in all the environments investigated, with a negligible effect of pH. The membrane interactions of hIAPP17-29 and rIAPP17-29 were assessed by recording differential scanning calorimetry (DSC) measurements aimed at elucidating the peptide-induced changes in the thermotropic behaviour of zwitterionic (DPPC) and negatively charged (DPPC/DPPS 3:1) model membranes (DPPC=1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPS=1,2-dipalmitoyl-sn-glycero-3-phosphoserine). Results of DSC experiments demonstrated the high potential of hIAPP17-29 to interact with DPPC membranes. hIAPP17-29 exhibited a negligible affinity for negatively charged DPPC/DPPS model membranes at neutral pH. On the other hand, rIAPP17-29 did not interact with neutral or negatively charged membranes. The role played by His18 in the modulation of the biophysical properties of this hIAPP region was assessed by synthesising and studying the R18HrIAPP17-29 peptide; the replacement of a single Arg with a His residue is not sufficient to induce either amyloidogenic propensity or membrane interaction in this region. The results show that the 17-29 domain of hIAPP has many properties of the full-length protein "in vitro" and this opens up new perspectives for both research and eventually therapy. PMID:17902185

  1. Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis

    PubMed Central

    Blohm, Philipp; Frishman, Goar; Smialowski, Pawel; Goebels, Florian; Wachinger, Benedikt; Ruepp, Andreas; Frishman, Dmitrij

    2014-01-01

    Knowledge about non-interacting proteins (NIPs) is important for training the algorithms to predict protein–protein interactions (PPIs) and for assessing the false positive rates of PPI detection efforts. We present the second version of Negatome, a database of proteins and protein domains that are unlikely to engage in physical interactions (available online at http://mips.helmholtz-muenchen.de/proj/ppi/negatome). Negatome is derived by manual curation of literature and by analyzing three-dimensional structures of protein complexes. The main methodological innovation in Negatome 2.0 is the utilization of an advanced text mining procedure to guide the manual annotation process. Potential non-interactions were identified by a modified version of Excerbt, a text mining tool based on semantic sentence analysis. Manual verification shows that nearly a half of the text mining results with the highest confidence values correspond to NIP pairs. Compared to the first version the contents of the database have grown by over 300%. PMID:24214996

  2. Interaction of fission products and SiC in TRISO fuel particles: a limiting HTGR design parameter

    SciTech Connect

    Stansfield, O.M.; Homan, F.J.; Simon, W.A.; Turner, R.F.

    1983-09-01

    The fuel particle system for the steam cycle cogeneration HTGR being developed in the US consists of 20% enriched UC/sub 0/./sub 3/O/sub 1/./sub 7/ and ThO/sub 2/ kernels with TRISO coatings. The reaction of fission products with the SiC coating is the limiting thermochemical coating failure mechanism affecting performance. The attack of the SiC by palladium (Pd) is considered the controlling reaction with systems of either oxide or carbide fuels. The lanthanides, such as cerium, neodymium, and praseodymium, also attack SiC in carbide fuel particles. In reactor design, the time-temperature relationships at local points in the core are used to calculate the depth of SiC-Pd reaction. The depth of penetration into the SiC during service varies with core power density, power distribution, outlet gas temperature, and fuel residence time. These parameters are adjusted in specifying the core design to avoid SiC coating failure.

  3. Precision measurements of the {sup 60}Co {beta}-asymmetry parameter in search for tensor currents in weak interactions

    SciTech Connect

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

    2010-11-15

    The {beta}-asymmetry parameter A-tilde for the Gamow-Teller decay of {sup 60}Co was measured by polarizing the radioactive nuclei with the brute-force low-temperature nuclear-orientation method. The {sup 60}Co activity was cooled down to milliKelvin temperatures in a {sup 3}He-{sup 4}He dilution refrigerator in an external 13-T magnetic field. The {beta} particles were observed by a 500-{mu}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, A-tilde=-1.014(12){sub stat}(16){sub 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.

  4. Modeling host interactions with hepatitis B virus using primary and induced pluripotent stem cell-derived hepatocellular systems.

    PubMed

    Shlomai, Amir; Schwartz, Robert E; Ramanan, Vyas; Bhatta, Ankit; de Jong, Ype P; Bhatia, Sangeeta N; Rice, Charles M

    2014-08-19

    Hepatitis B virus (HBV) chronically infects 400 million people worldwide and is a leading driver of end-stage liver disease and liver cancer. Research into the biology and treatment of HBV requires an in vitro cell-culture system that supports the infection of human hepatocytes, and accurately recapitulates virus-host interactions. Here, we report that micropatterned cocultures of primary human hepatocytes with stromal cells (MPCCs) reliably support productive HBV infection, and infection can be enhanced by blocking elements of the hepatocyte innate immune response associated with the induction of IFN-stimulated genes. MPCCs maintain prolonged, productive infection and represent a facile platform for studying virus-host interactions and for developing antiviral interventions. Hepatocytes obtained from different human donors vary dramatically in their permissiveness to HBV infection, suggesting that factors--such as divergence in genetic susceptibility to infection--may influence infection in vitro. To establish a complementary, renewable system on an isogenic background in which candidate genetics can be interrogated, we show that inducible pluripotent stem cells differentiated into hepatocyte-like cells (iHeps) support HBV infection that can also be enhanced by blocking interferon-stimulated gene induction. Notably, the emergence of the capacity to support HBV transcriptional activity and initial permissiveness for infection are marked by distinct stages of iHep differentiation, suggesting that infection of iHeps can be used both to study HBV, and conversely to assess the degree of iHep differentiation. Our work demonstrates the utility of these infectious systems for studying HBV biology and the virus' interactions with host hepatocyte genetics and physiology. PMID:25092305

  5. Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

    NASA Astrophysics Data System (ADS)

    Reif, Maria M.; Hünenberger, Philippe H.

    2011-04-01

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006), 10.1529/biophysj.106.083667; M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998), 10.1021/jp982638r; Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, ? G_hyd^{ominus }[H+] = -1100, -1075 or -1050 kJ mol-1, resulting in three sets L, M, and H for the SPC water model and three sets LE, ME, and HE for the SPC/E water model (alternative sets can easily be interpolated to intermediate ? G_hyd^{ominus }[H+] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is also evaluated and found to be very limited. Ultimately, it is expected that comparison with other experimental ionic properties (e.g., derivative single-ion solvation properties, as well as data concerning ionic crystals, melts, solutions at finite concentrations, or nonaqueous solutions) will permit to validate one specific set and thus, the associated ? G_hyd^{ominus }[H+] value (atomistic consistency assumption). Preliminary results (first-peak positions in the ion-water radial distribution functions, partial molar volumes of ionic salts in water, and structural properties of ionic crystals) support a value of ? G_hyd^{ominus }[H+] close to -1100 kJ.mol-1.

  6. Deriving k·p parameters from full-Brillouin-zone descriptions: A finite-element envelope function model for quantum-confined wurtzite nanostructures

    SciTech Connect

    Zhou, Xiangyu; Ghione, Giovanni; Bertazzi, Francesco Goano, Michele; Bellotti, Enrico

    2014-07-21

    We present a multiband envelope-function model for wurtzite nanostructures based on a rigorous numerical procedure to determine operator ordering and band parameters from nonlocal empirical pseudopotential calculations. The proposed approach, implemented within a finite-element scheme, leads to well-posed, numerically stable envelope equations that accurately reproduce full-Brillouin-zone subband dispersions of quantum systems. Although demonstrated here for III-nitride nonlocal empirical pseudopotentials, the model provides a general theoretical framework applicable to ab initio electronic structures of wurtzite semiconductors.

  7. Novel oxaliplatin derivatives with 1-(substituted benzyl)azetidine-3,3-dicarboxylate anions. Synthesis, cytotoxicity, and interaction with DNA.

    PubMed

    Sun, Yanyan; Cao, Zhe; Gou, Shaohua; Hu, Tingting

    2014-01-01

    A series of oxaliplatin derivatives with (1R,2R)-N(1) -alkyl-1,2-cyclohexane-1,2-diamine (alkyl=Bu or (i) Pr) as carrier ligands and 1-(methoxy- or methyl-substituted benzyl)azetidine-3,3-dicarboxylate anions as leaving groups were synthesized and spectrally characterized. Generally, Complexes 10-15 with an (i) Pr substituent at N(1) showed higher activities in vitro than carboplatin against MCF-7 human breast carcinoma and A549 human non-small-cell lung cell lines, although they were less potent than oxaliplatin. The typical complex 14 exhibited cytotoxicity superior to that of carboplatin and comparable to that of oxaliplatin against two selected tumor cell lines. Additionally, agarose gel electrophoresis was applied to investigate the DNA-cleavage ability of complex 14, which demonstrated that it has a different mode of DNA distortion from that of oxaliplatin. PMID:24443431

  8. Synthesis, interaction with DNA and antiproliferative activities of two novel Cu(II) complexes with norcantharidin and benzimidazole derivatives

    NASA Astrophysics Data System (ADS)

    Song, Wen-Ji; Lin, Qiu-Yue; Jiang, Wen-Jiao; Du, Fang-Yuan; Qi, Qing-Yuan; Wei, Qiong

    2015-02-01

    Two novel complexes [Cu(L)2(Ac)2]·3H2O (1) (L = N-2-methyl benzimidazole demethylcantharate imide, C16H15N3O3, Ac = acetate, C2H3O2) and [Cu(bimz)2(DCA)] (2) (bimz = benzimidazole, C7H6N2; DCA = demethylcantharate, C8H8O5) were synthesized and characterized by elemental analysis, infrared spectra and X-ray diffraction techniques. Cu(II) ion was four-coordinated in complex 1, Cu(II) ion was five-coordinated in complex 2. A large amount of intermolecular hydrogen-bonding and ?-? stacking interactions were observed in these complex structures. The DNA-binding properties of these complexes were investigated using electronic absorption spectra, fluorescence spectra, viscosity measurements and agarose gel electrophoresis. The interactions between the complexes and bovine serum albumin (BSA) were investigated by fluorescence spectra. The antiproliferative activities of the complexes against human hepatoma cells (SMMC7721) were tested in vitro. And the results showed that these complexes could bind to DNA in moderate intensity via partial intercalation, and complexes 1 and 2 could cleave plasmid DNA through hydroxyl radical mechanism. Title complexes could effectively quench the fluorescence of BSA through static quenching. Meanwhile, title complexes had stronger antiproliferative effect compared to L and Na2(DCA) within the tested concentration range. And complex 1 possessed more antiproliferative active than complex 2.

  9. Thiourea-catalysed ring opening of episulfonium ions with indole derivatives by means of stabilizing non-covalent interactions

    NASA Astrophysics Data System (ADS)

    Lin, Song; Jacobsen, Eric N.

    2012-10-01

    Small organic and metal-containing molecules (molecular mass <1,000) can catalyse synthetically useful reactions with the high levels of stereoselectivity typically associated with macromolecular enzymatic catalysts. Whereas enzymes are generally understood to accelerate reactions and impart selectivity as they stabilize specific transition structures through networks of cooperative interactions, enantioselectivity with chiral, small-molecule catalysts is rationalized typically by the steric destabilization of all but one dominant pathway. However, it is increasingly apparent that stabilizing effects also play an important role in small-molecule catalysis, although the mechanistic characterization of such systems is rare. Here, we show that arylpyrrolidino amido thiourea catalysts catalyse the enantioselective nucleophilic ring opening of episulfonium ions by indoles. Evidence is provided for the selective transition-state stabilization of the major pathway by the thiourea catalyst in the rate- and selectivity-determining step. Enantioselectivity is achieved through a network of attractive anion binding, cation-? and hydrogen-bond interactions between the catalyst and the reacting components in the transition-structure assembly.

  10. Simulations of cloud-radiation interaction using large-scale forcing derived from the CINDY/DYNAMO northern sounding array

    NASA Astrophysics Data System (ADS)

    Wang, Shuguang; Sobel, Adam H.; Fridlind, Ann; Feng, Zhe; Comstock, Jennifer M.; Minnis, Patrick; Nordeen, Michele L.

    2015-09-01

    The recently completed CINDY/DYNAMO field campaign observed two Madden-Julian oscillation (MJO) events in the equatorial Indian Ocean from October to December 2011. Prior work has indicated that the moist static energy anomalies in these events grew and were sustained to a significant extent by radiative feedbacks. We present here a study of radiative fluxes and clouds in a set of cloud-resolving simulations of these MJO events. The simulations are driven by the large-scale forcing data set derived from the DYNAMO northern sounding array observations, and carried out in a doubly periodic domain using the Weather Research and Forecasting (WRF) model. Simulated cloud properties and radiative fluxes are compared to those derived from the S-PolKa radar and satellite observations. To accommodate the uncertainty in simulated cloud microphysics, a number of single-moment (1M) and double-moment (2M) microphysical schemes in the WRF model are tested. The 1M schemes tend to underestimate radiative flux anomalies in the active phases of the MJO events, while the 2M schemes perform better, but can overestimate radiative flux anomalies. All the tested microphysics schemes exhibit biases in the shapes of the histograms of radiative fluxes and radar reflectivity. Histograms of radiative fluxes and brightness temperature indicate that radiative biases are not evenly distributed; the most significant bias occurs in rainy areas with OLR less than 150 W/m2 in the 2M schemes. Analysis of simulated radar reflectivities indicates that this radiative flux uncertainty is closely related to the simulated stratiform cloud coverage. Single-moment schemes underestimate stratiform cloudiness by a factor of 2, whereas 2M schemes simulate much more stratiform cloud.

  11. Using the Quake-Catcher Network (QCN) to derive source parameters and the site attenuation term, kappa (?), using aftershocks of the 2010 Darfield, New Zealand earthquake

    NASA Astrophysics Data System (ADS)

    Neighbors, C.; Cochran, E. S.; Ryan, K. J.; Funning, G.; Kaiser, A. E.

    2013-12-01

    We utilize a dense network of Quake-Catcher Network (QCN) MEMs accelerometers to investigate source parameters and the shallow site attenuation parameter, kappa (?), for aftershocks of the 3 September 2010 Mw7.1 Darfield earthquake in Christchurch, NZ. Approximately 190 QCN accelerometers captured over 180 aftershocks ? Mw4.0 from 9 September 2010 to 31 July 2011. Sensors were deployed in local residences as part of the QCN Rapid Aftershock Mobilization Project (RAMP), collecting vast amounts of data at dense spatial scales. The low cost, 14-bit QCN sensors perform within ANSS Class C sensor standards (Evans et al., 2013), and, the time series and response spectra of the sensors compare favorably to the strong-motion 24-bit NZ GeoNet sensors (Cochran et al., 2011). To find ?, we measure deviations from the ?-2 fall-off on the acceleration amplitude spectrum of Fourier-transformed S-wave windows containing 80% of the S-wave energy. We use both manual and automated methods to fit the slope of the fall-off (i.e., ?) following Anderson and Hough (1984). A known issue with this method is that ? should be measured above the corner frequency (f0) to avoid bias from source effects. Studies have recently reported larger than average stress drops for these aftershocks (e.g., Kaiser and Oth, 2013), which may yield significant variation from the theoretically determined f0. Here, we aim to find the site attenuation, ?, by simultaneously solving for f0 and the seismic moment (M0) for each station and event. For robust results, we employ several methods to find the source and site parameters. Initially, we use a linearized least-squares fitting routine for each event-station pair (e.g., Anderson and Humphrey, 1991). This method does not require a single M0 for an event recorded at multiple stations, resulting in disagreements across M0 and f0 for any given event. Consequently, we also employ a more physically meaningful approach that calculates a single M0 and f0 for a given event using a linearized general inversion scheme (e.g., Sarker and Abers, 1998; Stachnik et al., 2004). Due to a strong trade-off between f0 and ?, we lastly try the nonlinear least-squares Gauss-Newton algorithm, which obtains a constant M0 and produces a more reasonable f0 and well-fitted ?. Initial results show ? estimates range from 0.01 to 0.1 sec and our calculated moment magnitudes (Mw) agree with the USGS NEIC catalog. Another goal of this study is to determine if the QCN data can be confidently used to find source parameters. With the vast amount of strong-motion data collected, QCN offers an ideal dataset to determine source parameters from spectral fitting; particularly in Christchurch, where smaller datasets may contain a proportionally higher number of recordings that are biased by local effects, including site amplification and nonlinear response like liquefaction. For a single event, preliminary findings show that QCN sensors yield higher M0 values than GeoNet stations, thus prompting further investigation.

  12. Molecular interactions of DNA-topoisomerase I and II inhibitor with DNA and topoisomerases and in ternary complexes: binding modes and biological effects for intoplicine derivatives.

    PubMed

    Nabiev, I; Chourpa, I; Riou, J F; Nguyen, C H; Lavelle, F; Manfait, M

    1994-08-01

    Molecular interactions of intoplicine, dual DNA-topoisomerases (Topo) I and II inhibitor, with topoisomerases, plasmid DNA, in ternary cleavable complexes with enzymes and plasmid DNA, and in the reversed cleavable complexes were examined by means of surface-enhanced Raman scattering (SERS) and CD spectroscopy and by biochemical techniques. Detailed spectral analysis of intoplicine derivatives allowed us to assign SERS vibrational modes of chromophores and to propose the models for these complexes. Intoplicine was found to be able to interact specifically with the Topo II alone, but with Topo I only when in the presence of DNA. It shows at least two modes of binding to the DNA: the first was found to be dominant for its derivative 1c (most potent Topo I inhibitor), and the second was dominant for derivative 2a (most potent Topo II inhibitor). The possibility of forming these two types of complexes simultaneously is suggested to be one of the main factors enabling the drug to be a dual Topo I and Topo II inhibitor. The "deep intercalation mode" of the drug from the DNA minor groove with the long axis of the chromophore oriented roughly parallel to the dyad axis has been suggested to be responsible for induction of distortions of the DNA structure by the intercalating drug. Being involved in the formation of Topo I-mediated cleavable ternary complex, the molecules participating in the deep intercalation mode within the DNA do not change their molecular interactions as compared with their complex with the DNA alone. The stabilization of the Topo I-mediated cleavable complex was shown to be followed by the local denaturation of DNA in the AT-rich regions of the helix. When the ternary cleavable complex was reversed, the drug was shown to be in the complex with the plasmid. The "outside binding mode" from the DNA major groove via the hydroxyl group of the A-ring of the chromophore has been suggested to be responsible for Topo II inhibition. These molecules did not induce significant distortions of the DNA structure. Being involved in the formation of Topo II-mediated cleavable ternary complex, the drug changed its molecular interactions as compared with the complex with DNA alone.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:8043587

  13. Interactions between butterfly-shaped pulses in the inhomogeneous media

    SciTech Connect

    Liu, Wen-Jun; Huang, Long-Gang; Pan, Nan; Lei, Ming

    2014-10-15

    Pulse interactions affect pulse qualities during the propagation. Interactions between butterfly-shaped pulses are investigated to improve pulse qualities in the inhomogeneous media. In order to describe the interactions between butterfly-shaped pulses, analytic two-soliton solutions are derived. Based on those solutions, influences of corresponding parameters on pulse interactions are discussed. Methods to control the pulse interactions are suggested. - Highlights: • Interactions between butterfly-shaped pulses are investigated. • Methods to control the pulse interactions are suggested. • Analytic two-soliton solutions for butterfly-shaped pulses are derived.

  14. Effect of nonlinear optical three-wave interaction on the lasing parameters of a dual-wavelength vertical-external-cavity surface-emitting laser

    SciTech Connect

    Morozov, M Yu; Morozov, Yu A; Krasnikova, I V

    2013-09-30

    The influence of nonlinear optical interaction in a semiconductor dual-wavelength vertical-external-cavity surface-emitting laser on the main parameters of dual-wavelength radiation and lasing in the long-wavelength part of the mid-IR range, obtained in this laser as a result of nonlinear wave mixing, is investigated. An increase in the pump power leads to saturation of the short-wavelength lasing intensity and to a more rapid rise in the long-wavelength lasing intensity in comparison with the linear increase in lasing intensity in these regions in the absence of nonlinear interaction. Under the conditions of nonlinear interaction, the carrier concentration in the active layers is not stabilised near the lasing threshold but changes with an increase in the pump intensity and provides the corresponding gain in the laser active region, thus maintaining steadystate lasing. Some ways for modifying the laser active region in order to obtain the most efficient lasing in the mid-IR range are proposed. (nonlinear optical phenomena)

  15. BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors

    PubMed Central

    Wang, Junbai; Morigen

    2009-01-01

    Background We have incorporated Bayesian model regularization with biophysical modeling of protein-DNA interactions, and of genome-wide nucleosome positioning to study protein-DNA interactions, using a high-throughput dataset. The newly developed method (BayesPI) includes the estimation of a transcription factor (TF) binding energy matrices, the computation of binding affinity of a TF target site and the corresponding chemical potential. Results The method was successfully tested on synthetic ChIP-chip datasets, real yeast ChIP-chip experiments. Subsequently, it was used to estimate condition-specific and species-specific protein-DNA interaction for several yeast TFs. Conclusion The results revealed that the modification of the protein binding parameters and the variation of the individual nucleotide affinity in either recognition or flanking sequences occurred under different stresses and in different species. The findings suggest that such modifications may be adaptive and play roles in the formation of the environment-specific binding patterns of yeast TFs and in the divergence of TF binding sites across the related yeast species. PMID:19857274

  16. Neural stem cells induce bone-marrow-derived mesenchymal stem cells to generate neural stem-like cells via juxtacrine and paracrine interactions

    SciTech Connect

    Alexanian, Arshak R. . E-mail: aalexan@mcw.edu

    2005-11-01

    Several recent reports suggest that there is far more plasticity that previously believed in the developmental potential of bone-marrow-derived cells (BMCs) that can be induced by extracellular developmental signals of other lineages whose nature is still largely unknown. In this study, we demonstrate that bone-marrow-derived mesenchymal stem cells (MSCs) co-cultured with mouse proliferating or fixed (by paraformaldehyde or methanol) neural stem cells (NSCs) generate neural stem cell-like cells with a higher expression of Sox-2 and nestin when grown in NS-A medium supplemented with N2, NSC conditioned medium (NSCcm) and bFGF. These neurally induced MSCs eventually differentiate into {beta}-III-tubulin and GFAP expressing cells with neuronal and glial morphology when grown an additional week in Neurobasal/B27 without bFGF. We conclude that juxtacrine interaction between NSCs and MSCs combined with soluble factors released from NSCs are important for generation of neural-like cells from bone-marrow-derived adherent MSCs.

  17. Use of the Combination Index to determine interactions between plant-derived phenolic acids on hepatotoxicity endpoints in human and rat hepatoma cells.

    PubMed

    Liu, Yitong; Flynn, Thomas J; Ferguson, Martine S; Hoagland, Erica M

    2013-03-15

    The beneficial or adverse effects of isolated phytochemicals are not always concordant with effects of the botanical dietary supplements from which they were derived. This disparity could be due to interactions between the various phytochemicals present in the whole plant. The phenolic acids, rosmarinic acid (RA), caffeic acid (CA) and ferulic acid (FA) are widely present in foods and dietary supplements, and they are assumed to exert various beneficial biological effects. However, there is little data on the potential biological interactions of these three phenolic acids which commonly occur together and are linked metabolically. In the present study, liver toxicity of the three phenolic acids was assessed on the three compounds singly and in various binary and one ternary combinations. A series of in vitro endpoints relevant to liver toxicity were evaluated in both a human (HepG2/C3A) and rat (MH1C1) hepatocyte cell line. The Combination Index (CI) was calculated for each endpoint from both the concentration responses of the single compounds and the responses of the various binary and ternary mixtures. Both synergistic and antagonistic interactions were observed for some endpoints and some combinations of test agents. Interactions were most prevalent in measures of oxidative stress and cytochrome P450 activities in both cell types. There was only a 53% concordance between the rat and human cells which may be suggestive of species differences. The data suggest an approach for better characterizing the beneficial or adverse effects of complex botanical products through evaluation of interactions between individual phytochemical components. PMID:23380082

  18. 3-Hydroxy-4-pyridinone derivatives designed for fluorescence studies to determine interaction with amyloid protein as well as cell permeability.

    PubMed

    Telpoukhovskaia, Maria A; Cawthray, Jacqueline F; Rodríguez-Rodríguez, Cristina; Scott, Lauren E; Page, Brent D G; Patrick, Brian O; Orvig, Chris

    2015-09-01

    Finding a cure for Alzheimer's disease is an urgent goal. Multifunctional metal binders are used to elucidate its pathological features and investigated as potential therapeutics. The use of physicochemical and TD-DFT calculations constituted successful strategy in the design of 1-(4-(benzo[d]oxazol-2-yl)phenyl)-3-hydroxy-2-methylpyridin-4(1H)-one (HL21) and 1-(4-(benzo[d]thiazol-2-yl)phenyl)-3-hydroxy-2-methylpyridin-4(1H)-one (HL22). We report the synthesis and full characterization of these compounds, including X-ray crystallography. Using fluorescent signal as the readout, it was determined that HL22 interacts with amyloid-beta protein fibrils, and permeates into bEnd.3 cells used as a mimic of the blood-brain barrier. This provides the first example of direct investigation of our hydroxypyridinone compounds within a biological setting. PMID:26141772

  19. Interactions between muscle stem cells, mesenchymal-derived cells and immune cells in muscle homeostasis, regeneration and disease

    PubMed Central

    Farup, J; Madaro, L; Puri, P L; Mikkelsen, U R

    2015-01-01

    Recent evidence has revealed the importance of reciprocal functional interactions between different types of mononuclear cells in coordinating the repair of injured muscles. In particular, signals released from the inflammatory infiltrate and from mesenchymal interstitial cells (also known as fibro-adipogenic progenitors (FAPs)) appear to instruct muscle stem cells (satellite cells) to break quiescence, proliferate and differentiate. Interestingly, conditions that compromise the functional integrity of this network can bias muscle repair toward pathological outcomes that are typically observed in chronic muscular disorders, that is, fibrotic and fatty muscle degeneration as well as myofiber atrophy. In this review, we will summarize the current knowledge on the regulation of this network in physiological and pathological conditions, and anticipate the potential contribution of its cellular components to relatively unexplored conditions, such as aging and physical exercise. PMID:26203859

  20. Images of gravitational and magnetic phenomena derived from two-dimensional back-projection Doppler tomography of interacting binary stars

    SciTech Connect

    Richards, Mercedes T.; Cocking, Alexander S.; Fisher, John G.; Conover, Marshall J. E-mail: asc5097@psu.edu

    2014-11-10

    We have used two-dimensional back-projection Doppler tomography as a tool to examine the influence of gravitational and magnetic phenomena in interacting binaries that undergo mass transfer from a magnetically active star onto a non-magnetic main-sequence star. This multitiered study of over 1300 time-resolved spectra of 13 Algol binaries involved calculations of the predicted dynamical behavior of the gravitational flow and the dynamics at the impact site, analysis of the velocity images constructed from tomography, and the influence on the tomograms of orbital inclination, systemic velocity, orbital coverage, and shadowing. The H? tomograms revealed eight sources: chromospheric emission, a gas stream along the gravitational trajectory, a star-stream impact region, a bulge of absorption or emission around the mass-gaining star, a Keplerian accretion disk, an absorption zone associated with hotter gas, a disk-stream impact region, and a hot spot where the stream strikes the edge of a disk. We described several methods used to extract the physical properties of the emission sources directly from the velocity images, including S-wave analysis, the creation of simulated velocity tomograms from hydrodynamic simulations, and the use of synthetic spectra with tomography to sequentially extract the separate sources of emission from the velocity image. In summary, the tomography images have revealed results that cannot be explained solely by gravitational effects: chromospheric emission moving with the mass-losing star, a gas stream deflected from the gravitational trajectory, and alternating behavior between stream state and disk state. Our results demonstrate that magnetic effects cannot be ignored in these interacting binaries.

  1. The phenomenology of neutrinos with Majorana mass terms and standard-model interactions derived in the charge-parity basis

    E-print Network

    R. Plaga

    2012-12-14

    (abridged) The physical mechanisms that make a neutrino with standard-model (SM) weak interactions a "lepton-number conservation (LNC) violating" neutrino such as the Majorana neutrino are analysed in a basis of two Majorana states that have opposite charge-parity ("charge-parity basis"). A small Majorana mass that is larger than any Dirac mass makes the neutrino not a Majorana but a "pseudo-Majorana" particle that has no definite chirality and therefore has a different phenomenology than the physical neutrino. A combination of a large Majorana and Dirac mass of nearly equal value makes the neutrino a Majorana neutrino. However if this Majorana neutrino has SM interactions, its weak transition amplitudes squared are a factor 2 smaller than the ones observed for the physical neutrino. Only with a small Dirac mass that is larger than any Majorana mass (and in the massless case), the physical neutrino's phenomenology is correctly predicted by the SM. Such a mass combination makes the neutrino a Dirac- or (the most likely possibility for the physical neutrino) Pontecorvo's pseudo-Dirac particle which features neutrino-antineutrino oscillations, that violate LNC. Pseudo-Dirac neutrinos enable a completely negligible rate for neutrinoless double-beta decay if there is no Majorana-mass independent decay mechanism. Off-diagonal components of the mass matrix in the charge-parity basis make the neutrino a mixture of Dirac field with a different particle and anti-particle mass (i.e. a mass that violates CPT invariance) and a pseudo-Dirac field. Such a neutrino leads to a phenomenology similar to the one with additional generations of sterile neutrinos.

  2. N2O vibration-rotation parameters derived from measurements in the 900-1090- and 1580-2380/cm regions

    NASA Technical Reports Server (NTRS)

    Toth, Robert A.

    1987-01-01

    Fourier-transform spectrometric measurements of the N2O IR spectrum in the 900-1090 and 1580-2380/cm regions were obtained at a 0.005/cm resolution, and line frequencies of eight species for several ground state bands and hot bands are analyzed to obtain values of band centers and upper-state effective rotational constants. Several bands are reported for the first time. Least-squares fits for the 0400-0000, 0420(e)-0000, and 0510-0110 bands of the (N-14)2O-16 species suggest perturbation of the high-J levels of the upper states. Resonance interactions were noted in transitions including the 1001-1000 bands of (N-14)2O-16 and N-15N-14O-16.

  3. Reconciliation of essential process parameters for an enhanced predictability of Arctic stratospheric ozone loss and its climate interactions

    NASA Astrophysics Data System (ADS)

    von Hobe, M.; Bekki, S.; Borrmann, S.; Cairo, F.; D'Amato, F.; Di Donfrancesco, G.; Dörnbrack, A.; Ebersoldt, A.; Ebert, M.; Emde, C.; Engel, I.; Ern, M.; Frey, W.; Griessbach, S.; Grooß, J.-U.; Gulde, T.; Günther, G.; Hösen, E.; Hoffmann, L.; Homonnai, V.; Hoyle, C. R.; Isaksen, I. S. A.; Jackson, D. R.; Jánosi, I. M.; Kandler, K.; Kalicinsky, C.; Keil, A.; Khaykin, S. M.; Khosrawi, F.; Kivi, R.; Kuttippurath, J.; Laube, J. C.; Lefèvre, F.; Lehmann, R.; Ludmann, S.; Luo, B. P.; Marchand, M.; Meyer, J.; Mitev, V.; Molleker, S.; Müller, R.; Oelhaf, H.; Olschewski, F.; Orsolini, Y.; Peter, T.; Pfeilsticker, K.; Piesch, C.; Pitts, M. C.; Poole, L. R.; Pope, F. D.; Ravegnani, F.; Rex, M.; Riese, M.; Röckmann, T.; Rognerud, B.; Roiger, A.; Rolf, C.; Santee, M. L.; Scheibe, M.; Schiller, C.; Schlager, H.; Siciliani de Cumis, M.; Sitnikov, N.; Søvde, O. A.; Spang, R.; Spelten, N.; Stordal, F.; Sumi?ska-Ebersoldt, O.; Viciani, S.; Volk, C. M.; vom Scheidt, M.; Ulanovski, A.; von der Gathen, P.; Walker, K.; Wegner, T.; Weigel, R.; Weinbuch, S.; Wetzel, G.; Wienhold, F. G.; Wintel, J.; Wohltmann, I.; Woiwode, W.; Young, I. A. K.; Yushkov, V.; Zobrist, B.; Stroh, F.

    2012-11-01

    Significant reductions in stratospheric ozone occur inside the polar vortices each spring when chlorine radicals produced by heterogeneous reactions on cold particle surfaces in winter destroy ozone mainly in two catalytic cycles, the ClO dimer cycle and the ClO/BrO cycle. Chlorofluorocarbons (CFCs), which are responsible for most of the chlorine currently present in the stratosphere, have been banned by the Montreal Protocol and its amendments, and the ozone layer is predicted to recover to 1980 levels within the next few decades. During the same period, however, climate change is expected to alter the temperature, circulation patterns and chemical composition in the stratosphere, and possible geo-engineering ventures to mitigate climate change may lead to additional changes. To realistically predict the response of the ozone layer to such influences requires the correct representation of all relevant processes. The European project RECONCILE has comprehensively addressed remaining questions in the context of polar ozone depletion, with the objective to quantify the rates of some of the most relevant, yet still uncertain physical and chemical processes. To this end RECONCILE used a broad approach of laboratory experiments, two field missions in the Arctic winter 2009/10 employing the high altitude research aircraft M55-Geophysica and an extensive match ozone sonde campaign, as well as microphysical and chemical transport modelling and data assimilation. Some of the main outcomes of RECONCILE are as follows: (1) vortex meteorology: the 2009/10 Arctic winter was unusually cold at stratospheric levels during the six-week period from mid-December 2009 until the end of January 2010, with reduced transport and mixing across the polar vortex edge; polar vortex stability and how it is influenced by dynamic processes in the troposphere has led to unprecedented, synoptic-scale stratospheric regions with temperatures below the frost point; in these regions stratospheric ice clouds have been observed, extending over >106km2 during more than 3 weeks. (2) Particle microphysics: heterogeneous nucleation of nitric acid trihydrate (NAT) particles in the absence of ice has been unambiguously demonstrated; conversely, the synoptic scale ice clouds also appear to nucleate heterogeneously; a variety of possible heterogeneous nuclei has been characterised by chemical analysis of the non-volatile fraction of the background aerosol; substantial formation of solid particles and denitrification via their sedimentation has been observed and model parameterizations have been improved. (3) Chemistry: strong evidence has been found for significant chlorine activation not only on polar stratospheric clouds (PSCs) but also on cold binary aerosol; laboratory experiments and field data on the ClOOCl photolysis rate and other kinetic parameters have been shown to be consistent with an adequate degree of certainty; no evidence has been found that would support the existence of yet unknown chemical mechanisms making a significant contribution to polar ozone loss. (4) Global modelling: results from process studies have been implemented in a prognostic chemistry climate model (CCM); simulations with improved parameterisations of processes relevant for polar ozone depletion are evaluated against satellite data and other long term records using data assimilation and detrended fluctuation analysis. Finally, measurements and process studies within RECONCILE were also applied to the winter 2010/11, when special meteorological conditions led to the highest chemical ozone loss ever observed in the Arctic. In addition to quantifying the 2010/11 ozone loss and to understand its causes including possible connections to climate change, its impacts were addressed, such as changes in surface ultraviolet (UV) radiation in the densely populated northern mid-latitudes.

  4. Antimicrobial films based on cellulose-derived hydrocolloids. A synergetic effect of host-guest interactions on quality and functionality.

    PubMed

    Rutenberg, Roi; Bernstein, Solange; Paster, Nachman; Fallik, Eli; Poverenov, Elena

    2016-01-01

    A series of active films based on biodegradable cellulose-derived hydrocolloids capable of controlled release of antimicrobial propionic acid (PA) was prepared. ?-Cyclodextrin (?-CD), usually used for encapsulation of lipophilic compounds, was utilized in this research to host the hydrophilic PA. It was found that addition of ?-CD to the film forming solutions notably enhanced the hydrocolloid matrix capacity and resulted in up to a ten-fold increase in the amount of uploaded PA. In addition, ?-CD resulted in a two-fold prolongation of the effective PA release duration. ?-CD alone caused undesired effects on the physical, mechanical and morphological properties of the hydrocolloid films. Interestingly, when ?-CD was combined with PA in the film formulation, its undesired effects were significantly subdued. The antifungal activity of the films was demonstrated on fresh harvested wheat grains. Films containing ?-CD and PA were found to be effective in preventing fungal growth on wheat grains. Thus, incorporation of ?-CD and PA in hydrocolloids matrices demonstrated a synergetic effect and resulted in the formation of biodegradable active films that benefit good physical and mechanical properties, high active agent content, prolonged release ability and effective antimicrobial properties. PMID:26143711

  5. Embryo-Specific Gene Expression in Microspore-Derived Embryos of Brassica napus. An Interaction between Abscisic Acid and Jasmonic Acid1, 2

    PubMed Central

    Hays, Dirk B.; Wilen, Ronald W.; Sheng, Chuxing; Moloney, Maurice M.; Pharis, Richard P.

    1999-01-01

    The induction of napin and oleosin gene expression in Brassica napus microspore-derived embryos (MDEs) was studied to assess the possible interaction between abscisic acid (ABA) and jasmonic acid (JA). Napin and oleosin transcripts were detected sooner following treatment with ABA than JA. Treatment of MDEs with ABA plus JA gave an additive accumulation of both napin and oleosin mRNA, the absolute amount being dependent on the concentration of each hormone. Endogenous ABA levels were reduced by 10-fold after treatment with JA, negating the possibility that the observed additive interaction was due to JA-induced ABA biosynthesis. Also, JA did not significantly increase the uptake of [3H-ABA] from the medium into MDEs. This suggests that the additive interaction was not due to an enhanced carrier-mediated ABA uptake by JA. Finally, when JA was added to MDEs that had been treated with the ABA biosynthesis inhibitor fluridone, napin mRNA did not increase. Based on these results with the MDE system, it is possible that embryos of B. napus use endogenous JA to modulate ABA effects on expression of both napin and oleosin. In addition, JA could play a causal role in the reduction of ABA that occurs during late stages of seed development. PMID:10069845

  6. Estrogen and brain-derived neurotrophic factor (BDNF) in hippocampus: complexity of steroid hormone-growth factor interactions in the adult CNS.

    PubMed Central

    Scharfman, Helen E.; MacLusky, Neil J.

    2007-01-01

    In the CNS, there are widespread and diverse interactions between growth factors and estrogen. Here we examine the interactions of estrogen and brain-derived neurotrophic factor (BDNF), two molecules that have historically been studied separately, despite the fact that they seem to share common targets, effects, and mechanisms of action. The demonstration of an estrogen-sensitive response element on the BDNF gene provided an impetus to explore a direct relationship between estrogen and BDNF, and predicted that the effects of estrogen, at least in part, might be due to the induction of BDNF. This hypothesis is discussed with respect to the hippocampus, where substantial evidence has accumulated in favor of it, but alternate hypotheses are also raised. It is suggested that some of the interactions between estrogen and BDNF, as well as the controversies and implications associated with their respective actions, may be best appreciated in light of the ability of BDNF to induce neuropeptide Y (NPY) synthesis in hippocampal neurons. Taken together, this tri-molecular cascade, estrogen-BDNF-NPY, may be important in understanding the hormonal regulation of hippocampal function. It may also be relevant to other regions of the CNS where estrogen is known to exert profound effects, such as amygdala and hypothalamus; and may provide greater insight into neurological disorders and psychiatric illness, including Alzheimer’s disease, depression and epilepsy. PMID:17055560

  7. Indole-3-acetaldoxime-derived compounds restrict root colonization in the beneficial interaction between Arabidopsis roots and the endophyte Piriformospora indica.

    PubMed

    Nongbri, Pyniarlang L; Johnson, Joy Michal; Sherameti, Irena; Glawischnig, Erich; Halkier, Barbara Ann; Oelmüller, Ralf

    2012-09-01

    The growth-promoting and root-colonizing endophyte Piriformospora indica induces camalexin and the expression of CYP79B2, CYP79B3, CYP71A13, PAD3, and WRKY33 required for the synthesis of indole-3-acetaldoxime (IAOx)-derived compounds in the roots of Arabidopsis seedlings. Upregulation of the mRNA levels by P. indica requires cytoplasmic calcium elevation and mitogen-activated protein kinase 3 but not root-hair-deficient 2, radical oxygen production, or the 3-phosphoinositide-dependent kinase 1/oxidative signal-inducible 1 pathway. Because P. indica-mediated growth promotion is impaired in cyp79B2 cyp79B3 seedlings, while pad3 seedlings-which do not accumulate camalexin-still respond to the fungus, IAOx-derived compounds other than camalexin (e.g., indole glucosinolates) are required during early phases of the beneficial interaction. The roots of cyp79B2 cyp79B3 seedlings are more colonized than wild-type roots, and upregulation of the defense genes pathogenesis-related (PR)-1, PR-3, PDF1.2, phenylalanine ammonia lyase, and germin indicates that the mutant responds to the lack of IAOx-derived compounds by activating other defense processes. After 6 weeks on soil, defense genes are no longer upregulated in wild-type, cyp79B2 cyp79B3, and pad3 roots. This results in uncontrolled fungal growth in the mutant roots and reduced performance of the mutants. We propose that a long-term harmony between the two symbionts requires restriction of root colonization by IAOx-derived compounds. PMID:22852809

  8. The neutral atmosphere of Mars at ionospheric heights: A method to derive neutral atmospheric parameters from MaRS electron density profiles

    NASA Astrophysics Data System (ADS)

    Peter, Kerstin; Pätzold, Martin; Molina-Cuberos, Gregorio; Witasse, Olivier; Tellmann, Silvia; Häusler, Bernd; Bird, Michael

    2015-04-01

    The radio-science experiment MaRS (Mars Radio Science) on the Mars Express spacecraft sounds the atmosphere and ionosphere of Mars since 2004. More than 600 vertical profiles of the Mars ionospheric electron density and lower atmosphere neutral density and temperature have been aquired. These simultaneous soundings of the ionosphere and the lower neutral atmosphere make it possible to get information on the behavior of the Mars neutral atmosphere at ionospheric heights, which is directly not accessible by radio sounding but indirectly from the observed ionospheric electron density profiles. A simple 1D neutral atmospheric model is combined with a 1D ionospheric model for altitude ranges from 80 km to 160 km. The start-scenario of the model neutral atmosphere depends on the observed neutral atmospheric density at lower altitudes. The modelled neutral atmosphere profile as input for the ionospheric model is iterated until an agreement with the true observed electron density has been achieved. Information on the state of the upper neutral atmosphere are derived from the agreement between the modeled and observed electron density profiles.

  9. Determination of electrostatic parameters of a coumarin derivative compound C17H13NO3 by x-ray and density functional theory

    NASA Astrophysics Data System (ADS)

    Youcef, Megrouss; Nadia, Benhalima; Rawia, Bahoussi; Nouredine, Boukabcha; Abdelkader, Chouaih; Fodil, Hamzaoui

    2015-10-01

    This work is devoted to the experimental determination of the electrostatic properties of the molecular 4-methyl-7-(salicylidene amino) coumarin (C17H13NC3) using high resolution x-ray diffraction data. The experimental results are compared with those obtained theoretically from calculation type ab initio. The experimental investigation is carried out using the molecular electron charge density distribution based on the multipolar model of Hansen and Coppens. However the theoretical calculations are conducted by using the molecular orbital B3LYP method and the Hartree-Fock (HF) approximation with the basis set 6-31G (d,p) implemented in the Gaussian program. In addition to the structural analysis, the thermal agitation is also analyzed in terms of rigid blocks to ensure a better precision of the results. Subsequently, the electrostatic atomic and molecular properties such as the net charges, the molecular dipolar moment to highlight the nature of charge transfer existing within the molecule studied are derived. Moreover, the obtained electrostatic potential enables the localization of the electropositive and the electronegative parts of the investigated molecule. The present work reports in detail the obtained electrostatic properties of this biologically important molecule.

  10. Free energy calculation using molecular dynamics simulation combined with the three dimensional reference interaction site model theory. I. Free energy perturbation and thermodynamic integration along a coupling parameter

    NASA Astrophysics Data System (ADS)

    Miyata, Tatsuhiko; Ikuta, Yasuhiro; Hirata, Fumio

    2010-07-01

    This article proposes a free energy calculation method based on the molecular dynamics simulation combined with the three dimensional reference interaction site model theory. This study employs the free energy perturbation (FEP) and the thermodynamic integration (TDI) along the coupling parameters to control the interaction potential. To illustrate the method, we applied it to a complex formation process in aqueous solutions between a crown ether molecule 18-Crown-6 (18C6) and a potassium ion as one of the simplest model systems. Two coupling parameters were introduced to switch the Lennard-Jones potential and the Coulomb potential separately. We tested two coupling procedures: one is a "sequential-coupling" to couple the Lennard-Jones interaction followed by the Coulomb coupling, and the other is a "mixed-coupling" to couple both the Lennard-Jones and the Coulomb interactions together as much as possible. The sequential-coupling both for FEP and TDI turned out to be accurate and easily handled since it was numerically well-behaved. Furthermore, it was found that the sequential-coupling had relatively small statistical errors. TDI along the mixed-coupling integral path was to be carried out carefully, paying attention to a numerical behavior of the integrand. The present model system exhibited a nonmonotonic behavior in the integrands for TDI along the mixed-coupling integral path and also showed a relatively large statistical error. A coincidence within a statistical error was obtained among the results of the free energy differences evaluated by FEP, TDI with the sequential-coupling, and TDI with the mixed-coupling. The last one is most attractive in terms of the computer power and is accurate enough if one uses a proper set of windows, taking the numerical behavior of the integrands into account. TDI along the sequential-coupling integral path would be the most convenient among the methods we tested, since it seemed to be well-balanced between the computational load and the accuracy. The numerical results reported in this article qualitatively agree with the experimental data for the potassium ion recognition by the 18C6 in aqueous solution.

  11. Free energy calculation using molecular dynamics simulation combined with the three dimensional reference interaction site model theory. I. Free energy perturbation and thermodynamic integration along a coupling parameter.

    PubMed

    Miyata, Tatsuhiko; Ikuta, Yasuhiro; Hirata, Fumio

    2010-07-28

    This article proposes a free energy calculation method based on the molecular dynamics simulation combined with the three dimensional reference interaction site model theory. This study employs the free energy perturbation (FEP) and the thermodynamic integration (TDI) along the coupling parameters to control the interaction potential. To illustrate the method, we applied it to a complex formation process in aqueous solutions between a crown ether molecule 18-Crown-6 (18C6) and a potassium ion as one of the simplest model systems. Two coupling parameters were introduced to switch the Lennard-Jones potential and the Coulomb potential separately. We tested two coupling procedures: one is a "sequential-coupling" to couple the Lennard-Jones interaction followed by the Coulomb coupling, and the other is a "mixed-coupling" to couple both the Lennard-Jones and the Coulomb interactions together as much as possible. The sequential-coupling both for FEP and TDI turned out to be accurate and easily handled since it was numerically well-behaved. Furthermore, it was found that the sequential-coupling had relatively small statistical errors. TDI along the mixed-coupling integral path was to be carried out carefully, paying attention to a numerical behavior of the integrand. The present model system exhibited a nonmonotonic behavior in the integrands for TDI along the mixed-coupling integral path and also showed a relatively large statistical error. A coincidence within a statistical error was obtained among the results of the free energy differences evaluated by FEP, TDI with the sequential-coupling, and TDI with the mixed-coupling. The last one is most attractive in terms of the computer power and is accurate enough if one uses a proper set of windows, taking the numerical behavior of the integrands into account. TDI along the sequential-coupling integral path would be the most convenient among the methods we tested, since it seemed to be well-balanced between the computational load and the accuracy. The numerical results reported in this article qualitatively agree with the experimental data for the potassium ion recognition by the 18C6 in aqueous solution. PMID:20687640

  12. Analytic derivation of an approximate SU(3) symmetry inside the symmetry triangle of the interacting boson approximation model

    SciTech Connect

    Bonatsos, Dennis; Karampagia, S.; Casten, R. F.

    2011-05-15

    Using a contraction of the SU(3) algebra to the algebra of the rigid rotator in the large-boson-number limit of the interacting boson approximation (IBA) model, a line is found inside the symmetry triangle of the IBA, along which the SU(3) symmetry is preserved. The line extends from the SU(3) vertex to near the critical line of the first-order shape/phase transition separating the spherical and prolate deformed phases, and it lies within the Alhassid-Whelan arc of regularity, the unique valley of regularity connecting the SU(3) and U(5) vertices in the midst of chaotic regions. In addition to providing an explanation for the existence of the arc of regularity, the present line represents an example of an analytically determined approximate symmetry in the interior of the symmetry triangle of the IBA. The method is applicable to algebraic models possessing subalgebras amenable to contraction. This condition is equivalent to algebras in which the equilibrium ground state and its rotational band become energetically isolated from intrinsic excitations, as typified by deformed solutions to the IBA for large numbers of valence nucleons.

  13. CsPbCO3F: a strong second-harmonic generation material derived from enhancement via p-? interaction.

    PubMed

    Zou, Guohong; Huang, Ling; Ye, Ning; Lin, Chensheng; Cheng, Wendan; Huang, Hui

    2013-12-11

    The combination of Pb(2+) cations with lone-pair electrons and F(-) anions with the largest electronegativity into the carbonate generates a new nonlinear optical material, CsPbCO3F, with the largest powder second-harmonic generation (SHG) response among carbonates of about 13.4 times that of KDP (KH2PO4), and transparency over the near-UV to middle-IR region. The optical characterization of the compound indicates that it is phase matchable. Its crystal structure exhibits the stacking of [CsF]? and [Pb(CO3)]? layers, and the coplanar alignment of [CO3] triangles which are oriented in the same direction. Yet the Pb(2+) cation has an inert or nonstereoactive lone-pair, as indicated by its more spherical shape. Theoretical calculations confirm that the extremely large SHG efficiency indeed originates from enhancement via p-? interaction between Pb(2+) and [CO3](2-) within the [Pb(CO3)] layers. PMID:24261671

  14. Specific interactions between the Candida albicans ABC transporter Cdr1p ectodomain and a d-octapeptide derivative inhibitor

    PubMed Central

    Niimi, Kyoko; Harding, David R. K.; Holmes, Ann R.; Lamping, Erwin; Niimi, Masakazu; Tyndall, Joel D. A.; Cannon, Richard D.; Monk, Brian C.

    2012-01-01

    Summary Over-expression of the Candida albicans ATP-binding cassette transporter CaCdr1p causes clinically significant resistance to azole drugs including fluconazole (FLC). Screening of a ~1.89 × 106 member d-octapeptide combinatorial library that concentrates library members at the yeast cell surface identified RC21v3, a 4-methoxy-2,3,6-trimethylbenzenesulphonyl derivative of the d-octapeptide d-NH2-FFKWQRRR-CONH2, as a potent and stereospecific inhibitor of CaCdr1p. RC21v3 chemosensitized Saccharomyces cerevisiae strains over-expressing CaCdr1p but not other fungal ABC transporters, the C. albicans MFS transporter CaMdr1p or the azole target enzyme CaErg11p, to FLC. RC21v3 also chemosensitized clinical C. albicans isolates over-expressing CaCDR1 to FLC, even when CaCDR2 was over-expressed. Specific targeting of CaCdr1p by RC21v3 was confirmed by spontaneous RC21v3 chemosensitization resistant suppressor mutants of S. cerevisiae expressing CaCdr1p. The suppressor mutations introduced a positive charge beside, or within, extracellular loops 1, 3, 4 and 6 of CaCdr1p or an aromatic residue near the extracytoplasmic end of transmembrane segment 5. The mutations did not affect CaCdr1p localization or Cdr1p ATPase activity but some increased susceptibility to the CaCdr1p substrates FLC, rhodamine 6G, rhodamine 123 and cycloheximide. The suppressor mutations showed that the drug-like CaCdr1p inhibitors FK506, enniatin, milbemycin ?11 and milbemycin ?9 have modes of action similar to RC21v3. PMID:22788839

  15. Specific interactions between the Candida albicans ABC transporter Cdr1p ectodomain and a D-octapeptide derivative inhibitor.

    PubMed

    Niimi, Kyoko; Harding, David R K; Holmes, Ann R; Lamping, Erwin; Niimi, Masakazu; Tyndall, Joel D A; Cannon, Richard D; Monk, Brian C

    2012-08-01

    Overexpression of the Candida albicans ATP-binding cassette transporter CaCdr1p causes clinically significant resistance to azole drugs including fluconazole (FLC). Screening of a ~1.89 × 10(6) member D-octapeptide combinatorial library that concentrates library members at the yeast cell surface identified RC21v3, a 4-methoxy-2,3,6-trimethylbenzenesulphonyl derivative of the D-octapeptide D-NH(2) -FFKWQRRR-CONH(2) , as a potent and stereospecific inhibitor of CaCdr1p. RC21v3 chemosensitized Saccharomyces cerevisiae strains overexpressing CaCdr1p but not other fungal ABC transporters, the C. albicans MFS transporter CaMdr1p or the azole target enzyme CaErg11p, to FLC. RC21v3 also chemosensitized clinical C. albicans isolates overexpressing CaCDR1 to FLC, even when CaCDR2 was overexpressed. Specific targeting of CaCdr1p by RC21v3 was confirmed by spontaneous RC21v3 chemosensitization-resistant suppressor mutants of S. cerevisiae expressing CaCdr1p. The suppressor mutations introduced a positive charge beside, or within, extracellular loops 1, 3, 4 and 6 of CaCdr1p or an aromatic residue near the extracytoplasmic end of transmembrane segment 5. The mutations did not affect CaCdr1p localization or CaCdr1p ATPase activity but some increased susceptibility to the CaCdr1p substrates FLC, rhodamine 6G, rhodamine 123 and cycloheximide. The suppressor mutations showed that the drug-like CaCdr1p inhibitors FK506, enniatin, milbemycin ?11 and milbemycin ?9 have modes of action similar to RC21v3. PMID:22788839

  16. Zinc(II) interactions with brain-derived neurotrophic factor N-terminal peptide fragments: inorganic features and biological perspectives.

    PubMed

    Travaglia, Alessio; La Mendola, Diego; Magrì, Antonio; Pietropaolo, Adriana; Nicoletti, Vincenzo G; Grasso, Giuseppe; Malgieri, Gaetano; Fattorusso, Roberto; Isernia, Carla; Rizzarelli, Enrico

    2013-10-01

    Brain-derived neurotrophic factor (BDNF) is a neurotrophin essential for neuronal differentiation, growth, and survival; it is involved in memory formation and higher cognitive functions. The N-terminal domain of BDNF is crucial for the binding selectivity and activation of its specific TrkB receptor. Zn(2+) ion binding may influence BDNF activity. Zn(2+) complexes with the peptide fragment BDNF(1-12) encompassing the sequence 1-12 of the N-terminal domain of BDNF were studied by means of potentiometry, electrospray mass spectrometry, NMR, and density functional theory (DFT) approaches. The predominant Zn(2+) complex species, at physiological pH, is [ZnL] in which the metal ion is bound to an amino, an imidazole, and two water molecules (NH2, N(Im), and 2O(water)) in a tetrahedral environment. DFT-based geometry optimization of the zinc coordination environment showed a hydrogen bond between the carboxylate and a water molecule bound to zinc in [ZnL]. The coordination features of the acetylated form [AcBDNF(1-12)] and of a single mutated peptide [BDNF(1-12)D3N] were also characterized, highlighting the role of the imidazole side chain as the first anchoring site and ruling out the direct involvement of the aspartate residue in the metal binding. Zn(2+) addition to the cell culture medium induces an increase in the proliferative activity of the BDNF(1-12) peptide and of the whole protein on the SHSY5Y neuroblastoma cell line. The effect of Zn(2+) is opposite to that previously observed for Cu(2+) addition, which determines a decrease in the proliferative activity for both peptide and protein, suggesting that these metals might discriminate and modulate differently the activity of BDNF. PMID:24070197

  17. Time corrections to teleseismic P delays derived from SKS splitting parameters and implications for western U.S. P-wave tomography

    NASA Astrophysics Data System (ADS)

    O'Driscoll, Leland J.; Humphreys, Eugene D.; Schmandt, Brandon

    2011-10-01

    Upper mantle anisotropy will affect teleseismic P-wave arrival times and create artifacts in isotropic travel-time tomography. Compiled SKS splitting results indicate variations in the strength and orientation of azimuthal anisotropy beneath the western U.S. We use SKS splitting parameters and a hexagonally anisotropic elastic tensor (fast symmetry axis) to estimate azimuthal anisotropy contributions to P-wave delay times and evaluate the effects on isotropic P-wave tomography. Estimated anisotropy correction times have a root-mean-square (RMS) value of 0.16 s, which is 37% of P-wave delay time RMS. The magnitude of azimuthal anisotropy, rather than its azimuth, has the strongest effect on P delay times; however, if the anisotropy symmetry axis has a plunge, P-wave travel times may be strongly affected by both magnitude and azimuth. Applying azimuthal anisotropy corrections significantly increases tomographic P-wave velocity beneath the High Lava Plains and central California coast, and decreases velocity beneath the Great Basin.

  18. Use of Descartes Folium Equation for Deriving a Relation between Total Aperture of Fractures after Uniaxial Compression and Strain Parameters of Different Rocks Exhibiting Negative Total Volumetric Strains

    NASA Astrophysics Data System (ADS)

    Palchik, V.

    2014-11-01

    The axial, crack and total volumetric strains, porosity, elastic constants, crack damage stresses, uniaxial compressive strengths, as well as fracture apertures and number of fracture traces in rock samples surface after compression were defined for different chalk, basalt, dolomite, granite, limestone and sandstone samples exhibiting negative total volumetric strain at failure. It is established that the total (summed) aperture of vertical fractures obtained on the lateral surface of rock sample is related to three characteristic strain parameters: axial strain at the onset of negative total volumetric strain, axial failure strain and negative total volumetric strain at failure. The relation is based on Descartes folium equation, where the length of the loop of folium is equal to axial strain coordinate at the onset of negative total volumetric strain. This relation shows that the total aperture increases according to power law with increasing difference between axial failure strain and axial strain at the onset of negative total volumetric strain. Simultaneously, an increase in this difference leads to an increase in the value of negative total volumetric strain at failure. It is found that a direct correlation between total aperture of fractures and negative total volumetric strain at failure is relatively weak. Nevertheless, total aperture of fractures tends to increase with increasing absolute value of negative total volumetric strain at failure. It is revealed that there is no connection between the number of fracture traces and negative total volumetric strain at failure.

  19. Revised structure activity parameters derived from new rate coefficient determinations for the reactions of chlorine atoms with a series of seven ketones at 290 K and 1 atm

    NASA Astrophysics Data System (ADS)

    Farrugia, L. N.; Bejan, I.; Smith, S. C.; Medeiros, D. J.; Seakins, P. W.

    2015-11-01

    Rate coefficients of Cl atom reactions with several ketones have been investigated at 298 K and 1 atm using relative rate methods, monitoring substrates with both GC and FTIR and with two reference compounds. The following rate coefficients (1010 k/cm3 molecule-1 s-1) were obtained: k(2-pentanone) = (1.08 ± 0.05), k(3-pentanone) = (0.89 ± 0.12), k(3-methyl-2-butanone) = (0.68 ± 0.06), k(4-methyl-2-pentanone) = (1.10 ± 0.10), k(5-methyl-2-hexanone) = (1.65 ± 0.14), k(3-methyl-2-pentanone) = (0.94 ± 0.10) and k(3,3-dimethyl-2-butanone) = (0.48 ± 0.05). The results are discussed in terms of Cl reactivity trends and existing literature. k(3-methyl-2-pentanone) and k(3,3-dimethyl-2-butanone) are poorly predicted with current structure activity relationships and revised parameters are proposed. In regions of high [Cl], these reactions can significantly reduce the fraction of ketones reaching the free troposphere.

  20. Sandstone and shale compaction curves derived from sonic and gamma ray logs in offshore wells, North Slope, Alaska; parameters for basin modeling

    USGS Publications Warehouse

    Rowan, Elisabeth L.; Hayba, Daniel O.; Nelson, Philip H.; Burns, W. Matthew; Houseknecht, David W.

    2003-01-01

    Representative compaction curves for the principle lithologies are essential input for reliable models of basin history. Compaction curves influence estimates of maximum burial and erosion. Different compaction curves may produce significantly different thermal histories. Default compaction curves provided by basin modeling packages may or may not be a good proxy for the compaction properties in a given area. Compaction curves in the published literature span a wide range, even within one lithology, e.g., sandstone (see Panel 3). An abundance of geophysical well data for the North Slope, from both government and private sources, provides us with an unusually good opportunity to develop compaction curves for the Cretaceous-Tertiary Brookian sandstones, siltstones, and shales. We examined the sonic and gamma ray logs from 19 offshore wells (see map), where significant erosion is least likely to have occurred. Our data are primarily from the Cretaceous-Tertiary Brookian sequence and are less complete for older sequences. For each well, the fraction of shale (Vsh) at a given depth was estimated from the gamma ray log, and porosity was computed from sonic travel time. By compositing porosities for the near-pure sand (Vsh99%)from many individual wells we obtained data over sufficient depth intervals to define sandstone and shale 'master' compaction curves. A siltstone curve was defined using the sonic-derived porosities for Vsh values of 50%. These compaction curves generally match most of the sonic porosities with an error of 5% or less. Onshore, the curves are used to estimate the depth of maximum burial at the end of Brookian sedimentation. The depth of sonic-derived porosity profiles is adjusted to give the best match with the 'master' compaction curves. The amount of the depth adjustment is the erosion estimate. Using our compaction curves, erosion estimates on the North Slope range from zero in much of the offshore, to as much as 1500 ft along the coast, and to more than 10,000 ft in the foothills (Panel 3). Compaction curves provide an alternative to vitrinite reflectance for estimating erosion. Vitrinite reflectance data are often very sparse in contrast to well log data and are subject to inconsistencies when measurements are made by different labs. The phenomenon of 'recycling' can also make the reflectance values of dispersed vitrinite problematic for quantifying erosion. Recycling is suspected in dispersed vitrinite in North Slope rocks, particularly in the younger, Cretaceous-Tertiary section. The compaction curves defined here are being integrated into our burial history and thermal models to determine the timing of source rock maturation. An example on Panel 3 shows the results of calculating the maturity of the Shublik Fm. at the Tulaga well using two different sets of shale and siltstone compaction curves. Finally, accurate compaction curves improve a model's ability to realistically simulate the pressure regime during burial, including overpressures.

  1. Pulmonary Arterial Hypertension: MR Imaging-derived First-Pass Bolus Kinetic Parameters Are Biomarkers for Pulmonary Hemodynamics, Cardiac Function, and Ventricular Remodeling

    PubMed Central

    Skrok, Jan; Shehata, Monda L.; Mathai, Stephen; Girgis, Reda E.; Zaiman, Ari; Mudd, James O.; Boyce, Danielle; Lechtzin, Noah; Lima, João A. C.; Bluemke, David A.; Hassoun, Paul M.

    2012-01-01

    Purpose: To prospectively compare contrast material–enhanced (CE) magnetic resonance (MR) imaging–derived right-to-left ventricle pulmonary transit time (PTT), left ventricular (LV) full width at half maximum (FWHM), and LV time to peak (TTP) between patients with pulmonary arterial hypertension (PAH) and healthy volunteers and to correlate these measurements with survival markers in patients with PAH. Materials and Methods: This HIPAA-compliant study received institutional review board approval. Written informed consent was obtained from all participants. Forty-three patients (32 with PAH [29 women; median age, 55.4 years], 11 with scleroderma but not PAH [seven women; median age, 58.9 years]) underwent right-sided heart catheterization and 3-T CE cardiac MR imaging. Eighteen age- and sex-matched healthy control subjects (12 women; median age, 51.7 years) underwent only CE MR imaging. A short-axis saturation-recovery gradient-echo section was acquired in the basal third of both ventricles, and right-to-left-ventricle PTT, LV FWHM, and LV TTP were calculated. Statistical analysis included Kruskal-Wallis test, Wilcoxon rank sum test, Spearman correlation coefficient, multiple linear regression analysis, and Lin correlation coefficient analysis. Results: Patients had significantly longer PTT (median, 8.2 seconds; 25th–75th percentile, 6.9–9.9 seconds), FWHM (median, 8.2 seconds; 25th–75th percentile, 5.7–11.4 seconds), and TTP (median, 4.8 seconds; 25th–75th percentile, 3.9–6.5 seconds) than did control subjects (median, 6.4 seconds; 25th–75th percentile, 5.7–7.1 seconds; median, 5.2 seconds; 25th–75th percentile, 4.1–6.1 seconds; median, 3.2 seconds; 25th–75th percentile, 2.8–3.8 seconds, respectively; P < .01 for each) and subjects with scleroderma but not PAH (median, 6.5 seconds; 25th–75th percentile, 5.6–7.0 seconds; median, 5.0 seconds; 25th–75th percentile, 4.0–7.3 seconds; median, 3.6 seconds; 25th–75th percentile, 2.7–4.0 seconds, respectively; P < .02 for each). PTT, LV FWHM, and LV TTP correlated with pulmonary vascular resistance index (P < .01), right ventricular stroke volume index (P ? .01), and pulmonary artery capacitance (P ? .02). In multiple linear regression models, PTT, FWHM, and TTP were associated with mean pulmonary arterial pressure and cardiac index. Conclusion: CE MR-derived PTT, LV FWHM, and LV TTP are noninvasive compound markers of pulmonary hemodynamics and cardiac function in patients with PAH. Their predictive value for patient outcome warrants further investigation. © RSNA, 2012 Supplemental materialhttp://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.12111001/-/DC1 PMID:22509050

  2. The effect of shattered artifacts on derivation of bulk cloud parameters from optical array probe data collected during ISDAC and IDEAS-4

    NASA Astrophysics Data System (ADS)

    McFarquhar, Greg; Jackson, Robert; Stith, Jeff; Rogers, David; Cooper, William

    2013-04-01

    Many existing parameterizations of ice clouds in climate and weather models are based on observations of number concentrations of ice crystals with maximum dimension D < 500 micrometers from forward scattering and optical array probes that have been artificially amplified by the detection of small crystals generated by the shattering of large crystals on probe tips and inlets. This produces uncertainties in the model representation of ice sedimentation and single-scattering radiative properties and of liquid to ice conversion rates in mixed phase clouds. In addition to uncertainties in how past data are affected by shattered artifacts, recent studies have reached varying conclusions regarding the efficacy of shatter reducing tips and correction algorithms to remove shattered artifacts. Here, the effect of shattering on bulk microphysical properties derived from the two-dimensional cloud probe (2DC), such as total ice crystal concentration, ice crystal number distribution function N(D), extinction, ice water content, effective radius and median mass diameter, is quantified. Such properties, computed from data acquired by 2DCs with standard and shatter reducing tips on the National Research Council of Canada Convair-580 during the Indirect and Semi-Direct Aerosol Campaign (ISDAC) and on the National Center for Atmospheric Research C-130 during the Instrumentation Development and Education in Airborne Science phase 4 (IDEAS-4), are compared as a function of true air speed, pitch, roll, and attack angles, ice crystal habit, degree of riming, median diameter, and temperature. In general, use of algorithms to remove shattered artifacts reduces N(D< 500 micrometers) by a factor of 2 or greater. But, the 2DC shatter reducing tips eliminate more shattered artifacts than does application of shatter correction algorithms. Thus, both techniques must be used in concert to maximize the removal of artifacts. Therefore, considerable improvements in model parameterizations are possible with improved measurements of ice.

  3. Study of Target Dependence of Clan Model Parameter in 84^Kr_36 - Emulsion Interactions at 1 GeV per nucleon

    E-print Network

    M K Singh; A K Soma; V Singh; R Pathak

    2013-07-16

    The article focuses on study of clan model parameters and their target dependence in light of void probability scaling for heavy (Ag and Br) and light (C, N and O) groups of targets present in nuclear emulsion detector using 84 Kr 36 at around 1 A GeV. The variation of scaled rapidity gap (rap gap) probability with single moment combination has been studied. We found that experimental points are lying approximately on the negative binomial distribution (NBD) curve, indicating a scaling behavior. The average clan multiplicities for interactions, increases with the pseudo-rapidity interval was also observed. The values of average multiplicity for AgBr targets are larger than those for CNO target and also average number of particles per clan increases with increase in pseudo-rapidity interval. We further observed that for a particular target, average number of particles per clan increases with an increase in the size of projectile nucleus.

  4. Mechanism of interaction of optimized Limulus-derived cyclic peptides with endotoxins: thermodynamic, biophysical and microbiological analysis

    PubMed Central

    Andrä, Jörg; Howe, Jörg; Garidel, Patrick; Rössle, Manfred; Richter, Walter; Leiva-León, José; Moriyon, Ignacio; Bartels, Rainer; Gutsmann, Thomas; Brandenburg, Klaus

    2007-01-01

    On the basis of formerly investigated peptides corresponding to the endotoxin-binding domain from LALF [Limulus anti-LPS (lipopolysaccharide) factor], a protein from Limulus polyphemus, we have designed and synthesized peptides of different lengths with the aim of obtaining potential therapeutic agents against septic shock syndrome. For an understanding of the mechanisms of action, we performed a detailed physicochemical and biophysical analysis of the interaction of rough mutant LPS with these peptides by applying FTIR (Fourier-transform infrared) spectroscopy, SAXS (small-angle X-ray scattering), calorimetric techniques [DSC (differential scanning calorimetry) and ITC (isothermal titration calorimetry)] and FFTEM (freeze-fracture transmission electron microscopy). Also, the action of the peptides on bacteria of different origin in microbial assays was investigated. Using FTIR and DSC, our results indicated a strong fluidization of the lipid A acyl chains due to peptide binding, with a decrease in the endothermic melting enthalpy change of the acyl chains down to a complete disappearance in the 1:0.5 to 1:2 [LPS]:[peptide] molar ratio range. Via ITC, it was deduced that the binding is a clearly exothermic process which becomes saturated at a 1:0.5 to 1:2 [LPS]:[peptide] molar ratio range. The results obtained with SAXS indicated a drastic change of the aggregate structures of LPS into a multilamellar stack, which was visualized in electron micrographs as hundreds of lamellar layers. This can be directly correlated with the inhibition of the LPS-induced production of tumour necrosis factor ? in human mononuclear cells, but not with the action of the peptides on bacteria. PMID:17501719

  5. Synthesis, antibacterial, antifungal activity and interaction of CT-DNA with a new benzimidazole derived Cu(II) complex.

    PubMed

    Arjmand, Farukh; Mohani, Bhawana; Ahmad, Shamim

    2005-11-01

    The ligand [C(16)H(10)O(2)N(4)S(2)] L has been synthesized by the condensation reaction of 2-mercaptobenzimidazole and diethyloxalate. The ligand L was allowed to react with bis(ethylenediamine)Cu(II)/Ni(II) complexes to yield [C(20)H(22)N(8)S(2)Cu]Cl(2)1 and [C(20)H(22)N(8)S(2)Ni]Cl(2)2 complexes. The Ni(II) complex was synthesized only to elucidate the structure of the complex. The complexes 1 and 2 were characterized by elemental analyses, IR, NMR, EPR, UV-vis spectroscopy and molar conductance measurements. Both the complexes are ionic in nature and possess square-planar geometry. The binding of the complex 1 to calf thymus DNA was investigated spectrophotometrically. The absorption spectra of complex 1 exhibits a slight red shift with "hyperchromic effect" in presence of CTDNA. Electrochemical analysis and viscosity measurements were also carried out to ascertain the mode of binding. The complex 1 in the absence and in presence of CT DNA in aqueous solution exhibits one quasi-reversible redox wave corresponding to Cu(II)/Cu(I) redox couple at a scan rate of 0.2 V s(-1). The shift in DeltaE(p), E(1/2) and I(pa)/I(pc) values ascertain the interaction of calf thymus DNA with copper(II) complex. There is decrease in viscosity of CTDNA which indicates that the complex 1 binds to CTDNA through a partial intercalative mode. The antibacterial and antifungal studies of the [C(7)H(6)N(2)S], [C(4)H(16)N(4)Cu]Cl(2,) [C(16)H(10)N(4)S(2)O(2)] and [C(20)H(22)N(8)S(2)Cu]Cl(2) were carried out against S. aureus, E. coli and A. niger. All the results reveal that the complex 1 is highly active against the bacterial strains and also inhibits fungal growth. PMID:16006016

  6. Abstracts and parameter index database for reports pertaining to the unsaturated zone and surface water-ground water interactions at the Idaho National Engineering Laboratory

    SciTech Connect

    Bloomsburg, G.; Finnie, J.; Horn, D.; King, B.; Liou, J.

    1993-05-01

    This report is a product generated by faculty at the University of Idaho in support of research and development projects on Unsaturated Zone Contamination and Transport Processes, and on Surface Water-Groundwater Interactions and Regional Groundwater Flow at the Idaho National Engineering Laboratory. These projects are managed by the State of Idaho`s INEL Oversight Program under a grant from the US Department of Energy. In particular, this report meets project objectives to produce a site-wide summary of hydrological information based on a literature search and review of field, laboratory and modeling studies at INEL, including a cross-referenced index to site-specific physical, chemical, mineralogic, geologic and hydrologic parameters determined from these studies. This report includes abstracts of 149 reports with hydrological information. For reports which focus on hydrological issues, the abstracts are taken directly from those reports; for reports dealing with a variety of issues beside hydrology, the abstracts were generated by the University of Idaho authors concentrating on hydrology-related issues. Each abstract is followed by a ``Data`` section which identifies types of technical information included in a given report, such as information on parameters or chemistry, mineralogy, stream flows, water levels. The ``Data`` section does not include actual values or data.

  7. Uncertainties in pharmacokinetic modeling for perchloroethylene. I. Comparison of model structure, parameters, and predictions for low-dose metabolism rates for models derived by different authors.

    PubMed

    Hattis, D; White, P; Marmorstein, L; Koch, P

    1990-09-01

    In recent years physiologically based pharmacokinetic models have come to play an increasingly important role in risk assessment for carcinogens. The hope is that they can help open the black box between external exposure and carcinogenic effects to experimental observations, and improve both high-dose to low-dose and interspecies projections of risk. However, to date, there have been only relatively preliminary efforts to assess the uncertainties in current modeling results. In this paper we compare the physiologically based pharmacokinetic models (and model predictions of risk-related overall metabolism) that have been produced by seven different sets of authors for perchloroethylene (tetrachloroethylene). The most striking conclusion from the data is that most of the differences in risk-related model predictions are attributable to the choice of the data sets used for calibrating the metabolic parameters. Second, it is clear that the bottom-line differences among the model predictions are appreciable. Overall, the ratios of low-dose human to bioassay rodent metabolism spanned a 30-fold range for the six available human/rat comparisons, and the seven predicted ratios of low-dose human to bioassay mouse metabolism spanned a 13-fold range. (The greater range for the rat/human comparison is attributable to a structural assumption by one author group of competing linear and saturable pathways, and their conclusion that the dangerous saturable pathway constitutes a minor fraction of metabolism in rats.) It is clear that there are a number of opportunities for modelers to make different choices of model structure, interpretive assumptions, and calibrating data in the process of constructing pharmacokinetic models for use in estimating "delivered" or "biologically effective" dose for carcinogenesis risk assessments. We believe that in presenting the results of such modeling studies, it is important for researchers to explore the results of alternative, reasonably likely approaches for interpreting the available data--and either show that any conclusions they make are relatively insensitive to particular interpretive choices, or to acknowledge the differences in conclusions that would result from plausible alternative views of the world. PMID:2236748

  8. The Mineralogical Record of Oxygen Fugacity Variation and Alteration in Northwest Africa 8159: Evidence for Interaction Between a Mantle Derived Martian Basalt and a Crustal Component(s)

    NASA Technical Reports Server (NTRS)

    Shearer, Charles K.; Burger, Paul V.; Bell, Aaron S.; McCubbin, Francis M.; Agee, Carl; Simon, Justin I.; Papike, James J.

    2015-01-01

    A prominent geochemical feature of basaltic magmatism on Mars is the large range in initial Sr isotopic ratios (approx. 0.702 - 0.724) and initial epsilon-Nd values (approx. -10 to greater than +50). Within this range, the shergottites fall into three discreet subgroups. These subgroups have distinct bulk rock REE patterns, mineral chemistries (i.e. phosphate REE patterns, Ni, Co, V in olivine), oxygen fugacity of crystallization, and stable isotopes, such as O. In contrast, nakhlites and chassignites have depleted epsilon-Nd values (greater than or equal to +15), have REE patterns that are light REE enriched, and appear to have crystallized near the FMQ buffer. The characteristics of these various martian basalts have been linked to different reservoirs in the martian crust and mantle, and their interactions during the petrogenesis of these magmas. These observations pose interesting interpretive challenges to our understanding of the conditions of the martian mantle (e.g. oxygen fugacity) and the interaction of mantle derived magmas with the martian crust and surface. Martian meteorite NWA 8159 is a unique fine-grained augite basalt derived from a highly depleted mantle source as reflected in its initial epsilon-Nd value, contains a pronounced light REE depleted pattern, and crystallized presumably under very oxidizing conditions. Although considerably older than both shergottites and nahklites, it has been petrogenetically linked to both styles of martian magmatism. These unique characteristics of NWA 8159 may provide an additional perspective for deciphering the petrogenesis of martian basalts and the nature of the crust of Mars.

  9. Magnetic hyperthermia properties of nanoparticles inside lysosomes using kinetic Monte Carlo simulations: Influence of key parameters and dipolar interactions, and evidence for strong spatial variation of heating power

    NASA Astrophysics Data System (ADS)

    Tan, R. P.; Carrey, J.; Respaud, M.

    2014-12-01

    Understanding the influence of dipolar interactions in magnetic hyperthermia experiments is of crucial importance for fine optimization of nanoparticle (NP) heating power. In this study we use a kinetic Monte Carlo algorithm to calculate hysteresis loops that correctly account for both time and temperature. This algorithm is shown to correctly reproduce the high-frequency hysteresis loop of both superparamagnetic and ferromagnetic NPs without any ad hoc or artificial parameters. The algorithm is easily parallelizable with a good speed-up behavior, which considerably decreases the calculation time on several processors and enables the study of assemblies of several thousands of NPs. The specific absorption rate (SAR) of magnetic NPs dispersed inside spherical lysosomes is studied as a function of several key parameters: volume concentration, applied magnetic field, lysosome size, NP diameter, and anisotropy. The influence of these parameters is illustrated and comprehensively explained. In summary, magnetic interactions increase the coercive field, saturation field, and hysteresis area of major loops. However, for small amplitude magnetic fields such as those used in magnetic hyperthermia, the heating power as a function of concentration can increase, decrease, or display a bell shape, depending on the relationship between the applied magnetic field and the coercive/saturation fields of the NPs. The hysteresis area is found to be well correlated with the parallel or antiparallel nature of the dipolar field acting on each particle. The heating power of a given NP is strongly influenced by a local concentration involving approximately 20 neighbors. Because this local concentration strongly decreases upon approaching the surface, the heating power increases or decreases in the vicinity of the lysosome membrane. The amplitude of variation reaches more than one order of magnitude in certain conditions. This transition occurs on a thickness corresponding to approximately 1.3 times the mean distance between two neighbors. The amplitude and sign of this variation is explained. Finally, implications of these various findings are discussed in the framework of magnetic hyperthermia optimization. It is concluded that feedback on two specific points from biology experiments is required for further advancement of the optimization of magnetic NPs for magnetic hyperthermia. The present simulations will be an advantageous tool to optimize magnetic NPs heating power and interpret experimental results.

  10. A 3D interactive method for estimating body segmental parameters in animals: application to the turning and running performance of Tyrannosaurus rex.

    PubMed

    Hutchinson, John R; Ng-Thow-Hing, Victor; Anderson, Frank C

    2007-06-21

    We developed a method based on interactive B-spline solids for estimating and visualizing biomechanically important parameters for animal body segments. Although the method is most useful for assessing the importance of unknowns in extinct animals, such as body contours, muscle bulk, or inertial parameters, it is also useful for non-invasive measurement of segmental dimensions in extant animals. Points measured directly from bodies or skeletons are digitized and visualized on a computer, and then a B-spline solid is fitted to enclose these points, allowing quantification of segment dimensions. The method is computationally fast enough so that software implementations can interactively deform the shape of body segments (by warping the solid) or adjust the shape quantitatively (e.g., expanding the solid boundary by some percentage or a specific distance beyond measured skeletal coordinates). As the shape changes, the resulting changes in segment mass, center of mass (CM), and moments of inertia can be recomputed immediately. Volumes of reduced or increased density can be embedded to represent lungs, bones, or other structures within the body. The method was validated by reconstructing an ostrich body from a fleshed and defleshed carcass and comparing the estimated dimensions to empirically measured values from the original carcass. We then used the method to calculate the segmental masses, centers of mass, and moments of inertia for an adult Tyrannosaurus rex, with measurements taken directly from a complete skeleton. We compare these results to other estimates, using the model to compute the sensitivities of unknown parameter values based upon 30 different combinations of trunk, lung and air sac, and hindlimb dimensions. The conclusion that T. rex was not an exceptionally fast runner remains strongly supported by our models-the main area of ambiguity for estimating running ability seems to be estimating fascicle lengths, not body dimensions. Additionally, the craniad position of the CM in all of our models reinforces the notion that T. rex did not stand or move with extremely columnar, elephantine limbs. It required some flexion in the limbs to stand still, but how much flexion depends directly on where its CM is assumed to lie. Finally we used our model to test an unsolved problem in dinosaur biomechanics: how fast a huge biped like T. rex could turn. Depending on the assumptions, our whole body model integrated with a musculoskeletal model estimates that turning 45 degrees on one leg could be achieved slowly, in about 1-2s. PMID:17363001

  11. Aminoacyl-tRNA synthetase-interacting multifunctional protein 1 suppresses tumor growth in breast cancer-bearing mice by negatively regulating myeloid-derived suppressor cell functions.

    PubMed

    Hong, Hye-Jin; Lim, Hui Xuan; Song, Ju Han; Lee, Arim; Kim, Eugene; Cho, Daeho; Cohen, Edward P; Kim, Tae Sung

    2016-01-01

    Myeloid-derived suppressor cells (MDSCs) are one of the most important cell types that contribute to negative regulation of immune responses in the tumor microenvironment. Recently, aminoacyl-tRNA synthetase-interacting multifunctional protein 1 (AIMP1), a novel pleiotropic cytokine, was identified as an antitumor protein that inhibits angiogenesis and induces antitumor responses. However, the effect of AIMP1 on MDSCs in the tumor environment remains unclear. In the present study, we demonstrated that AIMP1 significantly inhibited tumor growth in 4T1 breast cancer-bearing mice and reduced MDSCs population of tumor sites and spleens of tumor-bearing mice. AIMP1 reduced expansion of MDSCs from bone marrow-derived cells in the tumor-conditioned media. AIMP1 also negatively regulated suppressive activities of MDSCs by inhibiting IL-6 and NO production, and Arg-1 expression. Furthermore, treatment of breast cancer-bearing mice with AIMP1 decreased the capacity of MDSCs to suppress T cell proliferation and Treg cell induction. Western blot and inhibition experiments showed that downregulation of MDSCs functions by AIMP1 may result from attenuated activation of STATs, Akt, and ERK. These findings indicate that AIMP1 plays an essential role in negative regulation of suppressive functions of MDSCs. Therefore, it has a significant potential as a therapeutic agent for cancer treatment. PMID:26613952

  12. A SnoRNA-derived piRNA interacts with human interleukin-4 pre-mRNA and induces its decay in nuclear exosomes

    PubMed Central

    Zhong, Fudi; Zhou, Nan; Wu, Kang; Guo, Yubiao; Tan, Weiping; Zhang, Hong; Zhang, Xue; Geng, Guannan; Pan, Ting; Luo, Haihua; Zhang, Yijun; Xu, Zhibin; Liu, Jun; Liu, Bingfeng; Gao, Wenchao; Liu, Chao; Ren, Liangliang; Li, Jun; Zhou, Jie; Zhang, Hui

    2015-01-01

    PIWI interacting RNAs (piRNAs) are highly expressed in germline cells and are involved in maintaining genome integrity by silencing transposons. These are also involved in DNA/histone methylation and gene expression regulation in somatic cells of invertebrates. The functions of piRNAs in somatic cells of vertebrates, however, remain elusive. We found that snoRNA-derived and C (C?)/D? (D)-box conserved piRNAs are abundant in human CD4 primary T-lymphocytes. piRNA (piR30840) significantly downregulated interleukin-4 (IL-4) via sequence complementarity binding to pre-mRNA intron, which subsequently inhibited the development of Th2 T-lymphocytes. Piwil4 and Ago4 are associated with this piRNA, and this complex further interacts with Trf4-Air2-Mtr4 Polyadenylation (TRAMP) complex, which leads to the decay of targeted pre-mRNA through nuclear exosomes. Taken together, we demonstrate a novel piRNA mechanism in regulating gene expression in highly differentiated somatic cells and a possible novel target for allergy therapeutics. PMID:26405199

  13. A 3D in vitro model of patient-derived prostate cancer xenograft for controlled interrogation of in vivo tumor-stromal interactions.

    PubMed

    Fong, Eliza L S; Wan, Xinhai; Yang, Jun; Morgado, Micaela; Mikos, Antonios G; Harrington, Daniel A; Navone, Nora M; Farach-Carson, Mary C

    2016-01-01

    Patient-derived xenograft (PDX) models better represent human cancer than traditional cell lines. However, the complex in vivo environment makes it challenging to employ PDX models to investigate tumor-stromal interactions, such as those that mediate prostate cancer (PCa) bone metastasis. Thus, we engineered a defined three-dimensional (3D) hydrogel system capable of supporting the co-culture of PCa PDX cells and osteoblastic cells to recapitulate the PCa-osteoblast unit within the bone metastatic microenvironment in vitro. Our 3D model not only maintained cell viability but also preserved the typical osteogenic phenotype of PCa PDX cells. Additionally, co-culture cellularity was maintained over that of either cell type cultured alone, suggesting that the PCa-osteoblast cross-talk supports PCa progression in bone, as is hypothesized to occur in patients with prostatic bone metastasis. Strikingly, osteoblastic cells co-cultured with PCa PDX tumoroids organized around the tumoroids, closely mimicking the architecture of PCa metastases in bone. Finally, tumor-stromal signaling mediated by the fibroblast growth factor axis tightly paralleled that in the in vivo counterpart. Together, these findings indicate that this 3D PCa PDX model recapitulates important pathological properties of PCa bone metastasis, and validate the use of this model for controlled and systematic interrogation of complex in vivo tumor-stromal interactions. PMID:26599623

  14. Elucidating the guest-host interactions and complex formation of praziquantel and cyclodextrin derivatives by (13)C and (15)N solid-state NMR spectroscopy.

    PubMed

    Arrúa, Eva C; Ferreira, M João G; Salomon, Claudio J; Nunes, Teresa G

    2015-12-30

    Praziquantel is the drug of choice to treat several parasitic infections including the neglected tropical disease schistosomiasis. Due to its low aqueous solubility, cyclodextrins have been tested as potential host candidates to prepare praziquantel inclusion complexes with improved solubility. For the first time, the interactions of praziquantel with ?-cyclodextrin and ?-cyclodextrin derivatives (methyl-?-cyclodextrin and hydroxypropyl-?-cyclodextrin) were investigated using high resolution solid-state NMR spectroscopy. The results of this work confirmed that solid-state NMR experiments provided structural characterization, demonstrating the formation of inclusion complexes most probably with PZQ adopting an anti conformation, also the most likely in amorphous raw PZQ. Further information on the interaction of praziquantel with methyl-?-cyclodextrin was obtained from proton rotating-frame relaxation time measurements, sensitive to kilohertz-regime motions but modulated by spin-diffusion. Evidences were presented in all cases for praziquantel complexation through the aromatic ring. In addition, 1:2 drug:carrier molar ratio appears to be the most probable and therefore suitable stoichiometry to improve pharmaceutical formulations of this antischistosomal drug. PMID:26602291

  15. A?1-25-Derived Sphingolipid-Domain Tracer Peptide SBD Interacts with Membrane Ganglioside Clusters via a Coil-Helix-Coil Motif.

    PubMed

    Wang, Yaofeng; Kraut, Rachel; Mu, Yuguang

    2015-01-01

    The Amyloid-? (A?)-derived, sphingolipid binding domain (SBD) peptide is a fluorescently tagged probe used to trace the diffusion behavior of sphingolipid-containing microdomains in cell membranes through binding to a constellation of glycosphingolipids, sphingomyelin, and cholesterol. However, the molecular details of the binding mechanism between SBD and plasma membrane domains remain unclear. Here, to investigate how the peptide recognizes the lipid surface at an atomically detailed level, SBD peptides in the environment of raft-like bilayers were examined in micro-seconds-long molecular dynamics simulations. We found that SBD adopted a coil-helix-coil structural motif, which binds to multiple GT1b gangliosides via salt bridges and CH-? interactions. Our simulation results demonstrate that the CH-? and electrostatic forces between SBD monomers and GT1b gangliosides clusters are the main driving forces in the binding process. The presence of the fluorescent dye and linker molecules do not change the binding mechanism of SBD probes with gangliosides, which involves the helix-turn-helix structural motif that was suggested to constitute a glycolipid binding domain common to some sphingolipid interacting proteins, including HIV gp120, prion, and A?. PMID:26540054

  16. A?1-25-Derived Sphingolipid-Domain Tracer Peptide SBD Interacts with Membrane Ganglioside Clusters via a Coil-Helix-Coil Motif

    PubMed Central

    Wang, Yaofeng; Kraut, Rachel; Mu, Yuguang

    2015-01-01

    The Amyloid-? (A?)-derived, sphingolipid binding domain (SBD) peptide is a fluorescently tagged probe used to trace the diffusion behavior of sphingolipid-containing microdomains in cell membranes through binding to a constellation of glycosphingolipids, sphingomyelin, and cholesterol. However, the molecular details of the binding mechanism between SBD and plasma membrane domains remain unclear. Here, to investigate how the peptide recognizes the lipid surface at an atomically detailed level, SBD peptides in the environment of raft-like bilayers were examined in micro-seconds-long molecular dynamics simulations. We found that SBD adopted a coil-helix-coil structural motif, which binds to multiple GT1b gangliosides via salt bridges and CH–? interactions. Our simulation results demonstrate that the CH–? and electrostatic forces between SBD monomers and GT1b gangliosides clusters are the main driving forces in the binding process. The presence of the fluorescent dye and linker molecules do not change the binding mechanism of SBD probes with gangliosides, which involves the helix-turn-helix structural motif that was suggested to constitute a glycolipid binding domain common to some sphingolipid interacting proteins, including HIV gp120, prion, and A?. PMID:26540054

  17. A SnoRNA-derived piRNA interacts with human interleukin-4 pre-mRNA and induces its decay in nuclear exosomes.

    PubMed

    Zhong, Fudi; Zhou, Nan; Wu, Kang; Guo, Yubiao; Tan, Weiping; Zhang, Hong; Zhang, Xue; Geng, Guannan; Pan, Ting; Luo, Haihua; Zhang, Yijun; Xu, Zhibin; Liu, Jun; Liu, Bingfeng; Gao, Wenchao; Liu, Chao; Ren, Liangliang; Li, Jun; Zhou, Jie; Zhang, Hui

    2015-12-01

    PIWI interacting RNAs (piRNAs) are highly expressed in germline cells and are involved in maintaining genome integrity by silencing transposons. These are also involved in DNA/histone methylation and gene expression regulation in somatic cells of invertebrates. The functions of piRNAs in somatic cells of vertebrates, however, remain elusive. We found that snoRNA-derived and C (C')/D' (D)-box conserved piRNAs are abundant in human CD4 primary T-lymphocytes. piRNA (piR30840) significantly downregulated interleukin-4 (IL-4) via sequence complementarity binding to pre-mRNA intron, which subsequently inhibited the development of Th2 T-lymphocytes. Piwil4 and Ago4 are associated with this piRNA, and this complex further interacts with Trf4-Air2-Mtr4 Polyadenylation (TRAMP) complex, which leads to the decay of targeted pre-mRNA through nuclear exosomes. Taken together, we demonstrate a novel piRNA mechanism in regulating gene expression in highly differentiated somatic cells and a possible novel target for allergy therapeutics. PMID:26405199

  18. Brain-derived neurotrophic factor-estrogen interactions in the hippocampal mossy fiber pathway: implications for normal brain function and disease.

    PubMed

    Harte-Hargrove, L C; Maclusky, N J; Scharfman, H E

    2013-06-01

    The neurotrophin brain-derived neurotrophic factor (BDNF) and the steroid hormone estrogen exhibit potent effects on hippocampal neurons during development and in adulthood. BDNF and estrogen have also been implicated in the etiology of diverse types of neurological disorders or psychiatric illnesses, or have been discussed as potentially important in treatment. Although both are typically studied independently, it has been suggested that BDNF mediates several of the effects of estrogen in the hippocampus, and that these interactions play a role in the normal brain as well as disease. Here we focus on the mossy fiber (MF) pathway of the hippocampus, a critical pathway in normal hippocampal function, and a prime example of a location where numerous studies support an interaction between BDNF and estrogen in the rodent brain. We first review the temporal and spatially regulated expression of BDNF and estrogen in the MFs, as well as their receptors. Then we consider the results of studies that suggest that 17?-estradiol alters hippocampal function by its influence on BDNF expression in the MF pathway. We also address the hypothesis that estrogen influences the hippocampus by mechanisms related not only to the mature form of BDNF, acting at trkB receptors, but also by regulating the precursor, proBDNF, acting at p75NTR. We suggest that the interactions between BDNF and 17?-estradiol in the MFs are potentially important in the normal function of the hippocampus, and have implications for sex differences in functions that depend on the MFs and in diseases where MF plasticity has been suggested to play an important role, Alzheimer's disease, epilepsy and addiction. PMID:23276673

  19. Metal cation dependence of interactions with amino acids: bond dissociation energies of Rb(+) and Cs(+) to the acidic amino acids and their amide derivatives.

    PubMed

    Armentrout, P B; Yang, Bo; Rodgers, M T

    2014-04-24

    Metal cation-amino acid interactions are key components controlling the secondary structure and biological function of proteins, enzymes, and macromolecular complexes comprising these species. Determination of pairwise interactions of alkali metal cations with amino acids provides a thermodynamic vocabulary that begins to quantify these fundamental processes. In the present work, we expand a systematic study of such interactions by examining rubidium and cesium cations binding with the acidic amino acids (AA), aspartic acid (Asp) and glutamic acid (Glu), and their amide derivatives, asparagine (Asn) and glutamine (Gln). These eight complexes are formed using electrospray ionization and their bond dissociation energies (BDEs) are determined experimentally using threshold collision-induced dissociation with xenon in a guided ion beam tandem mass spectrometer. Analyses of the energy-dependent cross sections include consideration of unimolecular decay rates, internal energy of the reactant ions, and multiple ion-neutral collisions. Quantum chemical calculations are conducted at the B3LYP, MP2(full), and M06 levels of theory using def2-TZVPPD basis sets, with results showing reasonable agreement with experiment. At 0 and 298 K, most levels of theory predict that the ground-state conformers for M(+)(Asp) and M(+)(Asn) involve tridentate binding of the metal cation to the backbone carbonyl, amino, and side-chain carbonyl groups, although tridentate binding to the carboxylic acid group and side-chain carbonyl is competitive for M(+)(Asn). For the two longer side-chain amino acids, Glu and Gln, multiple structures are competitive. A comparison of these results to those for the smaller alkali cations, Na(+) and K(+), provides insight into the trends in binding energies associated with the molecular polarizability and dipole moment of the side chain. For all four metal cations, the BDEs are inversely correlated with the size of the metal cation and follow the order Asp < Glu < Asn < Gln. PMID:24528155

  20. Kinetics of Peridotite and Pyroxenite-derived Melts Interaction: Implications for the Style and Extent of Melt-rock Reaction in the Mantle

    NASA Astrophysics Data System (ADS)

    Lo Cascio, M.; Liang, Y.

    2006-12-01

    Distinct geochemical and petrologic features of ocean floor basalts and mantle peridotites suggest that the upper mantle is lithologically heterogeneous, consisting predominantly of peridotite and a small amount of eclogite [1]. An important issue of this marble cake mantle, is the nature of the peridotite and pyroxenite interface during mantle melting. It has been suggested that during mantle melting eclogite and peridotite develop a reactive boundary layer composed of a second generation eclogite and a layer of orthopyroxenite [2]. The existence of such a boundary layer has also been used to explain the observation that oceanic basalts are extracted with only limited interaction with the surrounding peridotite [3]. In spite of recent progresses, the kinetics of peridotite and pyroxenite-derived melts reaction is still not well understood. It is likely that there are two regimes of peridotite-pyroxenite melt interaction: a high T/low P regime where both the peridotite and pyroxenite are partially molten; and a low T/high P regime where only pyroxenite is partially molten. In this study we explored the kinetics of such interactions in both regimes by conducting lherzolite dissolution experiments using a pyroxenite-derived melt at 1300°C and 1-2 GPa. Dissolution couples were formed by juxtaposing pre-synthesized rods of a basaltic andesite (54.6% SiO2, Mg# 0.42), whose composition is similar to pyroxenite derived liquid at 1300°C and 2 GPa [1,4], and a lherzolite (ol+opx+cpx) in a Pt and graphite lined Mo capsule. The lherzolite solidus is below 1300°C at 1 GPa [5], but above 1300°C at 2 GPa. Lherzolite hardly dissolves (~35 ?m in 6 hours) into the melt at 2 GPa and a thin opx layer (<10 ?m thick) decorated with a few garnet crystals is observed at the lherzolite-melt interface. From the concentration profiles of Al2O3 and MgO in the melt, we estimated the effective binary diffusion coefficient at 10^{-12}m2/s. Assuming an average mantle upwelling rate of ~50 mm/yr and peridotite solidus located ~50 km above that of the pyroxenite [5], it can be shown that partially molten pyroxenite veins that are less than 1 m wide are likely to be homogenized with the surrounding mantle before reaching the lherzolite solidus. Therefore, only pyroxenite veins on the order of a 1 m or more will remain isolate from the surrounding. When the solidus of lherzolite is crossed, a reactive boundary layer made of pyroxene and/or olivine develops and the style of peridotite-pyroxenite interaction changes from dissolution and assimilation to porous flow dominated melt-rock reaction. The latter can potentially spread the pyroxenite signature to a much large volume. Result of this study will have important implications for the size and distribution of heterogeneities in the mantle. [1] Petermann and Hirschmann, 2003, J. Pet., 44, doi: 10.1093/petrology/egg074; [2] Yaxley and Green, 1998, Schweiz. Mineral. Petrogr. Mitt., 78; [3] Hauri and Kurz, 1997, EPSL, 153; [4] Takahashi and Nakajima, 2002, Geoph. Mon. 128; [5] Morgan and Liang, 2005, CMP, 150, doi: 10.1007/s00410-005-0033-8; [6] Petermann and Hirschmann, 2003, JGR., 108, doi: 10.1029/2000JB000118.

  1. Estradiol, testosterone, dehydroepiandrosterone and androstenedione: novel derivatives and enantiomers. Interactions with rat liver microsomal cytochrome P450 and antioxidant/radical scavenger activities in vitro.

    PubMed

    Klinger, W; Lupp, A; Karge, E; Baumbach, H; Eichhorn, F; Feix, A; Füldner, F; Gernhardt, S; Knels, L; Kost, B; Mertens, G; Werner, F; Oettel, M; Römer, W; Schwarz, S; Elger, W; Schneider, B

    2002-03-10

    Interactions of 27 steroids, among them 17 derivatives such as ethers, sulfates and amidosulfonates derived from 17 beta- and 17 alpha-estradiol, from testosterone and alpha- and beta-dihydrotesosterone and from dehydroepiandrosterone with rat liver microsomal cytochromes P450 (P450) were investigated in vitro by assessing binding to P450 and effects on P450 mediated monooxygenase functions as measured by different model reactions: ethoxyresorufin O-deethylation (EROD), ethoxycoumarin O-deethylation (ECOD) and ethylmorphine N-demethylation (EMND). With the exception of 17 alpha-estradiol-3-dimethylamidosulfonate, estrone, its -3-methylether and -3-amidosulfonate and testosterone, all other steroids displayed type I or reverse type I binding to P450. All steroids inhibited EROD activity in micromolar concentrations. An additional strong inhibition of ECOD and EMND activities was only demonstrated for the androgens and progestins. Estriol, estrone and mestranol displayed less inhibitory actions on the model reactions than estradiol. No major differences in comparison to the parent compounds were noted with the other derivatives. The only exceptions were 17 beta-(8,9-dehydro-14 alpha,15 alpha-methylene)estradiol, which displayed stronger effects than estradiol, and dehydroepiandrosterone-3-sulfate, which was less effective than dehydroepiandrosterone. Possible antioxidant properties of the steroids were examined by the stimulated lipid peroxidation (LPO), H2O2 production, and lucigenin (LC) and luminol (LM) amplified chemiluminescence (CL) using rat liver microsomes. Additionally, the influence on rat whole blood chemiluminescence (WB-CL) was assessed. All the estrogens, but not their methylethers and amidosulfonates inhibited LPO in micromolar concentrations. The effects on the other oxidase model reactions or on WB-CL were less distinct. Only ethinylestradiol and 17 beta-(8,9-dehydro-14 alpha,15 alpha-methylene)estradiol displayed a strong inhibitory action on all model reactions. With the exception of dehydroepiandrosterone-3-sulfate, which in general had only weak effects, the androgen and progestin derivatives, in contrast, strongly decreased H2O2 formation and LM- and LC-CL, but were mostly ineffective on LPO and WB-CL. PMID:11869824

  2. Effect of self-interaction on the phase diagram of a Gibbs-like measure derived by a reversible Probabilistic Cellular Automata

    NASA Astrophysics Data System (ADS)

    Cirillo, Emilio N. M.; Louis, Pierre-Yves; Ruszel, Wioletta M.; Spitoni, Cristian

    2014-07-01

    Cellular Automata are discrete-time dynamical systems on a spatially extended discrete space which provide paradigmatic examples of nonlinear phenomena. Their stochastic generalizations, i.e., Probabilistic Cellular Automata (PCA), are discrete time Markov chains on lattice with finite single-cell states whose distinguishing feature is the \\emph{parallel} character of the updating rule. We study the ground states of the Hamiltonian and the low-temperature phase diagram of the related Gibbs measure naturally associated with a class of reversible PCA, called the \\textit{cross PCA}. In such a model the updating rule of a cell depends indeed only on the status of the five cells forming a cross centered at the original cell itself. In particular, it depends on the value of the center spin (\\textit{self-interaction}). The goal of the paper is that of investigating the role played by the self-interaction parameter in connection with the ground states of the Hamiltonian and the low-temperature phase diagram of the Gibbs measure associated with this particular PCA.

  3. Small-x evolution of jet quenching parameter

    NASA Astrophysics Data System (ADS)

    Abir, Raktim

    2015-09-01

    Concept of transverse deflection probability of a parton that travels through strongly interacting medium, recently introduced by D'Eramo, Liu and Rajagopal, has been used to derive high energy evolution equation for the jet quenching parameter in stochastic multiple scatterings regime. Jet quenching parameter, q ˆ (x), appears to evolve with x, with an exponent 0.9?bars, which is slightly less than that of xG (x) where G (x) is the gluon distribution function.

  4. Polarizable Simulations with Second order Interaction Model – force field and software for fast polarizable calculations: Parameters for small model systems and free energy calculations

    PubMed Central

    Kaminski, George A.; Ponomarev, Sergei Y.; Liu, Aibing B.

    2009-01-01

    We are presenting POSSIM (POlarizable Simulations with Second order Interaction Model) – a software package and a set of parameters designed for molecular simulations. The key feature of POSSIM is that the electrostatic polarization is taken into account using a previously introduced fast formalism. This permits cutting computational cost of using the explicit polarization by about an order of magnitude. In this article, parameters for water, methane, ethane, propane, butane, methanol and NMA are introduced. These molecules are viewed as model systems for protein simulations. We have achieved our goal of ca. 0.5 kcal/mol accuracy for gas-phase dimerization energies and no more than 2% deviations in liquid state heats of vaporization and densities. Moreover, free energies of hydration of the polarizable methane, ethane and methanol have been calculated using the statistical perturbation theory. These calculations are a model for calculating protein pKa shifts and ligand binding affinities. The free energies of hydration were found to be 2.12 kcal/mol, 1.80 kcal/mol and ?4.95 kcal/mol for methane, ethane and methanol, respectively. The experimentally determined literature values are 1.91 kcal/mol, 1.83 kcal/mol and ?5.11 kcal/mol. The POSSIM average error in these absolute free energies of hydration is only about 0.13 kcal/mol. Using the statistical perturbation theory with polarizable force fields is not widespread, and we believe that this work opens road to further development of the POSSIM force field and its applications for obtaining accurate energies in protein-related computer modeling. PMID:20209038

  5. Genetic parameters and genotype-environment interactions for skeleton deformities and growth traits at different ages on gilthead seabream (Sparus aurata L.) in four Spanish regions.

    PubMed

    Lee-Montero, I; Navarro, A; Negrín-Báez, D; Zamorano, M J; Borrell Pichs, Yaisel Juan; Berbel, C; Sánchez, J A; García-Celdran, M; Manchado, M; Estévez, A; Armero, E; Afonso, J M

    2015-04-01

    One of the most important problems of fish aquaculture is the high incidence of fish deformities, which are mainly skeletal. In this study, genetic parameters on gilthead seabream (Sparus aurata L.) for skeleton deformities at different ages (179, 269, 389, 539 and 689 days) and their correlations with growth traits were estimated, as were as their genotype × environment interactions (G × E) at harvesting age. A total of 4093 offspring from the mass spawning of three industrial broodstocks belonging to the PROGENSA(®) breeding programme were mixed and on-grown by different production systems in four Spanish regions: Canary Islands (tanks and cage), Andalusia (estuary), Catalonia (cage) and Murcia (cage). Parental assignment was inferred using the standardized SMsa1 microsatellite multiplex PCR. From three broodstocks, 139 breeders contributed to the spawn and a total of 297 full-sibling families (52 paternal and 53 maternal half-sibling families) were represented. Heritabilities at different ages were medium for growth traits (0.16-0.48) and vertebral deformities (0.16-0.41), and low for any type of deformity (0.07-0.26), head deformities (0.00-0.05) and lack of operculum (0.06-0.11). The genetic correlations between growth and deformity traits were medium and positive, suggesting that to avoid increasing deformities they should be taken into account in breeding programmes when growth is selected. The G × E interactions among the different facilities were weak for length and deformity and strong for growth rate during this period. These results highlight the potential for the gilthead seabream industry to reduce the prevalence of deformities by genetic improvement tools. PMID:25662001

  6. Interaction Effects of Light, Temperature and Nutrient Limitations (N, P and Si) on Growth, Stoichiometry and Photosynthetic Parameters of the Cold-Water Diatom Chaetoceros wighamii

    PubMed Central

    Spilling, Kristian; Ylöstalo, Pasi; Simis, Stefan; Seppälä, Jukka

    2015-01-01

    Light (20-450 ?mol photons m-2 s-1), temperature (3-11°C) and inorganic nutrient composition (nutrient replete and N, P and Si limitation) were manipulated to study their combined influence on growth, stoichiometry (C:N:P:Chl a) and primary production of the cold water diatom Chaetoceros wighamii. During exponential growth, the maximum growth rate (~0.8 d-1) was observed at high temperture and light; at 3°C the growth rate was ~30% lower under similar light conditions. The interaction effect of light and temperature were clearly visible from growth and cellular stoichiometry. The average C:N:P molar ratio was 80:13:1 during exponential growth, but the range, due to different light acclimation, was widest at the lowest temperature, reaching very low C:P (~50) and N:P ratios (~8) at low light and temperature. The C:Chl a ratio had also a wider range at the lowest temperature during exponential growth, ranging 16-48 (weight ratio) at 3°C compared with 17-33 at 11°C. During exponential growth, there was no clear trend in the Chl a normalized, initial slope (?*) of the photosynthesis-irradiance (PE) curve, but the maximum photosynthetic production (Pm) was highest for cultures acclimated to the highest light and temperature. During the stationary growth phase, the stoichiometric relationship depended on the limiting nutrient, but with generally increasing C:N:P ratio. The average photosynthetic quotient (PQ) during exponential growth was 1.26 but decreased to <1 under nutrient and light limitation, probably due to photorespiration. The results clearly demonstrate that there are interaction effects between light, temperature and nutrient limitation, and the data suggests greater variability of key parameters at low temperature. Understanding these dynamics will be important for improving models of aquatic primary production and biogeochemical cycles in a warming climate. PMID:25993327

  7. Interaction between cytokine gene polymorphisms and the effect of physical exercise on clinical and inflammatory parameters in older women: study protocol for a randomized controlled trial

    PubMed Central

    2012-01-01

    Background Aging is associated with chronic low-grade inflammatory activity with an elevation of cytokine levels. An association between regular physical activity and reduction of blood levels of anti-inflammatory cytokines is demonstrated in the literature pointing to an anti-inflammatory effect related to exercise. However, there is no consensus regarding which type of exercise and which parameters are the most appropriate to influence inflammatory markers. Evidence indicates that the single nucleotide polymorphism (SNP) can influence the synthesis of those cytokines affecting their production. Methods/Design The design of this study is a randomized controlled trial. The aim of this study is to investigate the interaction between the cytokine genes SNP and the effect of physical activity on older women. The main outcomes are: serum levels of sTNFR-1, sTNFR-2, interleukin (IL)-6, IL-10, measured by the ELISA method; genotyping of tumor necrosis factor- (TNF)-alpha (rs1800629), IL6 (rs1800795), IL10 (rs1800896) by the TaqMan Method (Applied Biosystems, Foster City, CA, USA); and physical performance assessed by Timed Up and Go and 10-Meter Walk Tests. Secondary outcomes include: Geriatric Depression Scale, Perceived Stress Scaleand aerobic capacity, assessed by the six-minute walk; and lower limb muscle strength, using an isokinetic dinamometer (Biodex Medical Systems, Inc., Shirley, NY,USA). Both exercise protocols will be performed three times a week for 10?weeks, 30 sessions in total. Discussion Investigating the interaction between genetic factors and exercise effects of both protocols of exercise on the levels of inflammatory cytokine levels can contribute to guide clinical practice related to treatment and prevention of functional changes due to chronic inflammatory activity in older adults. This approach could develop new perspectives on preventive and treatment proposals in physical therapy and in the management of the older patient. Trial registration (ReBEC) RBR9v9cwf PMID:22873651

  8. Interactions between the Etoposide Derivative F14512 and Human Type II Topoisomerases: Implications for the C4 Spermine Moiety in Promoting Enzyme-mediated DNA Cleavage†

    PubMed Central

    Gentry, Amanda C.; Pitts, Steven L.; Jablonsky, Michael J.; Bailly, Christian; Graves, David E.; Osheroff, Neil

    2011-01-01

    F14512 is a novel etoposide derivative that contains a spermine in place of the C4 glycosidic moiety. The drug was designed to exploit the polyamine transport system that is upregulated in some cancers. However, a preliminary study suggests that it is also a more efficacious topoisomerase II poison than etoposide [Barret et al. (2008) Cancer Res 68, 9845–9853]. Therefore, we undertook a more complete study of the actions of F14512 against human type II topoisomerases. As determined by saturation transfer difference [1H]-NMR spectroscopy, contacts between F14512 and human topoisomerase II? in the binary enzyme-drug complex are similar to those of etoposide. Although the spermine of F14512 does not interact with the enzyme, it converts the drug to a DNA binder [Barret et al. (2008)]. Consequently, the influence of the C4 spermine on drug activity was assessed. F14512 is a highly active topoisomerase II poison and stimulates DNA cleavage mediated by human topoisomerase II? or topoisomerase II?. The drug is more potent and efficacious than etoposide or TOP-53, an etoposide derivative that contains a C4 aminoalkyl group that strengthens drug-enzyme binding. Unlike the other drugs, F14512 maintains robust activity in the absence of ATP. The enhanced activity of F14512 correlates with a tighter binding and an increased stability of the ternary topoisomerase II-drug- DNA complex. The spermine-drug core linkage is critical for these attributes. These findings demonstrate the utility of a C4 DNA binding group and provide a rational basis for the development of novel and more active etoposide-based topoisomerase II poisons. PMID:21413765

  9. Dynamic determination of kinetic parameters for the interaction between polypeptide hormones and cell-surface receptors in the perfused rat liver by the multiple-indicator dilution method

    SciTech Connect

    Sato, H.; Sugiyama, Y.; Sawada, Y.; Iga, T.; Sakamoto, S.; Fuwa, T.; Hanano, M. )

    1988-11-01

    Hepatic elimination of epidermal growth factor (EGF) via receptor-mediated endocytosis was studied by a multiple-indicator dilution method in the isolated perfused rat liver, in which cell polarity and spatial organization are maintained. In this method EGF was given with inulin, an extracellular reference, as a bolus into the portal vein, and dilution curves of both compounds in the hepatic vein effluent were analyzed. Analysis of the dilution curve for EGF, compared with that for somatostatin, which showed no specific binding to isolated liver plasma membranes, resulted as follows: (i) both extraction ratio and distribution volume of {sup 125}I-labeled EGF decreased as the injected amount of unlabeled EGF increased; (ii) the ratio plot of the dilution curve for EGF exhibited an upward straight line initially for a short period of time, whereas the ratio plot of somatostatin gradually decreased. The multiple-indicator dilution method was used for other peptides also. Insulin and glucagon, known to have hepatocyte receptors, behaved similarly to EGF in shape of their ratio plots. The kinetic parameters calculated by this analysis were comparable with reported values obtained by in vitro direct binding measurements at equilibrium using liver homogenates. They conclude that the multiple-indicator dilution method is a good tool for analyzing the dynamics of peptide hormones-cell-surface receptor interaction under a condition in which spatial architecture of the liver is maintained.

  10. On the use of the proximity force approximation for deriving limits to short-range gravitational-like interactions from sphere-plane Casimir force experiments

    SciTech Connect

    Dalvit, Diego A. R.; Onofrio, Roberto

    2009-09-15

    We discuss the role of the proximity force approximation in deriving limits to the existence of Yukawian forces--predicted in the submillimeter range by many unification models--from Casimir force experiments using the sphere-plane geometry. Two forms of this approximation are discussed, the first used in most analyses of the residuals from the Casimir force experiments performed so far, and the second recently discussed in this context in R. Decca et al.[Phys. Rev. D 79, 124021 (2009)]. We show that the former form of the proximity force approximation overestimates the expected Yukawa force and that the relative deviation from the exact Yukawa force is of the same order of magnitude, in the realistic experimental settings, as the relative deviation expected between the exact Casimir force and the Casimir force evaluated in the proximity force approximation. This implies both a systematic shift making the actual limits to the Yukawa force weaker than claimed so far, and a degree of uncertainty in the {alpha}-{lambda} plane related to the handling of the various approximations used in the theory for both the Casimir and the Yukawa forces. We further argue that the recently discussed form for the proximity force approximation is equivalent, for a geometry made of a generic object interacting with an infinite planar slab, to the usual exact integration of any additive two-body interaction, without any need to invoke approximation schemes. If the planar slab is of finite size, an additional source of systematic error arises due to the breaking of the planar translational invariance of the system, and we finally discuss to what extent this may affect limits obtained on power-law and Yukawa forces.

  11. Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

    SciTech Connect

    Reif, Maria M.; Huenenberger, Philippe H.

    2011-04-14

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Huenenberger, J. Chem. Phys. 124, 224501 (2006); M. M. Reif and P. H. Huenenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li{sup +}, Na{sup +}, K{sup +}, Rb{sup +}, Cs{sup +}) and halide (F{sup -}, Cl{sup -}, Br{sup -}, I{sup -}) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998); Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, {Delta}G{sub hyd} {sup O-minus} [H{sup +}]=-1100, -1075 or -1050 kJ mol{sup -1}, resulting in three sets L, M, and H for the SPC water model and three sets L{sub E}, M{sub E}, and H{sub E} for the SPC/E water model (alternative sets can easily be interpolated to intermediate {Delta}G{sub hyd} {sup O-minus} [H{sup +}] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is also evaluated and found to be very limited. Ultimately, it is expected that comparison with other experimental ionic properties (e.g., derivative single-ion solvation properties, as well as data concerning ionic crystals, melts, solutions at finite concentrations, or nonaqueous solutions) will permit to validate one specific set and thus, the associated {Delta}G{sub hyd} {sup O-minus} [H{sup +}] value (atomistic consistency assumption). Preliminary results (first-peak positions in the ion-water radial distribution functions, partial molar volumes of ionic salts in water, and structural properties of ionic crystals) support a value of {Delta}G{sub hyd} {sup O-minus} [H{sup +}] close to -1100 kJ{center_dot}mol{sup -1}.

  12. Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

    SciTech Connect

    Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der

    2014-12-14

    Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.

  13. Synthesis, antiviral activity, 3D-QSAR, and interaction mechanisms study of novel malonate derivatives containing quinazolin-4(3H)-one moiety.

    PubMed

    Chen, Meihang; Li, Pei; Hu, Deyu; Zeng, Song; Li, Tianxian; Jin, Linhong; Xue, Wei; Song, Baoan

    2016-01-01

    A series of novel malonate derivatives containing quinazolin-4(3H)-one moiety were synthesized and evaluated for their antiviral activities against cucumber mosaic virus (CMV). Results indicated that the title compounds exhibited good antiviral activities. Notably, compounds g15, g16, g17, and g18 exhibited excellent curative activities in vivo against CMV, with 50% effective concentration (EC50) values of 208.36, 153.78, 181.47, and 164.72?g/mL, respectively, which were better than that of Ningnanmycin (256.35?g/mL) and Ribavirin (523.34?g/mL). Moreover, statistically valid three-dimensional quantitative structure-activity relationship (3D-QSAR) models with good correlation and predictive power were obtained with comparative molecular field analysis (CoMFA) steric and electrostatic fields (r(2)=0.990, q(2)=0.577) and comparative molecular similarity indices analysis (CoMSIA) with combined steric, electrostatic, hydrophobic and hydrogen bond acceptor fields (r(2)=0.977, q(2)=0.516), respectively. Based on those models, compound g25 was designed, synthesized, and showed better curative activity (146.30?g/mL) than that of compound g16. The interaction of between cucumber mosaic virus coat protein (CMV CP) and g25 with 1:1.83 ratio is typically spontaneous and exothermic with micromole binding affinity by isothermal titration calorimetry (ITC) and fluorescence spectroscopy investigation. PMID:26598463

  14. TATA box-dependent protein-DNA interactions are detected on heat shock and histone gene promoters in nuclear extracts derived from Drosophila melanogaster embryos

    SciTech Connect

    Gilmour, D.S.; Dietz, T.J.; Elgin, S.C.R.

    1988-08-01

    The authors monitored protein-DNA interactions that occur on the hsp26, hsp70, histone H3, and histone H4 promoters in nuclear extracts derived from frozen Drosophila melanogaster embryos. All four of these promoters were found to be transcribed in vitro at comparable levels by extracts from both heat-shocked and non-heat-shocked embryos. Factors were detected in both types of extracts that block exonuclease digestion from a downstream site at ca. +35 and -20 base pairs from the start of transcription of all four of these promoters. In addition, factors in extracts from heat-shocked embryos blocked exonuclease digestion at sites flanking the heat shock consensus sequences of hsp26 and hsp70. Competition experiments indicated that common factors cause the +35 and -20 barriers on all four promoters in both extracts. The formation of the barriers at +35 and -20 required a TATA box but did not appear to require specific sequences downstream of +7. The authors suggest that the factors responsible for the +35 and -20 barriers are components whose association with the promoter precedes transcriptional activation.

  15. Nuclear Matter Bulk Parameter Scales and Correlations

    NASA Astrophysics Data System (ADS)

    Santos, B. M.; Dutra, M.; Lourenço, O.; Delfino, A.

    2015-12-01

    We study the arising of correlations among some isovector bulk parameters in nonrelativistic and relativistic hadronic mean-field models. For the former, we investigate correlations in the nonrelativistic (NR) limit of relativistic point-coupling models. We provide analytical correlations, for the NR limit model, between the symmetry energy and its derivatives, namely, the symmetry energy slope, curvature, skewness and fourth order derivative, discussing the conditions in which they are linear ones. We also show that some correlations presented in the NR limit model are reproduced for relativistic models presenting cubic and quartic self-interactions in its scalar field. As a direct application of such linear correlations, we remark its association with possible crossing points in the density dependence of the linearly correlated bulk parameter.

  16. Characterization of coal- and petroleum-derived binder pitches and the interaction of pitch/coke mixtures in pre-baked carbon anodes

    NASA Astrophysics Data System (ADS)

    Suriyapraphadilok, Uthaiporn

    Carbon anodes are manufactured from calcined petroleum coke (i.e. sponge coke) and recycled anode butts as fillers, and coal tar pitch (SCTP) as the binder. During the manufacturing of carbon anodes, coal tar pitch is mixed with calcined petroleum coke. The mix of binder, filler and some additives is heated to about 50°C above the softening point of the pitch, typically 160°C. This temperature is sufficient to enable the pitch to wet the coke particles. The mix is then either extruded, vibrated, or pressed to form a green anode. The binding between coke and pitch is very important to the anode properties. There are different binder pitches used in this work, which were standard coal tar pitch (SCTP-2), petroleum pitch (PP-1), gasification pitch (GP-115), coal-extract pitch (WVU-5), and co-coking pitches (HTCCP and OXCCP). Petroleum pitch is a residue produced from heat-treatment and distillation of petroleum fractions. Production of coal-extract pitch involves a prehydrogenation of coal followed by extraction using a dipolar solvent. Gasification pitches are distilled by-product tars produced from the coal gasification process. Co-coking pitch was developed in this work and was obtained from the liquid distillate of co-coking process of coal and heavy petroleum residue. Understanding of composition and structures of pitches from different sources and processes would lead to greater understanding of the binding properties of pitch in carbon anodes and was one of the main focuses in this study. Characterization of pitches by using different techniques including gas chromatography/mass spectrometry (GC/MS), high performance liquid chromatography (HPLC), matrix-assisted laser desorption ionization/mass spectrometry (MALDI/MS), 1H and 13C solution-state nuclear magnetic resonance (NMR), and 13C solid-state NMR yield important chemistry and structural information. The binding, or in other words the interactions in the pitch/coke mixture, is another interest in this study. Pitch itself is a very complex material. Studying the binding between pitch and the porous coke even adds another level of complexity to this subject. The high-temperature 1H NMR has been shown to be a promising technique to study the molecular interaction between different materials. The fraction of the mobile protons in the sample and their mobility as measured by the spin-spin relaxation time ( T*2 ), which is inversely proportional to the peak width at half maximum height (DeltaH1/2), seem to have a potential to probe the extent of the interaction between pitch and coke. Understanding of the interaction between coke and some simple compounds which are commonly found in pitch, i.e. model compounds, should help identify the binding efficiency between pitch and coke. The knowledge of (1) pitch chemistry and structure, (2) interaction between model compounds and filler cokes would lead to an understanding of the binding efficiency between pitch and coke. The mass distribution by MALDI analysis showed that the majority of the compounds in these pitches is in the range of 200-700 Da. The hexane-soluble (HS) fractions of all of the pitch samples in this study mainly consist of four-ring polycyclic aromatic compounds (PACs) as observed by GC/MS and Pyrolysis-GC/MS techniques. Coal-derived pitches contained mainly cata- and peri-condensed PACs and a few alkyl- and heteroatomic-substituted PACs, whereas those peteroleum-derived pitches consisted of a number of alkyl-substituted PACs with high sulfur substitution. Solid-state NMR results show that SCTP-2 and PP-1 contain six and five fused rings on average, respectively, whereas GP-115 and WVU-5 contain two and three fused rings on average, respectively. The latter two pitches contained mostly methyl substituents with a few ethyls. WVU-5 contains a higher degree of naphthenic substituents as compared to other pitches as confirmed by the GC/MS analysis. HTCCP and OXCCP contained three peri-condensed fused rings on average per molecule. 1H in-situ high temperature NMR and the solid echo pulse program were employed t

  17. Tumor cell and connective tissue cell interactions in human colorectal adenocarcinoma. Transfer of platelet-derived growth factor-AB/BB to stromal cells.

    PubMed Central

    Sundberg, C.; Branting, M.; Gerdin, B.; Rubin, K.

    1997-01-01

    Mechanisms underlying stimulation of platelet-derived growth factor (PDGF) beta-receptors expressed on connective tissue cells in human colorectal adenocarcinoma were investigated in this study. PDGF-AB/BB, but not PDGF receptors, was expressed by tumor cells in situ, as well as in tumor cell isolates of low passage from human colorectal adenocarcinoma. In an experimental co-culture system, conditioned medium from tumor cells only marginally activated PDGF beta-receptors expressed on fibroblasts. In contrast, co-culturing of the two cell types led to a marked PDGF beta-receptor activation. Functional PDGF-AB/BB was found to be associated with heparinase-I-sensitive components on the tumor cell surface. PDGF-AB/BB, isolated from heparinase-I-sensitive cell surface components, induced a marked activation of PDGF beta-receptors. Furthermore, co-culturing tumor cells together with fibroblasts led to a sustained activation of PDGF beta-receptors expressed on fibroblasts. Double immunofluorescence staining of tissue sections from human colorectal adenocarcinoma, combined with computer-aided image analysis, revealed that nonproliferating tumor cells were the predominant cellular source of PDGF-AB/BB in the tumor stroma. In addition, PDGF-AB/BB-expressing tumor cells were found juxtapositioned to microvascular cells expressing activated PDGF beta-receptors. Confocal microscopy revealed a cytoplasmic and cell-membrane-associated expression of PDGF-AB/BB in tumor cells situated in the stroma. In contrast, epithelial cells situated in normal or tumorous acinar structures revealed only a cell-membrane-associated PDGF-AB/BB expression. The is vitro and in situ results demonstrate that tumor cells not only facilitate but also have the ability to modulate connective tissue cell responsiveness to PDGF-AB/BB in a paracrine fashion, through direct cell-cell interactions in human colorectal adenocarcinoma. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 PMID:9250160

  18. Specific interaction between the bovine papillomavirus E5 transforming protein and the beta receptor for platelet-derived growth factor in stably transformed and acutely transfected cells.

    PubMed Central

    Petti, L; DiMaio, D

    1994-01-01

    The E5 protein of bovine papillomavirus is a 44-amino-acid membrane protein which induces morphologic and tumorigenic transformation of fibroblasts. We previously showed that the E5 protein activates and forms a complex with the endogenous beta receptor for platelet-derived growth factor (PDGF) in transformed rodent fibroblasts and that the PDGF beta receptor can mediate tumorigenic transformation by the E5 protein in a heterologous cell system. Other workers have identified the receptor for epidermal growth factor (EGF) as a potential target of the E5 protein in NIH 3T3 cells. Here, we investigate the specificity of the interaction of the E5 protein with various growth factor receptors, with particular emphasis on the PDGF beta receptor and the EGF receptor. Under conditions where both the PDGF beta receptor and the EGF receptor are stably expressed in E5-transformed mouse and bovine fibroblasts and in E5-transformed epithelial cells, the E5 protein specifically forms a complex with and activates the PDGF receptor and not the EGF receptor. Under conditions of transient overexpression in COS cells, the E5 protein has the potential to associate with several growth factor receptors, including the EGF receptor. However, upon coexpression of PDGF beta receptors and EGF receptors in COS cells, the E5 protein preferentially forms a complex with the PDGF receptor. Therefore, we conclude that the PDGF beta receptor is the primary target for the E5 protein in a variety of cell types, including bovine fibroblasts. Images PMID:8189497

  19. Interactive Effects of Climate Change and Decomposer Communities on the Stabilization of Wood-Derived Carbon Pools: Catalyst for a New Study

    SciTech Connect

    Resh, Sigrid C.

    2014-11-17

    Globally, forest soils store ~two-thirds as much carbon (C) as the atmosphere. Although wood makes up the majority of forest biomass, the importance of wood contributions to soil C pools is unknown. Even with recent advances in the mechanistic understanding of soil processes, integrative studies tracing C input pathways and biological fluxes within and from soils are lacking. Therefore, our research objectives were to assess the impact of different fungal decay pathways (i.e., white-rot versus brown-rot)—in interaction with wood quality, soil temperature, wood location (i.e., soil surface and buried in mineral soil), and soil texture—on the transformation of woody material into soil CO2 efflux, dissolved organic carbon (DOC), and soil C pools. The use of 13C-depleted woody biomass harvested from the Rhinelander, WI free-air carbon dioxide enrichment (Aspen-FACE) experiment affords the unique opportunity to distinguish the wood-derived C from other soil C fluxes and pools. We established 168 treatment plots across six field sites (three sand and three loam textured soil). Treatment plots consisted of full-factorial design with the following treatments: 1. Wood chips from elevated CO2, elevated CO2 + O3, or ambient atmosphere AspenFACE treatments; 2. Inoculated with white rot (Bjerkandera adusta) or brown rot (Gloeophyllum sepiarium) pure fungal cultures, or the original suite of endemic microbial community on the logs; and 3. Buried (15cm in soil as a proxy for coarse roots) or surface applied wood chips. We also created a warming treatment using open-topped, passive warming chambers on a subset of the above treatments. Control plots with no added wood (“no chip control”) were incorporated into the research design. Soils were sampled for initial ?13C values, CN concentrations, and bulk density. A subset of plots were instrumented with lysimeters for sampling soil water and temperature data loggers for measuring soil temperatures. To determine the early pathways of decomposition, we measured soil surface CO2 efflux, dissolved organic C (DOC), and DO13C approximately monthly over two growing seasons from a subsample of the research plots. To determine the portion of soil surface CO2 efflux attributable to wood-derived C, we used Keeling plot techniques to estimate the associated ?13C values of the soil CO2 efflux. We measured the ?13CO2 once during the peak of each growing season. Initial values for soil ?13C values and CN concentrations averaged across the six sites were -26.8‰ (standard error = 0.04), 2.46% (se = 0.11), and 0.15% (se = 0.01), respectively. The labeled wood chips from the Aspen FACE treatments had an average ?13C value of -39.5‰ (se 0.10). The >12 ‰ isotopic difference between the soil and wood chip ?13C values provides the basis for tracking the wood-derived C through the early stages of decomposition and subsequent storage in the soil. Across our six research sites, average soil surface CO2 efflux ranged from 1.04 to 2.00 g CO2 m-2 h-1 for the first two growing seasons. No wood chip controls had an average soil surface CO2 efflux of 0.67 g CO2 m-2 h-1 or about half of that of the wood chip treatment plots. Wood-derived CO2 efflux was higher for loam textured soils relative to sands (0.70 and 0.54 g CO2 m-2 h-1, respectively; p = 0.045)), for surface relative to buried wood chip treatments (0.92 and 0.39 g CO2 m-2 h-1, respectively; p < 0.001), for warmed relative to ambient temperature treatments (0.99 and 0.78 g CO2 m-2 h-1, respectively; 0.004), and for natural rot relative to brown and white rots (0.93, 0.82, and 0.78 g CO2 m-2 h-1, respectively; p = 0.068). Our first two growing seasons of soil surface CO2 efflux data show that wood chip location (i.e., surface vs. buried chip application) is very important, with surface chips loosing twice the wood-derived CO2. The DOC data support this trend for greater loss of ecosystem C from surface chips. This has strong implications for the importance of root and buried wood for ecosystem C retention. This strong chip location effect

  20. Interaction of the N-(3-Methylpyridin-2-yl)amide Derivatives of Flurbiprofen and Ibuprofen with FAAH: Enantiomeric Selectivity and Binding Mode

    PubMed Central

    Deplano, Alessandro; Smaldone, Giovanni; Pedone, Emilia; Luque, F. Javier; Svensson, Mona; Novellino, Ettore; Congiu, Cenzo; Onnis, Valentina; Catalanotti, Bruno; Fowler, Christopher J.

    2015-01-01

    Background Combined fatty acid amide hydrolase (FAAH) and cyclooxygenase (COX) inhibition is a promising approach for pain-relief. The Flu-AM1 and Ibu-AM5 derivatives of flurbiprofen and ibuprofen retain similar COX-inhibitory properties and are more potent inhibitors of FAAH than the parent compounds. However, little is known as to the nature of their interaction with FAAH, or to the importance of their chirality. This has been explored here. Methodology/Principal Findings FAAH inhibitory activity was measured in rat brain homogenates and in lysates expressing either wild-type or FAAHT488A-mutated enzyme. Molecular modelling was undertaken using both docking and molecular dynamics. The (R)- and (S)-enantiomers of Flu-AM1 inhibited rat FAAH with similar potencies (IC50 values of 0.74 and 0.99 ?M, respectively), whereas the (S)-enantiomer of Ibu-AM5 (IC50 0.59 ?M) was more potent than the (R)-enantiomer (IC50 5.7 ?M). Multiple inhibition experiments indicated that both (R)-Flu-AM1 and (S)-Ibu-AM5 inhibited FAAH in a manner mutually exclusive to carprofen. Computational studies indicated that the binding site for the Flu-AM1 and Ibu-AM5 enantiomers was located between the acyl chain binding channel and the membrane access channel, in a site overlapping the carprofen binding site, and showed a binding mode in line with that proposed for carprofen and other non-covalent ligands. The potency of (R)-Flu-AM1 was lower towards lysates expressing FAAH mutated at the proposed carprofen binding area than in lysates expressing wild-type FAAH. Conclusions/Significance The study provides kinetic and structural evidence that the enantiomers of Flu-AM1 and Ibu-AM5 bind in the substrate channel of FAAH. This information will be useful in aiding the design of novel dual-action FAAH: COX inhibitors. PMID:26565710

  1. Normal and tumor-derived myoepithelial cells differ in their ability to interact with luminal breast epithelial cells for polarity and basement membrane deposition

    SciTech Connect

    Gudjonsson, Thorarinn; Ronnov-Jessen, Lone; Villadsen, Rene; Rank, Fritz; Bissell, Mina J.; Petersen, Ole William

    2001-10-04

    The signals that determine the correct polarity of breast epithelial structures in vivo are not understood. We have shown previously that luminal epithelial cells can be polarized when cultured within a reconstituted basement membrane gel. We reasoned that such cues in vivo may be given by myoepithelial cells. Accordingly, we used an assay where luminal epithelial cells are incorrectly polarized to test this hypothesis. We show that culturing human primary luminal epithelial cells within collagen-I gels leads to formation of structures with no lumina and with reverse polarity as judged by dual stainings for sialomucin, epithelial specific antigen or occludin. No basement membrane is deposited, and {beta}4-integrin staining is negative. Addition of purified human myoepithelial cells isolated from normal glands corrects the inverse polarity, and leads to formation of double-layered acini with central lumina. Among the laminins present in the human breast basement membrane (laminin-1, -5 and -10/11), laminin-1 was unique in its ability to substitute for myoepithelial cells in polarity reversal. Myoepithelial cells were purified also from four different breast cancer sources including a biphasic cell line. Three out of four samples either totally lacked the ability to interact with luminal epithelial cells, or conveyed only correction of polarity in a fraction of acini. This behavior was directly related to the ability of the tumor myoepithelial cells to produce {alpha}-1 chain of laminin. In vivo, breast carcinomas were either negative for laminin-1 (7/12 biopsies) or showed a focal, fragmented deposition of a less intensely stained basement membrane (5/12 biopsies). Dual staining with myoepithelial markers revealed that tumorassociated myoepithelial cells were either negative or weakly positive for expression of laminin-1, establishing a strong correlation between loss of laminin-1 and breast cancer. We conclude that the double-layered breast acinus may be recapitulated in culture and that one reason for the ability of myoepithelial cells to induce polarity is because they are the only source of laminin-1 in the breast in vivo. A further conclusion is that a majority of tumor-derived/-associated myoepithelial cells are deficient in their ability to impart polarity because they have lost their ability to synthesize sufficient or functional laminin-1. These results have important implications for the role of myoepithelial cells in maintenance of polarity in normal breast and how they may function as structural tumor suppressors.

  2. Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis

    PubMed Central

    2011-01-01

    Background There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis. Methodology/Principal Findings An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed - i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data - i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design - i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses. Conclusions/Significance Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research. PMID:21929759

  3. MeCP2 controls hippocampal brain-derived neurotrophic factor expression via homeostatic interactions with microRNA?132 in rats with depression.

    PubMed

    Su, Meilei; Hong, Jun; Zhao, Yongzhi; Liu, Shuai; Xue, Xiang

    2015-10-01

    Major depressive disorder (MDD) is a considerable public health concern, which affects patients worldwide. MDD is associated with psychosocial impairment, poor quality of life, and significant disability, morbidity and mortality. Stress is a major factor in depression, which impairs the structural and functional plasticity of the hippocampus. Previous studies have demonstrated that chronic unpredictable mild stress is able to downregulate the expression of brain?derived neurotrophic factor (BDNF) and methyl?CpG?binding protein 2 (MeCP2), and alter the expression levels of certain microRNAs (miR). The aim of the present study was to investigate the regulatory association between BDNF, MeCP2 and miR-132 in an animal model of chronic stress?induced depression. ELISA, western blot and qPCR were used to detect the expression levels of BDNF, MeCP2 and miR-132 in the peripheral blood samples of patients with MDD and in the hippocampi of depressed animals. In addition, a dual luciferase reporter gene system was used to determine whether miR-132 directly targets BDNF or MeCP2. The present study demonstrated that, as compared with normal subjects, miR?132 expression was increased in the peripheral blood samples of patients with MDD, whereas the expression of MeCP2 and BDNF was decreased; thus, the expression levels of MeCP2 and BDNF were negatively correlated with those of miR?132. In addition, in an animal model of chronic stress?induced depression, increased expression levels of miR?132, and decreased levels of MeCP2 and BDNF were detected in the hippocampi. Furthermore, knockdown of MeCP2 expression in primary hippocampal neurons increased the expression of miR?132 and decreased the expression levels of BDNF. The results of the present study demonstrated that miR?132 may directly target MeCP2, but not BDNF, and control its expression at the transcriptional and translational level. miR?132 was also shown to negatively regulate BDNF expression. The reduced expression levels of BDNF, as induced by MeCP2 knockdown, were enhanced by miR?132 mimics, and were rescued by miR?132 inhibitors. These results suggested that homeostatic interactions between MeCP2 and miR?132 may regulate hippocampal BDNF levels, which may have a role in the pathogenesis of MDD. PMID:26239616

  4. Density dependence of the MIT bag parameters from the field theory of hadrons

    E-print Network

    R. Aguirre; M. Schvellinger

    1997-03-25

    A self-consistent description of the MIT bag parameters as functions of the nuclear matter density is presented. The subnuclear degrees of freedom are treated in the Quark-Meson Coupling Model, considering the equilibrium conditions for the bag in the nuclear medium. The hadronic interaction is described in the framework of the quantum field theory of hadrons through several models. We have obtained the behavior of the bag radius and the bag parameters $B$ and $z_0$, taking their derivatives with respect to the mean field value of the scalar meson as free parameters. A discussion on the variation range of these derivatives is given.

  5. Ascaris suum-Derived Products Induce Human Neutrophil Activation via a G Protein-Coupled Receptor That Interacts with the Interleukin-8 Receptor Pathway 

    E-print Network

    Falcone, Franco; Rossi, Adriano G; Sharkey, Rose; Brown, Alan; Pritchard, David; Maizels, Rick

    2001-01-01

    Infection with tissue-migrating helminths is frequently associated with intense granulocyte infiltrations. Several host-derived factors are known to mediate granulocyte recruitment to the tissues, but less attention ...

  6. Analysis of the effect of design parameters and their interactions on the strength of dental restorations with endodontic posts, using finite element models and statistical analysis.

    PubMed

    González-Lluch, Carmen; Pérez-González, Antonio

    2016-03-01

    Many previous studies, both in vitro and with model simulations, have been conducted in an attempt to reach a full understanding of how the different design parameters of an endodontically restored tooth affect its mechanical strength. However, differences in the experimental set-up or modelling conditions and the limited number of parameters studied in each case prevent us from obtaining clear conclusions about the real significance of each parameter. In this work, a new approach is proposed for this purpose based on the combination of a validated three-dimensional parametric biomechanical model of the restored tooth and statistical analysis using full factorial analysis of variance. A two-step approach with two virtual tests (with, respectively, 128 and 81 finite element models) was used in the present work to study the effect of several design parameters on the strength of a restored incisor, using full factorial designs. Within the limitations of this study, and for cases where the parameters are within the ranges that were tested, the conclusions indicate that the material of the post is the most significant factor as far as its strength is concerned, the use of a low Young's modulus being preferable for this component. Once the post material has been chosen, the geometry of the post is of less importance than the Young's modulus selected for the core or, especially, for the crown. PMID:25922872

  7. The Hamiltonian three-parameter spaces of the q-state Potts model with three competing interactions on a Cayley tree

    NASA Astrophysics Data System (ADS)

    Uguz, Selman; Ganikhodjaev, Nasir; Dogan, Hasan

    2015-05-01

    In this paper, we study the phase diagrams for the integer q-state ( q ? 3) Potts model on a Cayley tree for order two with competing nearest-neighbor interactions J 1, prolonged next-nearestneighbor interactions J p and two-level triple-neighbor interactions J t . The exact phase diagrams of the Potts model with some competing interactions on a Cayley tree lattice of order two have been found. At vanishing temperature, the phase diagram is fully determined for all values and signs of J 1, J p and J t . Our aim is to generalize the results of Ganikhodjaev et al. to the q-state Potts model with competing nearest-neighbor, prolonged next-nearest-neighbor and two-level tripleneighbor interactions on a Cayley tree for order 2 and to compare these with previous results in the literature. Ganikhodjaev et al. reported on a new phase, denoted as a paramodulated (PM) phase, found at low temperatures and characterized by 2-periodic points of an one-dimensional dynamical system lying inside the modulated phase. An important note for such a phase is that inherently the Potts model has no analogues in the Ising setting. In this paper, we show that increasing the spin number from three ( q = 3) to arbitrary q > 3 can dramatically affect the resultant phases (expanding the paramodulated phase). We believe that the enlarging of the paramodulated (PM) phase is essentially connected to the symmetry in the spin numbers.

  8. Redefining solubility parameters: the partial solvation parameters.

    PubMed

    Panayiotou, Costas

    2012-03-21

    The present work reconsiders a classical and universally accepted concept of physical chemistry, the solubility parameter. Based on the insight derived from modern quantum chemical calculations, a new definition of solubility parameter is proposed, which overcomes some of the inherent restrictions of the original definition and expands its range of applications. The original single solubility parameter is replaced by four partial solvation parameters reflecting the dispersion, the polar, the acidic and the basic character of the chemical compounds as expressed either in their pure state or in mixtures. Simple rules are adopted for the definition and calculation of these four parameters and their values are tabulated for a variety of common substances. In contrast, however, to the well known Hansen solubility parameters, their design and evaluation does not rely exclusively on the basic rule of "similarity matching" for solubility but it makes also use of the other basic rule of compatibility, namely, the rule of "complementarity matching". This complementarity matching becomes particularly operational with the sound definition of the acidic and basic components of the solvation parameter based on the third ?-moments of the screening charge distributions of the quantum mechanics-based COSMO-RS theory. The new definitions are made in a simple and straightforward manner, thus, preserving the strength and appeal of solubility parameter stemming from its simplicity. The new predictive method has been applied to a variety of solubility data for systems of pharmaceuticals and polymers. The results from quantum mechanics calculations are critically compared with the results from Abraham's acid/base descriptors. PMID:22327537

  9. New tools derived from the solvatochromic 4-N,N-dimethylamino-1,8-naphthalimide fluorophore for the detection of biomolecular interactions

    E-print Network

    Loving, Galen

    2009-01-01

    The concept that complex cellular behavior is driven by an intricate network of biomolecular interactions, which emerged through billions of years of evolution, is one of the great wonders of nature. Living cells must ...

  10. Hexahalogenated and their mixed benzene derivatives as prototypes for the understanding of halogen···halogen intramolecular interactions: New insights from combined DFT, QTAIM-, and RDG-based NCI analyses.

    PubMed

    Varadwaj, Pradeep R; Varadwaj, Arpita; Jin, Bih-Yaw

    2015-12-01

    A large number of fully halogenated benzene derivatives containing the fluorine, chlorine, bromine, and iodine atoms have been experimentally synthesized both as single- and co-crystals (e.g., Desiraju et al., Chem. Eur. J. 2006, 12, 2222), yet the natures of the halogen ··· halogen interactions between the vicinal halogens in these compounds within the intramolecular domain are undisclosed. Given a fundamental understanding of these interactions is incredibly important in many areas of chemical, biological, supramolecular, and material sciences, we present here our newly discovered theoretical results that delineate whilst the nature of an F···F interaction in a pair of two adjacent fluorine atoms in either of the hexafluorobenzene and 1,4-dibromotetrafluorobenzene compounds examined is almost unclear, each of the latter three hexahalogenated benzene derivatives (viz., C6 Cl6 , C6 Br6 , and C6 I6 ), and each of the seven of their fully mixed hexahalogenated benzene analogues, are found to be stabilized by means of a number of halogen···halogen interactions, each a form of long-range attraction within the intramolecular domain. The Molecular Electrostatic Surface Potential model was found to be unsurprisingly unsuitable in unraveling any of the aforesaid attractions between the halogen atoms. However, such interactions successfully enunciated by a set of noncovalent interaction descriptors of geometrical, topological, and electrostatic origins. These latter properties were extracted combining the results of the Density Functional Theory electronic structure calculations with those revealed from Atoms in Molecules, and Reduced Density Gradient charge density-based topological calculations, and are expounded in detail to formalize the conclusions. © 2015 Wiley Periodicals, Inc. PMID:26505258

  11. Interaction between the magnetic and superconducting order parameters in a La1.94Sr0.06CuO4 wire studied via muon spin rotation

    E-print Network

    Keren, Amit

    studied via muon spin rotation Meni Shay, Amit Keren, Gad Koren, Amit Kanigel, Oren Shafir, and Lital-energy muon spin relaxation technique. The superconducting order parameter is characterized by transport. However, a local probe such as muon spin relaxation indicates that the magnetic volume fraction is 100

  12. First-order exchange coefficient coupling for simulating surface water-groundwater interactions: Parameter sensitivity and consistency with a physics-based approach

    USGS Publications Warehouse

    Ebel, B.A.; Mirus, B.B.; Heppner, C.S.; VanderKwaak, J.E.; Loague, K.

    2009-01-01

    Distributed hydrologic models capable of simulating fully-coupled surface water and groundwater flow are increasingly used to examine problems in the hydrologic sciences. Several techniques are currently available to couple the surface and subsurface; the two most frequently employed approaches are first-order exchange coefficients (a.k.a., the surface conductance method) and enforced continuity of pressure and flux at the surface-subsurface boundary condition. The effort reported here examines the parameter sensitivity of simulated hydrologic response for the first-order exchange coefficients at a well-characterized field site using the fully coupled Integrated Hydrology Model (InHM). This investigation demonstrates that the first-order exchange coefficients can be selected such that the simulated hydrologic response is insensitive to the parameter choice, while simulation time is considerably reduced. Alternatively, the ability to choose a first-order exchange coefficient that intentionally decouples the surface and subsurface facilitates concept-development simulations to examine real-world situations where the surface-subsurface exchange is impaired. While the parameters comprising the first-order exchange coefficient cannot be directly estimated or measured, the insensitivity of the simulated flow system to these parameters (when chosen appropriately) combined with the ability to mimic actual physical processes suggests that the first-order exchange coefficient approach can be consistent with a physics-based framework. Copyright ?? 2009 John Wiley & Sons, Ltd.

  13. The primal integrated realm and the derived interactive realm in relation to biosemiosis, and their link with the ideas of J.W. von Goethe

    PubMed Central

    Barlow, Peter W.

    2012-01-01

    Certain phenomena in Nature which might logically be regarded as indicating biosemiotic communication, with signal, receptor and interpretant, may, in fact, indicate no such thing. Instead, the respective phenomenological observations may point to an underlying system that JW von Goethe termed an "Urphänomen". From such Primal Phenomena emerge derived phenomena, or "Types", which are made substantial by processes that uniquely define Life and Living. Biosemiosis arises and takes place within the derived Types. Examples of Primal Phenomena and their derivatives are taken from recent observations on the putative influence of the lunisolar gravitational force upon animal and plant behavior, and from some aspects of plant development that show connection with Goethe’s idea of the ‘Urpflanze’. PMID:23181156

  14. Parameter estimating state reconstruction

    NASA Technical Reports Server (NTRS)

    George, E. B.

    1976-01-01

    Parameter estimation is considered for systems whose entire state cannot be measured. Linear observers are designed to recover the unmeasured states to a sufficient accuracy to permit the estimation process. There are three distinct dynamics that must be accommodated in the system design: the dynamics of the plant, the dynamics of the observer, and the system updating of the parameter estimation. The latter two are designed to minimize interaction of the involved systems. These techniques are extended to weakly nonlinear systems. The application to a simulation of a space shuttle POGO system test is of particular interest. A nonlinear simulation of the system is developed, observers designed, and the parameters estimated.

  15. Quasi-chemical theory of cosolvent hydrophobic preferential interactions.

    PubMed

    Priya, M Hamsa; Merchant, Safir; Asthagiri, Dilip; Paulaitis, Michael E

    2012-06-01

    Cosolvent hydrophobic preferential interactions with methane in aqueous methanol solutions are evaluated on the basis of the solute excess chemical potential derived from molecular simulations using the quasi-chemical (QC) theory generalization of the potential distribution theorem (PDT). We find that the methane-methanol preferential interaction parameter derived from QC theory quantitatively captures the favorable solvation of methane in methanol solutions in terms of important local solute-solvent (water and methanol) intermolecular interactions within a defined inner shell around the solute, and nonlocal solute interactions with solvent molecules outside this inner shell. Moreover, a unique inner shell can be defined such that the preferential interaction parameter is derived exclusively from the free energy of cavity formation in the aqueous cosolvent solution without the solute, where this cavity corresponds to the specified inner shell, and the mean interaction or binding energy of the solute with solvent molecules outside this inner shell. This inner-shell definition leads to a description of solute-cosolvent preferential interactions in which the molecular details of those interactions are derived from the effect of cosolvent on cavity statistics in the aqueous cosolvent solution alone. The finding suggests that solution thermodynamic behavior beyond steric exclusion (macromolecular crowding) contribute to the molecular mechanisms by which cosolvent preferential interactions influence protein stability and activity. PMID:22574766

  16. The interaction of climate observation, parameter estimation, and mitigation decisions: Modeling climate policy under uncertainty with a partially observable Markov decision process

    NASA Astrophysics Data System (ADS)

    Fertig, E.; Webster, M.

    2013-12-01

    Though climate sensitivity remains poorly constrained, the trajectory of future greenhouse gas emissions and observable climate data could lead to improved estimates. Updated parameter estimates could alter decisions on greenhouse mitigation policy, which in turn influences future observed climate data and parameter estimation. Previous research on global climate mitigation policy neglects the cyclic nature of climate observation, parameter estimation, and policy action, instead treating uncertainty in climate sensitivity with scenario analysis or assuming that it will be resolved completely at some point in the future. This paper advances quantitative analysis of decision making under uncertainty (DMUU) in climate sensitivity by modeling the observation/parameter estimation/policy action cycle as a partially observable Markov decision process (POMDP). In a POMDP framework, an objective function is maximized while both observable parameters and probability distributions over unobservable parameters are retained as system states. As time progresses and more data are collected, the probability distributions are updated with Bayesian analysis. To model anthropogenic climate change as a POMDP, we maximize social welfare using a modified DICE model. Climate sensitivity is never directly observable; instead it is modeled with a distribution that is subject to Bayesian updating after observation of stochastic changes in global mean temperature. The maximization problem is posed as a stochastic Bellman equation, which expresses total social welfare as the sum of immediate social welfare resulting from a current mitigation decision under current knowledge of climate sensitivity and the expected cost-to-go, which is the discounted future social welfare in the subsequent time interval as a function of both global mean temperature and the consequent probability distribution over climate sensitivity. While similar, smaller stochastic dynamic programming problems can be solved exactly through backward iteration, the size of the current problem makes this approach computationally prohibitive. We instead solve it using approximate dynamic programming (ADP), in which the cost-to-go function is approximated as an analytical function of the state variables. Results yield novel insight into the interdependence of anthropogenic climate perturbation and the state of knowledge of climate sensitivity, as well as the effect of potential knowledge accumulation on optimal climate mitigation policy. The model contains a stylized representation of the climate-economy system and results are not directly prescriptive for policy. The unique contribution of this paper is that it captures the interplay between observational data, knowledge acquisition, and climate perturbation in a multi-stage framework made tractable by ADP techniques, treating climate sensitivity closer to the way it manifests in reality: perpetually uncertain, but increasingly constrained by observational climate data.

  17. Structural Basis for a Novel Interaction between the NS1 Protein Derived from the 1918 Influenza Virus and RIG-I.

    PubMed

    Jureka, Alexander S; Kleinpeter, Alex B; Cornilescu, Gabriel; Cornilescu, Claudia C; Petit, Chad M

    2015-11-01

    The influenza non-structural protein 1 (NS1) plays a critical role in antagonizing the innate immune response to infection. One interaction that facilitates this function is between NS1 and RIG-I, one of the main sensors of influenza virus infection. While NS1 and RIG-I are known to interact, it is currently unclear whether this interaction is direct or if it is mediated by other biomolecules. Here we demonstrate a direct, strain-dependent interaction between the NS1 RNA binding domain (NS1(RBD)) of the influenza A/Brevig Mission/1918 H1N1 (1918(H1N1)) virus and the second caspase activation and recruitment domain of RIG-I. Solving the solution structure of the 1918(H1N1) NS1(RBD) revealed features in a functionally novel region that may facilitate the observed interaction. The biophysical and structural data herein suggest a possible mechanism by which strain-specific differences in NS1 modulate influenza virulence. PMID:26365801

  18. Highly electron-poor Buchwald-type ligand: application for Pd-catalysed direct arylation of thiophene derivatives and theoretical consideration of the secondary Pd(0)-arene interaction.

    PubMed

    Korenaga, Toshinobu; Sasaki, Ryo; Shimada, Kazuaki

    2015-11-10

    Highly electron-poor SPhos ligands bearing either 2,6-bis(trifluoromethyl)-4-pyridyl (BFPy) or 3,5-(CF3)2C6H3 groups were synthesised. The former ligand highly accelerated the Pd-catalysed direct arylation of 2-propylthiophene, 2-methylthiophene or benzo[b]thiophene with only 1 mol% of the catalyst. This high catalytic activity can be attributed to a combination of electronic properties and the secondary Pd-arene interaction of BFPySPhos. The secondary interactions of SPhos, PhSPhos and BFPySPhos were optimised at the oniom(mp2/lanl2dz?:?b3lyp/lanl2dz) level and were further evaluated using the NBO method by DFT at the M06-2X/6-31G(d) level with LanL2DZ + ECP. The deletion energy analysis showed that the transfer of electrons from Pd to aromatic ring is the dominating factor for the secondary Pd-arene interaction of SPhos-Pd(0) complexes. Although an electron-poor BFPySPhos does not particularly favour this type of interaction, this interaction is still substantial enough to sufficiently stabilise the BFPySPhos-Pd complex. PMID:26250605

  19. Dipole Interaction in Triplet Superconductivity with Horizontal Line Nodes: Orientation of the Superconducting Order Parameter in Sr2RuO4

    NASA Astrophysics Data System (ADS)

    Hasegawa, Yasumasa

    2003-10-01

    Dipole interaction in triplet superconductivity is studied. If Cooper pairs are formed by electrons at r and r+(±\\frac{a}{2},±\\frac{a}{2},±\\frac{c}{2}) in a body-centered tetragonal lattice (in this case line nodes run horizontally on a cylindrical Fermi surface), the dipole energy is low when the d-vector is perpendicular to the direction of the angular momentum of the Cooper pairs (l-vector). This result is in contrast with the dipole energies in the Anderson-Brinkman-Morel (ABM) state of superfluid 3He, where the d-vector is forced to be parallel or antiparallel to the l-vector by dipole interaction. The recent NQR experiment in Sr2RuO4 by Ishida et al. can be explained by this result.

  20. Synthesis, spectroscopic characterization and in vitro antimicrobial, anticancer and antileishmanial activities as well interaction with Salmon sperm DNA of newly synthesized carboxylic acid derivative, 4-(4-methoxy-2-nitrophenylamino)-4-oxobutanoic acid

    NASA Astrophysics Data System (ADS)

    Sirajuddin, Muhammad; Ali, Saqib; McKee, Vickie; Ullah, Hameed

    2015-03-01

    This paper stresses on the synthesis, characterization of novel carboxylic acid derivative and its application in pharmaceutics. Carboxylic acid derivatives have a growing importance in medicine, particularly in oncology. A novel carboxylic acid, 4-(4-methoxy-2-nitrophenylamino)-4-oxobutanoic acid, was synthesized and characterized by elemental analysis, FT-IR, NMR (1H, and 13C), mass spectrometry and single crystal X-ray structural analysis. The structure of the title compound, C11H12N2O6, shows the molecules dimerised by short intramolecular Osbnd H⋯O hydrogen bonds. The compound was screened for in vitro antimicrobial, anticancer, and antileishmanial activities as well as interaction with SS-DNA. The compound was also checked for in vitro anticancer activity against BHK-21, H-157 and HCEC cell lines, and showed significant anticancer activity. The compound was almost non-toxic towards human corneal epithelial cells (HCEC) and did not show more than 7.4% antiproliferative activity when used at the 2.0 ?g/mL end concentration. It was also tested for antileishmanial activity against the promastigote form of leishmania major and obtained attractive result. DNA interaction study exposes that the binding mode of the compound with SS-DNA is an intercalative as it results in hypochromism along with minor red shift. A new and efficient strategy to identify pharmacophores sites in carboxylic acid derivative for antibacterial/antifungal activity using Petra, Osiris and Molinspiration (POM) analyses was also carried out.

  1. Design, Synthesis, and Evaluation of Triazole Derivatives That Induce Nrf2 Dependent Gene Products and Inhibit the Keap1-Nrf2 Protein-Protein Interaction.

    PubMed

    Bertrand, Hélène C; Schaap, Marjolein; Baird, Liam; Georgakopoulos, Nikolaos D; Fowkes, Adrian; Thiollier, Clarisse; Kachi, Hiroko; Dinkova-Kostova, Albena T; Wells, Geoff

    2015-09-24

    The transcription factor Nrf2 regulates the expression of a large network of cytoprotective and metabolic enzymes and proteins. Compounds that directly and reversibly inhibit the interaction between Nrf2 and its main negative regulator Keap1 are potential pharmacological agents for a range of disease types including neurodegenerative conditions and cancer. We describe the development of a series of 1,4-diphenyl-1,2,3-triazole compounds that inhibit the Nrf2-Keap1 protein-protein interaction (PPI) in vitro and in live cells and up-regulate the expression of Nrf2-dependent gene products. PMID:26348784

  2. The recovery of microwave scattering parameters from scatterometric measurements with special application to the sea

    NASA Technical Reports Server (NTRS)

    Claassen, J. P.; Fung, A. K.

    1975-01-01

    As part of an effort to demonstrate the value of the microwave scatterometer as a remote sea wind sensor, the interaction between an arbitrarily polarized scatterometer antenna and a noncoherent distributive target was derived and applied to develop a measuring technique to recover all the scattering parameters. The results are helpful for specifying antenna polarization properties for accurate retrieval of the parameters not only for the sea but also for other distributive scenes.

  3. Stabilization of asphaltenes in aliphatic solvents using alkylbenzene-derived amphiphiles. 2. Study of the asphaltene-amphiphile interactions and structures using Fourier transform infrared spectroscopy and small-angle X-ray scattering techniques

    SciTech Connect

    Chang, C.L.; Fogler, H.S. )

    1994-06-01

    In the preceding paper in this issue, the influence of the chemical structure of a series of alkylbenzene-derived amphiphiles on the stabilization of asphaltenes was described. In this paper, we present the results of using Fourier transform infrared (FTIR) spectroscopy and small-angle X-ray scattering (SAXS) techniques to study the interaction between asphaltenes and two alkylbenzene-derived amphiphiles, p-alkylphenol and p-alkylbenzenesulfonic acid. FTIR spectroscopy was used to characterize and quantify the acid-base interactions between asphaltenes and amphiphiles. It was found that asphaltenes could hydrogen-bond to p-dodecylphenol amphiphiles. The hydrogen-bonding capacity of asphaltenes was estimated to be 1.6-2.0 mmol/g of asphaltene. On the other hand, the FTIR spectroscopic study indicated that asphaltenes had a complicated acid-base interaction with p-dodecylbenzenesulfonic acid (DBSA) amphiphiles with a stoichiometry of about 1.8 mmol of DBSA/g of asphaltene. The UV/vis spectroscopic study suggested that asphaltenes and DBSA could associate into large electronic conjugated complexes. Physical evidence of the association between asphaltenes and amphiphiles was obtained by SAXS measurements. 27 refs., 10 figs.

  4. Interactive state-parameter estimation of a crop carbon mass balance model through the assimilation of observed winter wheat carbon flux and stock data

    NASA Astrophysics Data System (ADS)

    Sus, O.; Williams, M. D.; Gruenwald, T.

    2010-12-01

    Next to the consideration of land management practises, modelling the carbon balance of croplands requires a crop carbon budget model that realistically simulates photosynthesis, ecosystem respiration, soil carbon dynamics, and phenology dependant on crop-specific parameters and carbon allocation patterns. A crop carbon mass balance model is a tool which can aid to answer questions related to cropland carbon sequestration potential, best-practise recommendations, seasonal patterns and amplitude of net carbon exchange (NEE), and prediction of biomass growth and crop yield. However, land management complicates modelling of cropland NEE by largely determining the onset and length of the growing season of agricultural areas. Human decision making on crop cultivars, sowing and harvest dates, and management practices is difficult to simulate, and corresponding reliable data for larger spatial and temporal scales is still sparse. Crop carbon budget models require a specific set of parameters, some of which are poorly understood and are thus of empirical rather than mechanistic nature. Here, we present a study that deals with the assimilation of observations of both carbon flux and stock data into a crop C budget model (SPAc). Our data assimilation procedure (the Ensemble Kalman Filter, EnKF) aims at updating both model states and parameters, so that we will gain insight into optimized parameter values and carbon stock/flux estimates within quantified confidence limits. We obtained measured data of NEE, LAI, and leaf, root, stem, and storage organ dry mass for a winter wheat season in 2005/2006 from the CarboEurope Fluxnet site at Klingenberg/Germany. We conducted several model experiments, for each of which we assimilated a unique combination of data sources. We find that the assimilation of NEE data leads to reduced model error (observed vs. modelled NEE) compared to a model run without data assimilation (a reduction of ~15-20% of RMSE). The assimilated dry mass data on the other hand increased model error (by ~1-5%, up to ~13% when root dry mass assimilated), but is helpful in constraining above- and belowground biomass. We further find that cumulative NEE at harvest is considerably underestimated after flux data assimilation (-198.1 observed, -212.7 no assimilation, -301.0 NEE assimilated). This underestimation can partly be compensated for when NEE and stock data are assimilated simultaneously. We find that assimilated NEE data is helpful in reducing overestimation of carbon assimilation in the early growing season. Moreover, the timing of crop senescence is clearly improved through NEE flux data assimilation. For the, statistically speaking, “best” model run (NEE only assimilated), we find an increase in the parameter leaf carbon per leaf area (resulting in the growth of thicker leaves as the crop matures), and a clear reduction of the fraction of autotrophic respiration through time (from initially 0.43 to 0.36 at maturity). The time evolution of phenological parameters leads to an extension (a reduction) of the length of the vegetative (reproductive) phase.

  5. Interaction of flavan-3-ol derivatives and different caseins is determined by more than proline content and number of proline repeats.

    PubMed

    Bohin, Maxime C; Vincken, Jean-Paul; Westphal, Adrie H; Tripp, Annelise M; Dekker, Peter; van der Hijden, Harry T W M; Gruppen, Harry

    2014-09-01

    Interactions of Type A and B flavan-3-ol dimers (procyanidins) and several monomeric flavan-3-ols, with ?-casein and ?-casein, were investigated. Binding affinities measured were related to the ligands structure, including several properties (e.g. intrinsic flexibility (number of rotatable bonds)