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1

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

2

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

NASA Astrophysics Data System (ADS)

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.

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

2014-09-01

3

Application of Statistically Derived CPAS Parachute Parameters  

NASA Technical Reports Server (NTRS)

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.

Romero, Leah M.; Ray, Eric S.

2013-01-01

4

Instantaneous phase and frequency derived without user-defined parameters  

NASA Astrophysics Data System (ADS)

We define an algorithm in the time domain for computing the unwrapped instantaneous phase and its derivative, the instantaneous frequency, using only derivatives and integrals. It does not require user-defined parameters, like most algorithms proposed so far. We validate and compare its performance with respect to open-source and commercial software by synthetic and real data examples.

Poggiagliolmi, E.; Vesnaver, A.

2014-12-01

5

Simultaneous Inference for Model Averaging of Derived Parameters.  

PubMed

Model averaging is a useful approach for capturing uncertainty due to model selection. Currently, this uncertainty is often quantified by means of approximations that do not easily extend to simultaneous inference. Moreover, in practice there is a need for both model averaging and simultaneous inference for derived parameters calculated in an after-fitting step. We propose a method for obtaining asymptotically correct standard errors for one or several model-averaged estimates of derived parameters and for obtaining simultaneous confidence intervals that asymptotically control the family-wise Type I error rate. The performance of the method in terms of coverage is evaluated using a simulation study and the applicability of the method is demonstrated by means of three concrete examples. PMID:24952957

Jensen, Signe M; Ritz, Christian

2014-06-20

6

Sinusoidal polynomial parameter estimation using the distribution derivative  

Microsoft Academic Search

In this paper, we present a method to estimate the parameters of a generalized sinusoidal model. A generalized sinusoid x is defined as a polynomial in the log domain, with complex coefficients alphai : x(t)=exp(Sigmai alphai t i), where i=0...Q. The method is based on the distribution derivative of the signal and operates in the transform domain. The method is

Michaël Betser

2009-01-01

7

Deriving sea-state parameters using RISAT-1 SAR data  

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

8

A study of photon interaction parameters in lung tissue substitutes  

PubMed Central

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

Manjunatha, H. C.

2014-01-01

9

Derivation of Delaware Bay tidal parameters from space shuttle photography  

SciTech Connect

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.

Zheng, Quanan; Yan, Xiaohai; Klemas, V. (Univ. of Delaware, Newark (United States))

1993-06-01

10

Derivation of Delaware Bay tidal parameters from Space Shuttle photography  

NASA Technical Reports Server (NTRS)

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, we calculate the tidal influx of the Delaware Bay, which is 2.76 x 10 exp 9 cu m. 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.

Zheng, Quanan; Yan, Xiao-Hai; Klemas, Vic

1993-01-01

11

Statefinder Parameters for Interacting Phantom Energy with Dark Matter  

E-print Network

We apply in this paper the statefinder parameters to the interacting phantom energy with dark matter. There are two kinds of scaling solutions in this model. It is found that the evolving trajectories of these two scaling solutions in the statefinder parameter plane are quite different, and that are also different from the statefinder diagnostic of other dark energy models.

Baorong Chang; Hongya Liu; Lixin Xu; Chengwu Zhang; Yongli Ping

2006-12-21

12

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

NASA Technical Reports Server (NTRS)

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

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

1992-01-01

13

The QCD Coupling Parameter Derived from the Uncertainty Principle and a Model for Quark Vacuum Fluctuations  

E-print Network

The magnitude of the strong interaction is characterized by $\\alpha_s$, the coupling parameter in Quantum Chromodynamics (QCD), a parameter with an unexplained value in the Standard Model. In this paper, a candidate explanation for $\\alpha_s$ is derived from (1) the lifetime of quark-antiquark pairs in vacuum fluctuations given by the Uncertainty Principle, (2) the variation of $\\alpha_s$ as a function of energy in QCD, and (3) classical relativistic dynamics of the quarks and antiquarks. A semiclassical model for heavy quark-antiquark vacuum fluctuations is described herein, based on (2) and (3). The model in this paper predicts the measured value of $\\alpha_s(M_{Z^0})$ to be 0.121, which is in agreement with recent measurements within statistical uncertainties.

David Batchelor

2010-07-30

14

Quality assessment parameters for EST-derived SNPs from catfish  

Technology Transfer Automated Retrieval System (TEKTRAN)

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

15

AC conductivity parameters of graphene derived from THz etalon transmittance.  

PubMed

THz frequency-domain transmittance measurements were carried out on chemical-vapor-deposited (CVD) graphene films transferred to high-resistivity silicon substrates, and packaged as back-gated graphene field effect transistors (G-FETs). The graphene AC conductivity ?(?), both real and imaginary parts, is determined between 0.2 and 1.2 THz from the transmittance using the transmission matrix method and curve-fitting techniques. Critical parameters such as the charge-impurity scattering width and chemical potential are calculated. It is found that not only the sheet charge density but also the scattering parameter can be modified by the back-gate voltage. PMID:25307168

Zhang, Weidong; Pham, Phi H Q; Brown, Elliott R; Burke, Peter J

2014-11-21

16

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

NASA Technical Reports Server (NTRS)

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.

Lurie, Boris J. (inventor)

1994-01-01

17

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

Microsoft Academic Search

A study is presented focusing on the potential value of parameters derived from radiosonde data or data from numerical atmospheric models for the forecasting of severe weather associated with convective storms. Parameters have been derived from soundings in the proximity of large hail, tornadoes (including tornadoes over water: waterspouts) and thunderstorms in the Netherlands. 66,365 radiosonde soundings from six stations

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

2007-01-01

18

Source parameters derived from seismic spectrum in the Jalisco block  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

19

Interactions of Arsenic and the Dissolved Substances Derived from  

E-print Network

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) contamination of local shallow groundwater from the application of MSMA. The distinction between "free

Florida, University of

20

Interactions between specific parameters of cannabis use and verbal memory.  

PubMed

Recently, the impact of different parameters of cannabis use, including the age of first use, the average frequency of use, the cumulative lifetime dose, the average dose per occasion, and the duration of regular use upon cognitive functions has been discussed. However, to date no study has systematically investigated the interactions of these parameters with regard to cognitive performance. To determine whether these interactions exist, 142 healthy young adult cannabis users participated in a neuropsychological assessment study with a German version of the Rey Auditory Verbal Learning Test (RAVLT). In line with previous studies on cannabis use and verbal memory, significant associations between certain components of verbal memory and frequency of use, cumulative lifetime dose and duration of regular use respectively were found. Remarkably, a multivariate analysis solely revealed a significant main effect of the duration of cannabis use with regard to immediate recall and recall after interference. Moreover, the findings suggest that age of first use, duration of use and frequency of cannabis use interact with regard to their impact on different measures of verbal memory. The findings of the present study provide first evidence that particular parameters of cannabis use interact with regard to their impact on cognitive functions in unintoxicated cannabis users. This finding might deliver more insight into the complex mechanisms underlying the impaired memory functions observed in cannabis users. PMID:20398718

Wagner, Daniel; Becker, Benjamin; Gouzoulis-Mayfrank, Euphrosyne; Daumann, Jörg

2010-08-16

21

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

22

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

E-print Network

Information Systems (GIS) and statistical analyses. We derived new glacier outlines from the 2003 SPOT imagesDecadal 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

23

Synthesis, characterization and DNA interaction studies of new triptycene derivatives  

PubMed Central

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

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

2014-01-01

24

Deriving forest canopy fuel parameters for loblolly pine forests in eastern Texas  

E-print Network

Deriving forest canopy fuel parameters for loblolly pine forests in eastern Texas Muge Agca, Sorin forest canopy fuel parameters including canopy bulk density and canopy base height for loblolly pines, the calculated average canopy bulk density values, across all 50 plots, were 0.18 and 0.07 kg/m3

25

Power Saving Optimization for Linear Collider Interaction Region Parameters  

SciTech Connect

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.

Seryi, Andrei; /SLAC

2009-10-30

26

Deriving physical parameters of unresolved star clusters. III. Application to M 31 PHAT clusters  

NASA Astrophysics Data System (ADS)

Context. This study is the third of a series that investigates the degeneracy and stochasticity problems present in the determination of physical parameters such as age, mass, extinction, and metallicity of partially resolved or unresolved star cluster populations situated in external galaxies when using broad-band photometry. Aims: This work tests the derivation of parameters of artificial star clusters using models with fixed and free metallicity for the WFC3+ACS photometric system. Then the method is applied to derive parameters of a sample of 203 star clusters in the Andromeda galaxy observed with the HST. Methods: Following Papers I and II, the star cluster parameters are derived using a large grid of stochastic models that are compared to the observed cluster broad-band integrated WFC3+ACS magnitudes. Results: We derive the age, mass, and extinction of the sample of M 31 star clusters with one fixed metallicity in agreement with previous studies. Using artificial tests we demonstrate the ability of the WFC3+ACS photometric system to derive the metallicity of star clusters. We show that the metallicity derived using photometry of 36 massive M 31 star clusters is in a good agreement with the metallicity previously derived using spectroscopy taken from literature.

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

2015-02-01

27

Two-dimensional acoustic pattern derived strain parameters closely correlate with one-dimensional tissue Doppler derived strain measurements  

Microsoft Academic Search

Background: Two-dimensional strain echocardiography (2D-SE) calcu- lates tissue velocities via frame-to-frame tracking of unique acoustic markers within the image and provides strain parameters in two dimensions. Novel 2D-SE software allows semi-automated strain measurements and increased averaging capabilities optimizing signalenoise ratio. Aim: We tested whether 2D-SE and the currently used and well-validated tissue Doppler derived strain echocardiography (TD-SE) yield similar information

Karen M. Modesto; Sanderson Cauduro; Angela Dispenzieri; Bijoy Khandheria; Marek Belohlavek; Peter Lysyansky; Zvi Friedman; Morie Gertz; Theodore P. Abraham

2006-01-01

28

Detecting RNA-RNA interactions using psoralen derivatives.  

PubMed

Psoralens are tricyclic compounds that intercalate into double-stranded DNA or RNA and, on irradiation with long-wavelength (365-nm) UV light, covalently link pyrimidines on adjacent strands. More rarely, psoralen cross-links can be observed at the ends of helices (i.e., double-stranded-single-stranded boundaries). Although psoralens can, in some instances, cross-link protein to RNA, their primary application is to detect RNA-RNA base-pairing interactions. The most useful psoralen derivative is 4'-aminomethyl trioxsalen (AMT), which is soluble in H2O. This protocol describes the use of AMT to detect RNA-RNA interactions in tissue culture cells or in extracts. Cross-linked RNAs are detectable by their reduced mobility in polyacrylamide gels. Cross-links can be reversed by exposure to short-wavelength (254 nm) UV light. PMID:25183819

Nilsen, Timothy W

2014-09-01

29

Ultlra-intense laser-matter interactions at extreme parameters  

SciTech Connect

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.

Hegellich, Bjorn M [Los Alamos National Laboratory

2010-11-24

30

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

NASA Astrophysics Data System (ADS)

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

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

31

Derivative-free optimization for parameter estimation in computational nuclear physics  

E-print Network

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.

Stefan M. Wild; Jason Sarich; Nicolas Schunck

2014-09-17

32

Developmental functions for saccadic eye movement parameters derived from pro- and antisaccade tasks  

Microsoft Academic Search

.   The few studies on the development of oculomotor functions conducted so far suggest strong developmental effects of age on\\u000a different parameters of saccade control in childhood and adolescence. The present study aimed at determining developmental\\u000a functions for a set of 22 parameters derivable from the examination of pro- and antisaccades elicited under the 200-ms gap\\u000a and overlap conditions (100

Christoph Klein

2001-01-01

33

Evaluation of energetic particle parameters in the near-Earth magnetotail derived from ux asymmetry observations  

E-print Network

Evaluation of energetic particle parameters in the near-Earth magnetotail derived from ¯ux-tail current of energetic ions, their pressure gradient and average drift velocity, as well as a ®eld intensity á GEOS 2 á Energetic particles 1 Introduction Quantitative measurements of particle and magnetic

Paris-Sud XI, Université de

34

Spectroscopic and in silico evaluation of interaction of DNA with six anthraquinone derivatives.  

PubMed

Anthraquinones consist of several hundreds of derivatives that differ in the nature and positions of substituent groups which are known to have several biological activities including antitumor properties. Interaction of molecules with DNA persists to be an extremely vital parameter while endeavouring to formulate therapeutics. In this study, few anthraquinone derivatives such as 1,2-dihydroxyanthraquinone (alizarin), 1,4-dihydroxyanthraquinone (quinizarin), 1,8-dihydroxyanthraquinone (danthron), 1,2,4-trihydroxyanthraquinone (purpurin), 1,4-diaminoanthraquinone, and 1-methylaminoanthraquinone were analyzed for its possible interaction with calf-thymus DNA through spectroscopy and in silico analysis. Our UV spectroscopic results indicate that all selected anthraquinones interact with DNA probably by external binding. Molar extinction coefficient has been calculated for chosen six anthraquinones. FT-IR results suggest that significant shifts of peaks as well as disappearance of certain characteristic peaks were indicators of the plausible interaction going on due to dye-DNA adduct formation. Among the six dyes used, purpurin showed better results and indicates the relatively strong binding affinity with DNA. Our molecular modeling results also show that purpurin has comparatively higher DNA interaction with a score of -6.18 compared with the ethidium bromide of -5.02 and intercalate the DNA. PMID:23645388

Ghosh, Pritha; Devi, G Poornima; Priya, R; Amrita, A; Sivaramakrishna, A; Babu, S; Siva, R

2013-07-01

35

Derivatives  

NSDL National Science Digital Library

Murray Bourne developed the Interactive Mathematics site while working as a mathematics lecturer at Ngee Ann Polytechnic in Singapore. The site contains numerous mathematics tutorials and resources for students and teachers alike. This specific page is focused on differentiation, or finding derivatives. Bourne walks users through an introduction to differentiation and limits, and then moves on to more specific applications like rate of change, derivatives of polynomials, and differentiating powers of a function. Each topic includes graphs and interactive materials designed to aid users in understanding the presented concepts. The information here is presented in a clear, straightforward manner that is appropriate for introductory and advanced calculus students alike.

Bourne, Murray

2008-04-22

36

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

PubMed

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

Roth, Robert E

2013-12-01

37

Fusion of CSP-derived features and Time-Domain Parameters for mind robotics control  

Microsoft Academic Search

In this paper, fusion of Common Spatial Pattern (CSP) analysis derived features and Time-Domain Parameters (TDP) is investigated for two-class motion imagery classification: left hand movement and right hand movement imagery. This fusion method is aiming at improving the performance of Brain- Computer Interface (BCI) systems in translating human thoughts into command to control certain robots, e.g. rehabilitation robots. In

Shuzhi Sam Ge; Xinyang Li; Yaozhang Pan

2011-01-01

38

Interaction of aldehydes derived from lipid peroxidation and membrane proteins.  

PubMed

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

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

39

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

NASA Technical Reports Server (NTRS)

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.

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

1990-01-01

40

Understanding Variability in the AVIRIS-Derived Parameters from Vegetation Cover  

NASA Technical Reports Server (NTRS)

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.

Goetz, Alexander F. H.

2000-01-01

41

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

NASA Technical Reports Server (NTRS)

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.

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

1993-01-01

42

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

PubMed

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

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

2014-05-01

43

Interaction of a calix[4]arene derivative with a DOPC bilayer: biomolecular simulations towards chloride transport.  

PubMed

The ability of a calix[4]arene derivative (CX-1), bearing four protonated NH3(+) groups located in the upper rim and aliphatic tails in the lower rim, to interact with a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) model bilayer and promote transmembrane chloride transport was investigated by molecular dynamics (MD) simulations. Unconstrained MD simulations show that the interaction of CX-1 with DOPC occurs via the NH3(+) groups, which are able to establish electrostatic interactions and multiple hydrogen bonds with the DOPC phosphate groups, while the aliphatic tails point towards the water phase (when CX-1 starts from the water phase) or to the membrane (when CX-1 is initially positioned within the bilayer). The interaction does not induce any relevant perturbation on the biophysical properties of the bilayer system (area per lipid, thickness, and hydration) apart from a systematic increase in the order parameter of the C2 carbon atom of the sn-1 lipid tail, meaning that the bilayer conserves its integrity. Since total internalization of CX-1 was not observed in the unconstrained MD time-scale, constant velocity steered molecular dynamics (SMD) simulations were performed in order to simulate the CX-1 permeation across the bilayer. At pulling velocities lower than 0.0075 nmps(-1), chloride transport was observed. The Potential of Mean Force (PMF), calculated with the weighted histogram analysis method, indicates a barrier of ca. 58kJmol(-1) for this mobile carrier to cross the membrane. PMID:24316169

Costa, Paulo J; Marques, Igor; Félix, Vítor

2014-03-01

44

The two-parameter soliton family for the interaction of a fundamental and its second harmonic  

E-print Network

The two-parameter soliton family for the interaction of a fundamental and its second harmonic R (October 30, 2000) For a system of interacting fundamental and second harmonics the soliton family is characterized by two independent parameters, a soliton potential and a soliton velocity. It is shown

45

Parameter identification for stochastic hybrid models of biological interaction networks  

E-print Network

with the structure of the model, identification is split in two subproblems: estimation of the genetic network regulating subtilin production from gene expression data, and estimation of population dynamics based on nutrient and population profiles. Techniques for parameter estimation from sparse and irregularly sampled

Ferrari-Trecate, Giancarlo

46

Deriving precise parameters for cool solar-type stars. Optimizing the iron line list  

NASA Astrophysics Data System (ADS)

Context. Temperature, surface gravity, and metallicitity are basic stellar atmospheric parameters necessary to characterize a star. There are several methods to derive these parameters and a comparison of their results often shows considerable discrepancies, even in the restricted group of solar-type FGK dwarfs. Aims: We want to check the differences in temperature between the standard spectroscopic technique based on iron lines and the infrared flux method (IRFM). We aim to improve the description of the spectroscopic temperatures especially for the cooler stars where the differences between the two methods are higher, as presented in a previous work. Methods: Our spectroscopic analysis was based on the iron excitation and ionization balance, assuming Kurucz model atmospheres in LTE. The abundance analysis was determined using the code MOOG. We optimized the line list using a cool star (HD 21749) with high resolution and high signal-to-noise spectrum, as a reference in order to check for weak, isolated lines. Results: We test the quality of the new line list by re-deriving stellar parameters for 451 stars with high resolution and signal-to-noise HARPS spectra, that were analyzed in a previous work with a larger line list. The comparison in temperatures between this work and the latest IRFM for the stars in common shows that the differences for the cooler stars are significantly smaller and more homogeneously distributed than in previous studies for stars with temperatures below 5000 K. Moreover, a comparison is presented between interferometric temperatures with our results that shows good agreement, even though the sample is small and the errors of the mean differences are large. We use the new line list to re-derive parameters for some of the cooler stars that host planets. Finally, we present the impact of the new temperatures on the [Cr i/Cr ii] and [Ti i/Ti ii] abundance ratios that previously showed systematic trends with temperature. We show that the slopes of these trends for the cooler stars become drastically smaller. Based on observations collected at the La Silla Paranal Observatory, ESO (Chile) with the HARPS spectrograph at the 3.6-m telescope (ESO runs ID 072.C-0488.Full Tables 2 and 3 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/555/A150Appendix A is available in electronic form at http://www.aanda.org

Tsantaki, M.; Sousa, S. G.; Adibekyan, V. Zh.; Santos, N. C.; Mortier, A.; Israelian, G.

2013-07-01

47

Temporal variations of ionospheric parameters derived from electron density profiles at high latitudes  

NASA Astrophysics Data System (ADS)

The ionosphere in the high latitude zone shows similar features to those of middle latitudes but additional factors make it more irregular and variable. The ionosonde, the basic technique for studying the ionosphere, has limitations when it is used at high latitudes avoiding to get a complete information from the ionograms. However the advent of moder sounders permits to produce better ionograms and to gather more information on the ionosphere. This study presents the diurnal and seasonal variations of ionospheric parameters derived from electron density profiles obtained at high latitudes for different solar activity conditions. The day-to-day variability is also examined. The database includes hourly values obtained at selected stations of the Northern and Southern hemispheres. The parameters analyzed are: the F2 peak parameters (foF2 and hmF2), the scale height at the F2 layer (Hm), the integrated total electron content (ITEC) and the equivalent slab thickness (EST).The results presented can be used to extract some properties of the electron density profiles at high latitudes in order to improve the IRI model for this latitudinal region.

Estela Mosert, Marta; McKinnell, Lee-Anne; Magdaleno, Sergio; Jadur, Camilo Alberto

48

The impact parameter dependence of swift electron-matter interactions  

SciTech Connect

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

Ritchie, R.H.

1988-01-01

49

A Poor Man's Derivation of Quantum Compass–Heisenberg Interaction: Superexchange Interaction in J–J Coupling Scheme  

NASA Astrophysics Data System (ADS)

The exchange interaction between 5d electrons in t2g orbitals is derived on the basis of the J–J coupling scheme, which is the appropriate basis in the case of a strong spin–orbit interaction. From simple calculations, it is found that the ferromagnetic Ising interaction (quantum compass model) occurs owing to a selection rule of hybridization between ?7 and ?8 orbitals, while the antiferromagnetic Heisenberg interaction appears from the hybridization between ?7 orbitals. It is also found that the ferromagnetic Ising interaction decreases as the spin–orbit interaction increases. Thus, the sign of the exchange interaction changes from the ferromagnetic Ising interaction to antiferromagnetic Heisenberg interaction as the spin–orbit interaction increases.

Matsuura, Hiroyasu; Ogata, Masao

2014-09-01

50

Novel polypyrrole derivatives to enhance conductive polymer-tissue interactions  

E-print Network

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 ...

George, Paul M. (Paul Matthew)

2005-01-01

51

Estimation of atomic interaction parameters by photon counting  

NASA Astrophysics Data System (ADS)

Detection of radiation signals is at the heart of precision metrology and sensing. In this article we show how the fluctuations in photon-counting signals can be exploited to optimally extract information about the physical parameters that govern the dynamics of the emitter. For a simple two-level emitter subject to photon counting, we show that the Fisher information and the Cramér-Rao sensitivity bound based on the full detection record can be evaluated from the waiting-time distribution in the fluorescence signal which can, in turn, be calculated for both perfect and imperfect detectors by a quantum trajectory analysis. We provide an optimal estimator achieving that bound.

Kiilerich, Alexander Holm; Mølmer, Klaus

2014-05-01

52

Improving mesoscale modeling using satellite-derived land surface parameters in the Pearl River Delta region, China  

NASA Astrophysics Data System (ADS)

surface parameters play an important role in mesoscale modeling by regulating the regional heat flux and hydrological cycle. Recently, significant urbanization and afforestation occurred in the Pearl River Delta (PRD) region, China, which exert an important effect on local meteorology and thermal circulation. But previous studies failed to capture the complex changes of the surface characteristics in the PRD and thus were difficult to accurately describe the land-atmosphere coupling. In this study, high-resolution Moderate Resolution Imaging Spectroradiometer observations are used to specify the land cover type, green vegetation fraction, and leaf area index in the Weather Research and Forecasting model. Comparisons with ground-based observations during eight episodes, as well as satellite measurements, all indicate an improved model performance when the satellite-derived land surface parameters are assimilated. Moreover, the remote sensing data accurately reflect the surface inhomogeneity and successfully represent the intensity and spatiotemporal characteristics of the urban heat island (UHI) effect. The UHI effect in turn modifies the local thermal circulation by enhancing the urban-rural horizontal advection and initiating the urban heat island circulation, as well as interacting with the sea/land breeze over the PRD. This work not only improves the understanding of local meteorological simulation and forecasting but also sets the stage for further research on the feedback between air quality and meteorological responses due to land cover changes.

Li, Mengmeng; Song, Yu; Huang, Xin; Li, Jianfeng; Mao, Yi; Zhu, Tong; Cai, Xuhui; Liu, Bing

2014-06-01

53

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

PubMed Central

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

Parthasarathy, Ranganathan; Singh, Viraj; Spencer, Paulette

2014-01-01

54

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

NASA Astrophysics Data System (ADS)

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.

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

55

CONSTRAINING THE SYMMETRY PARAMETERS OF THE NUCLEAR INTERACTION  

SciTech Connect

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

Lattimer, James M. [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States); Lim, Yeunhwan, E-mail: james.lattimer@stonybrook.edu, E-mail: yeunhwan.lim@gmail.com [Department of Physics Education, Daegu University, Gyeongsan 712-714 (Korea, Republic of)

2013-07-01

56

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

NASA Astrophysics Data System (ADS)

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

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

1993-09-01

57

Interactive Network Exploration to Derive Insights: Filtering, Clustering,  

E-print Network

of realistic networks generated by scientific article citations, cell phone calling patterns, banking, commercial, terrorist, or friendship interactions, where pro-social initiatives, commercial enterprises evolving struc- tures, where links act as pathways for volatile information or commodity flows. #12;2 B

Golbeck, Jennifer

58

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

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

59

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 ...

60

Fosinopril H(2)-receptor antagonists interaction studies by derivative spectroscopy.  

PubMed

Fosinopril sodium, a phosphinic acid derivative is an angiotensin converting enzyme (ACE) inhibitor, which had been employed for the treatment of hypertension and congestive heart failure; long tem use of ACE inhibitor often result in stress ulcers due to which H(2) receptor antagonists are also concurrently prescribed. The later compete with histamine for H(2) receptors and block gastric acid secretion and some cardiovascular effects of histamine. Our studies are focused on the in vitro availability of fosinopril in presence of commonly used H(2) receptor antagonists. Derivative spectroscopy has been employed for the quantitation of fosinopril and H(2) receptor antagonists followed by linear regression analysis. These studies were carried out in buffers of pH 7.4 and 9 at 37, 48 and 60( masculine)C. Stability constant and thermodynamic function had also been calculated in order to evaluate the reaction mechanism. Commonly prescribed H(2) receptor antagonists like cimetidine, ranitidine and famotidine were used in these studies. Present study clearly indicated that most of the H(2) receptor antagonists studied decreased the availability of fosinopril which conclude that availability of fosinopril can be affected by the concurrent administration of H(2) receptor antagonists. PMID:17337423

Sultana, Najma; Arayne, M Saeed; Sana, Aisha

2007-01-01

61

Interaction of one anthraquinone derivative with ctDNA analyzed by spectroscopic and modeling methods.  

PubMed

The interaction of one anthraquinone derivative (AOMan) with calf thymus deoxyribonucleic acid (ctDNA) was systematically investigated at physiological pH 7.4 by fluorescence spectroscopy and molecular modeling. Binding constants of ctDNA with AOMan were calculated at different temperatures. Thermodynamic parameters, enthalpy and entropy changes were calculated according to Van't Hoff equation, which indicated that the reaction was spontaneous and predominantly enthalpically driven. The increasing viscosity of ctDNA indicated that AOMan could intercalate into the base pairs of ctDNA. This conclusion was also demonstrated by the results obtained from KI quenching, denatured DNA studies and fluorescence polarization experiment. Furthermore, the molecular modeling results showed that anthraquinone ring tended to slide into the G-C rich region of ctDNA through the hydrogen bond, which are consistent with the results from experimental methods. Studying the binding interaction of target anthraquinones with DNA is one of the key steps in their DNA-changing action and the design of new drugs. PMID:24957254

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

2014-09-01

62

Force field development for organic molecules: Modifying dihedral and 1-n pair interaction parameters.  

PubMed

We comprehensively illustrate a general process of fitting all-atom molecular mechanics force field (FF) parameters based on quantum mechanical calculations and experimental thermodynamic data. For common organic molecules with free dihedral rotations, this FF format is comprised of the usual bond stretching, angle bending, proper and improper dihedral rotation, and 1-4 scaling pair interactions. An extra format of 1-n scaling pair interaction is introduced when a specific intramolecular rotation is strongly hindered. We detail how the preferred order of fitting all intramolecular FF parameters can be determined by systematically generating characteristic configurations. The intermolecular Van der Waals parameters are initially taken from the literature data but adjusted to obtain a better agreement between the molecular dynamics (MD) simulation results and the experimental observations if necessary. By randomly choosing the molecular configurations from MD simulation and comparing their energies computed from FF parameters and quantum mechanics, the FF parameters can be verified self-consistently. Using an example of a platform chemical 3-hydroxypropionic acid, we detail the comparison between the new fitting parameters and the existing FF parameters. In particular, the introduced systematic approach has been applied to obtain the dihedral angle potential and 1-n scaling pair interaction parameters for 48 organic molecules with different functionality. We suggest that this procedure might be used to obtain better dihedral and 1-n interaction potentials when they are not available in the current widely used FF. © 2014 Wiley Periodicals, Inc. PMID:25487650

Chen, Siyan; Yi, Shasha; Gao, Wenmei; Zuo, Chuncheng; Hu, Zhonghan

2015-03-01

63

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

SciTech Connect

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.

Hutchinson, T.A.; Scambos, T.A. [Univ. of Colorado, Boulder, CO (United States)

1997-11-01

64

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

NASA Astrophysics Data System (ADS)

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

Narbutis, D.; Semionov, D.; Stonkut?, R.; de Meulenaer, P.; Mineikis, T.; Bridžius, A.; Vansevi?ius, V.

2014-09-01

65

Interaction of piperidin derivative of Mannich base with DPPC liposomes.  

PubMed

The long chain Mannich bases, especially with the piperidine and morpholine groups, display very promising antimicrobial activity. In order to extend our knowledge on their impact on biological systems, we examined the interactions of the 5-pentadecyl-2-((piperidin-1-yl)methyl)phenol (PPDP) with model lipid membrane by means of differential scanning calorimetry (DSC) and fluorescence measurements. The small unilamellar vesicles of dipalmitoylophosphatidylcholine (DPPC) with different piperidine Mannich base concentration were investigated as a function of the increase of temperature. The phase separation accompanied by the rise of the transition enthalpy of both subcomponents, the increase of the function of the GP values of Laurdan versus the wavelength of excitation in the gel phase of PPDP/DPPC systems, and no remarkable differences in the fluorescence anisotropy of PPDP molecules in lipid environment for different mixtures of PPDP/DPPC was observed. Additionally, it was shown that PPDP itself interdigitated in solid state. PMID:23425432

Cie?lik-Boczula, Katarzyna; Petrus, Rafa? Micha?; Köhler, Gottfried; Lis, Tadeusz; Koll, Aleksander

2013-03-14

66

The Application of Connected QSRR and QSAR Strategies to Predict the Physicochemical Interaction of Acridinone Derivatives with DNA.  

PubMed

Acridinone derivatives as imidazoacridinones and triazoloacridinones are the new potent antitumor agents characterized by different mechanisms of action related to their ability to interact with DNA. The analysis undertaken in this study involves searching of QSAR (Quantitative Structure-Activity Relationship) and QSRR (Quantitative Structure-Retention Relationship) models, which would allow to predict the biological activity of acridinones expressed as ability to stabilize the secondary structure of DNA (?T), based on their structural parameters and chromatographic retention data. For this purpose, 20 acridinone derivatives were subjected to chromatographic analyses and molecular modeling, followed by statistical analyses using multiple linear regression method (MLR). As a novelty aspect, except for RP-HPLC approach, hydrophilic interaction chromatography (HILIC) columns were tested. As a result of performed analysis, appropriate QSAR and QSRR models were obtained, and each model was analyzed in terms of prediction of acridinones' ability to interact with DNA. Derived QSAR and QSRR models were characterized as one, with good prediction performance. Concluding, the proposed connected QSAR and QSRR strategies allow to predict in silico the ability of acridinones to interact with DNA without necessity of performing any biological experiments under in vitro and in vivo conditions. PMID:25387726

Paulina, Szatkowska; Marcin, Koba; Agata, Kuchcicka; Sylwia, Kurek; Emilia, Daghir; B?czek, Tomasz

2014-11-12

67

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

SciTech Connect

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.

González, M.; Lemus-Santana, A.A. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Rodríguez-Hernández, J. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Instituto de Ciencia y Tecnología de Materiales, Universidad de La Habana, Havana (Cuba); Aguirre-Velez, C.I. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Knobel, M. [Institute of Physics “Gleb Wataghin”, UNICAMP, 13083-970 Campinas, SP (Brazil); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico)

2013-08-15

68

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

SciTech Connect

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.

Belvedere, L.V. [Instituto de Fisica, Universidade Federal Fluminense, Av. Litoranea S/N, Boa Viagem, Niteroi, CEP 24210-340, Rio de Janeiro (Brazil)]. E-mail: belve@if.uff.br; Rodrigues, A.F. [Instituto de Fisica, Universidade Federal Fluminense, Av. Litoranea S/N, Boa Viagem, Niteroi, CEP 24210-340, Rio de Janeiro (Brazil)]. E-mail: armflavio@if.uff.br

2006-12-15

69

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

SciTech Connect

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.

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

2013-06-03

70

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

71

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

SciTech Connect

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

Ismail, M.; Adel, A. [Physics Department, Faculty of Science, Cairo University, Giza (Egypt)

2011-09-15

72

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

NASA Astrophysics Data System (ADS)

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

Ismail, M.; Adel, A.

2011-09-01

73

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

NASA Astrophysics Data System (ADS)

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.

Fielitz, Daniel; Wegler, Ulrich

2013-04-01

74

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

SciTech Connect

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.

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

2012-01-10

75

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

Microsoft Academic Search

We present spatial patterns of glacier fluctuations from the Cordillera Blanca, Peru, (glacier area, terminus elevations, median elevations and hypsography) at decadal timescales derived from 1970 aerial photography, 2003 SPOT5 satellite data, Geographic Information Systems (GIS) and statistical analyses. We derived new glacier outlines from the 2003 SPOT images, and ingested them in the Global Land and Ice Measurements from

Adina E. Racoviteanu; Yves Arnaud; Mark W. Williams; Julio Ordoñez

2008-01-01

76

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

ERIC Educational Resources Information Center

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…

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

2011-01-01

77

Entanglement dynamics in two-parameter qubit-qutrit states under Dzyaloshinskii-Moriya interaction  

NASA Astrophysics Data System (ADS)

We study entanglement dynamics in two-parameter qubit-qutrit states under the influence of Dzyaloshisnhkii-Moriya (DM) interaction. Our system consists of a qubit-qutrit pair as a closed system initially in two-parameter class of states, and one environmental qubit interacts with the qutrit of the closed system via DM interaction. We divide our analysis into two cases. In the first case, we study the entanglement dynamics in separable region, and in the second case we study the same in non-separable region. The DM interaction produces the entanglement in separable region with entanglement sudden death (ESD) and some states in this region remain unaffected by the same. In non-separable region, all the states are affected by DM interaction. The DM interaction excites the entanglement but does not produce ESD in this region. We observed that probability amplitude of environmental qubit does not affect the entanglement in two-parameter qubit-qutrit states in both the regions.

Sharma, Kapil K.; Pandey, S. N.

2014-09-01

78

Characterization of the Flory-Huggins interaction parameter of polymer thermodynamics  

NASA Astrophysics Data System (ADS)

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.

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

2014-12-01

79

The ionic model: Extension to spatial charge distributions, derivation of an interaction potential for silica polymorphs  

NASA Astrophysics Data System (ADS)

An interatomic interaction potential for silica polymorphs is derived based on the SCD model (cfr. Tijskens et al. 1994). This interaction potential incorporates all classical electrostatic interactions arising from the spherical part of the spatial extent of the atoms including many body interactions. The potential is derived from Hartree-Fock energies and electron densities for a set 72 [SiO4]4-- and [Si2O7]6--clusters with variable configuration. The long range impact of the surroundings on these clusters in the infinite system has been successfully mimicked by embedding the clusters in a finite three-dimensional array of point charges. This three-dimensional array of point charges is optimized as to reproduce the average site potential and its gradient occurring in II IV-coordinated silica polymorphs at the central atoms of the clusters. The resulting interaction potential consists of two functions of the configurational coordinates, ?, describing spherical “atomic” electron densities, ?a(x, ?) for A=Si, O. All classical electrostatic interactions are derived from these densities. A Born-Mayer type correction term ? E qm(?) models the quantum mechanical interactions and the electrostatic interactions arising from the non-spherosymmetrical component of the electron density. The new interaction potential model shows a slightly improved reproduction of the potential surface with respect to the classical Born-Mayer ionic model and demonstrates the importance of many body interactions as charge transfer and expansion/contraction of the atomic electron densities in these systems. Also the dependence of the quantum mechanical correction term ? E qm(?) on the Si-O-Si-bond angle proves covalent effects to be larger than suggested by the classical Born-Mayer ionic model thereby clarifying the controversy in literature on the importance of covalent effects in silica polymorphs and polymerised silicates in general.

Tijskens, E.; Viaene, W. A.; Geerlings, P.

1995-04-01

80

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

E-print Network

Compost mixture influence of interactive physical parameters on microbial kinetics and substrate 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 Composting is a feasible by selecting an initial compost recipe with physical properties that enhance microbial activity. The present

Paris-Sud XI, Université de

81

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...

82

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

NASA Astrophysics Data System (ADS)

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.

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

2014-03-01

83

ANTESCOFO: ANTICIPATORY SYNCHRONIZATION AND CONTROL OF INTERACTIVE PARAMETERS IN COMPUTER MUSIC  

E-print Network

(rather than pitch), control over vari- ous time scales used in music writing, and enables tempo- ralANTESCOFO: ANTICIPATORY SYNCHRONIZATION AND CONTROL OF INTERACTIVE PARAMETERS IN COMPUTER MUSIC Arshia Cont UCSD, Music Department, and Ircam - UMR CNRS STMS. cont@ircam.fr ABSTRACT Antescofo

Paris-Sud XI, Université de

84

Interactive genetic algorithm for cartooning parameter tuning , Sun-Young Lee*, , Min-Joon Yoo**,  

E-print Network

Interactive genetic algorithm for cartooning parameter tuning , Sun-Young Lee*, , Min-Joon Yoo**, , Jong-Chul Yoon**, , In-Kwon Lee on Graphics, vol. 25, no. 3, pp. 1221-1226 (2006) [2] Henry Kang, S. Lee and Charles K. Chui, "Coherent Line

Lee, In-Kwon

85

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...

86

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

NASA Astrophysics Data System (ADS)

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.

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

1993-07-01

87

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

NASA Astrophysics Data System (ADS)

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

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

2004-04-01

88

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

Microsoft Academic Search

BACKGROUND: The enumeration of tetrameric and other sequence motifs that are positively or negatively correlated with in vivo antisense DNA effects has been a useful addition to the arsenal of information needed to predict effective targets for antisense DNA control of gene expression. Such retrospective information derived from in vivo cellular experiments characterizes aspects of the sequence dependence of antisense

Donald M. Gray; Carla W. Gray; Byong-Hoon Yoo; Tzu-Fang Lou

2010-01-01

89

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

PubMed

In this paper, a novel model for evaluating the temperature of traveling-wave ultrasonic motor (TWUSM) is developed. The proposed model, where the interaction between the temperature rise and motor parameters is considered, differs from the previous reported models with constant parameters. In this model, losses and temperature rises of the motor were evaluated based on the temperature-related varying parameters: the feedback voltage Vaux of the stator, dielectric permittivity ? and dielectric loss factor tan?. At each new temperature, Vaux, ? and tan? were updated. The feasibility and effectiveness of this proposed model was verified by comparing the predicted temperatures with the measured one. The effects of driving voltage, driving frequency and ambient temperature on the predicted temperature were also analyzed. The results show that the proposed model has more accurate predicted temperature than that with constant parameters. This will be very useful for the optimal design, reducing the heat loss, improvement of control and reliability life of TWUSM. PMID:25481041

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

2015-03-01

90

Estimating Kinetic and Thermodynamic Parameters from Single Molecule Enzyme-Inhibitor Interactions  

PubMed Central

We report the application of recently developed microscopic models to estimate the apparent kinetic and thermodynamic parameters in a single molecule force spectroscopy study of the carbonic anhydrase enzyme and a complementary sulfonamide inhibitor. The most probable rupture force for the enzyme-inhibitor interaction shows a non-linear dependency on the log-loading rate. Estimates for the kinetic and thermodynamic parameters were obtained by fitting the non-linear dependency to linear cubic potential and cusp potential models and compared to the standard Bell-Evans model. The reliability of the estimated parameters was verified by modeling the experimental rupture force distributions by the theoretically predicted distributions at rupture. We also report that linkers that are attached to the enzyme and inhibitor show appreciable effects on the apparent kinetic and thermodynamic parameters. PMID:18808161

Porter-Peden, Laura; Kamper, Sarah G.; Wal, Mark Vander; Blankespoor, Ronald; Sinniah', Kumar

2008-01-01

91

Structural Interface Parameters Are Discriminatory in Recognising Near-Native Poses of Protein-Protein Interactions  

PubMed Central

Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native) structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets. PMID:24498255

Malhotra, Sony; Sankar, Kannan; Sowdhamini, Ramanathan

2014-01-01

92

Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions.  

PubMed

Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native) structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets. PMID:24498255

Malhotra, Sony; Sankar, Kannan; Sowdhamini, Ramanathan

2014-01-01

93

F2 Peak parameters, drifts and spread F derived from digisonde ionograms for the COPEX campaign in Brazil  

Microsoft Academic Search

Digisonde ionograms recorded in Brazil during the COPEX campaign of 2002 have been analyzed to determine the diurnal variations of the F2 peak parameters (foF2, hmF2 and the Chapman scale height, Hm) for the three COPEX stations, Boa Vista, Cachimbo and Campo Grande. Values of foF2 were derived at 15-min intervals for UT days 278–298. The autoscaled F2 traces for

Leo F. McNamara; John M. Retterer; M. A. Abdu; Inez S. Batista; Bodo W. Reinisch

2008-01-01

94

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

PubMed Central

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

2012-01-01

95

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

PubMed Central

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 ?iSASA. A procedure for the determination of values for the ?iSASA 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 ?iSASA 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 ?gSASA was obtained via partitioning of the atom–type ?iSASA 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

2012-01-01

96

Photometric parameter maps of the Moon derived from LROC WAC images  

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

97

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

NASA Astrophysics Data System (ADS)

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.

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

2007-05-01

98

Large scale ecosystem modeling using parameters derived from imaging spectrometer data  

NASA Astrophysics Data System (ADS)

The capability to predict the response of ecosystems to change relies on our ability to understand and model the effective functioning of biotic processes at large scales and the transport functions of the atmospheric/hydrospheric processes. To successfully evaluate changes in ecological processes at the required spatial and temporal scales remote sensing technology and ecosystem theory must be considered jointly. A review of developments in remote sensing analysis using high spectral resolution sensors has led to the selection of a potential set ofparameters to be used in ecosystem models. These parameters quantify the light interception properties that scale from leaf to landscape. Spectral mixture analysis forms a framework for the systematic separation of both vegetative and non-vegetative components at sub-pixel spatial resolution. The spectral concentrations of the vegetative components defined by the spectral mixture analysis are then used to drive canopy radiative transfer models from which the ecosystem parameters are inferred. 1.

Wessman, Carol A.; Curtiss, Brian; Ustin, Susan L.

1990-09-01

99

Novel interactions of fluorinated nucleotide derivatives targeting orotidine-5?-monophosphate decarboxylase  

PubMed Central

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

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

2011-01-01

100

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

NASA Astrophysics Data System (ADS)

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.

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

2014-06-01

101

Analysis of the gas-surface interaction parameters using a least squares differential correction method  

NASA Astrophysics Data System (ADS)

This paper proposes an experiment that can be carried out using general house-keeping data from a spinning satellite. The satellite used for this work is the Space Technology Research Vehicle (STRV-1) which is being developed at the Defence Research Agency, Farnborough, UK. This satellite will be launched into Geostationary Transfer Orbit from the ASAP ring of an Ariane 4 rocket. As the vehicle passes through perigee with a nominal spin rate of 10 rpm it will be subjected to torques due to the aerodynamic interactions. It is planned to use the change in spin axis direction to refine our knowledge of the gas surface interaction (GSI) parameters. Optimal attitudes for perigee passage are evaluated which will give a maximum perturbation, and the magnitude of the expected deviation is calculated. A least squares differential correction method is then described which will allow us to refine the GSI parameters, and finally a method of simulating spacecraft data is outlined.

Markwell, A. J.; Swinerd, G. G.

102

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

PubMed Central

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

2015-01-01

103

Interactions of curcumin and its derivatives with nucleic acids and their implications.  

PubMed

Curcumin (diferuloylmethane) is a yellow polyphenol found in the rhizome of the annual herb turmeric (Curcuma longa) belonging to the family Zingiberaceae. Its interaction with a huge number of molecular targets like cytokines, growth factors, transcription factors, receptors, pro-inflammatory enzymes, protein kinases and adhesion molecules has been studied extensively. Interaction of curcumin with nucleic acids has been the focus of extensive research in recent years. Curcumin is observed to be genotoxic and antigenotoxic agent in time and concentration dependent manner. Curcumin and its derivatives either alone or as metal complexes have been reported to bind directly to DNA. The interactions are mainly as DNA minor groove binding or as DNA intercalating agents. The similarity in the shape of curcumin to DNA minor groove binding drugs is the motivation for exploring its binding to DNA minor grooves. Thus curcumin is a "double edged sword": having therapeutic potential as a minor groove binder but at the same time it may cause DNA damage in the cell at high concentration. The purpose of this review is to summarize the current information related to interaction of curcumin metal complexes and its derivatives with nucleic acids and the implication such interaction can have on therapeutics. PMID:23095000

Kumar, Anil; Bora, Utpal

2013-02-01

104

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

NASA Astrophysics Data System (ADS)

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.

Peikert, Benjamin; Schaumann, Gabriele Ellen

2014-05-01

105

Derivate  

NSDL National Science Digital Library

In this activity, students input functions in order to calculate the derivative and tangent line of that function. This activity allows students to explore tangent lines of various functions. This activity includes supplemental materials, including background information about the topics covered, a description of how to use the application, and exploration questions for use with the java applet.

2010-01-01

106

Selection of operating parameters on the basis of hydrodynamics in centrifugal partition chromatography for the purification of nybomycin derivatives.  

PubMed

The selection of solvent systems in centrifugal partition chromatography (CPC) is the most critical point in setting up a separation. Therefore, lots of research was done on the topic in the last decades. But the selection of suitable operating parameters (mobile phase flow rate, rotational speed and mode of operation) with respect to hydrodynamics and pressure drop limit in CPC is still mainly driven by experience of the chromatographer. In this work we used hydrodynamic analysis for the prediction of most suitable operating parameters. After selection of different solvent systems with respect to partition coefficients for the target compound the hydrodynamics were visualized. Based on flow pattern and retention the operating parameters were selected for the purification runs of nybomycin derivatives that were carried out with a 200 ml FCPC(®) rotor. The results have proven that the selection of optimized operating parameters by analysis of hydrodynamics only is possible. As the hydrodynamics are predictable by the physical properties of the solvent system the optimized operating parameters can be estimated, too. Additionally, we found that dispersion and especially retention are improved if the less viscous phase is mobile. PMID:23290339

Adelmann, S; Baldhoff, T; Koepcke, B; Schembecker, G

2013-01-25

107

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

PubMed Central

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

Rowan-Robinson, M

1993-01-01

108

Fermi Orbital Derivatives in Self-Interaction Corrected Density Functional Theory: Applications to Closed Shell Atoms  

E-print Network

A recent modification of the Perdew-Zunger self-interaction-correction (SIC) to the density-functional formalism (Pederson, Ruzsinszky, Perdew) has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Lowdin orthonormalized Fermi-orbitals (Luken et al) which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested here on atoms. Total energies and ionization energies in closed-shell atoms, where correlation is less important, using the PW92 LDA functional are in very good to excellent agreement with experiment and non-relativistic Quantum-Monte-Carlo (QMC) results.

Pederson, Mark R

2014-01-01

109

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

PubMed Central

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

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

1979-01-01

110

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

NASA Astrophysics Data System (ADS)

Interactions of water molecules with soil organic matter (SOM) may affect the ability of SOM to participate in multiple physical, chemical and biological processes. Specifically, water-SOM interactions may have a profound effect on interactions of organic compounds with SOM which is often considered as a major natural sorbent controlling the environmental fate of organic pollutants in the soil environment. Quantification of water - SOM interactions may be carried out by using water vapor sorption isotherms. However, water sorption isotherms providing macroscopic thermodynamic data do not allow examining water-SOM interactions on a microenvironment scale. The examination of water-SOM interactions in a local SOM environment may be carried out by determining the response of the SOM hydration to sorption of probe organic compounds. Recently, the model-free approach was proposed which allows quantifying effects of sorbing organic molecules on water - SOM interactions, by using relatively more available data on the effect of water activity on organic compound - SOM interactions. Therefore, this thermodynamic approach was applied to the experimental data describing sorption of organic compounds by SOM, both from the vapor and liquid phases, at various water activities. Hence, the response of water interactions with the model SOM materials such as a humic acid and an organic matter-rich peat soil to the presence of various organic sorbates was evaluated. Depending on a molecular structure of organic sorbates probing various molecular environments in SOM, the SOM-bound water may be driven in or out of the SOM sorbents. Organic compounds containing the atoms of oxygen, nitrogen or sulfur and preferring a relatively "polar" SOM microenvironment demonstrate the distinct enhancing effect on water-SOM interactions. In contrast, the "low-polarity" organic compounds, e.g., hydrocarbons or their halogen-substituted derivatives, produce a weakening effect on water-SOM interactions. Importantly, the changes in water-SOM interactions induced by the presence of organic compounds may demonstrate the cooperative behavior: (1) several water molecules may be involved in an enhanced hydration of SOM, (2) at the presence of an organic sorbate, interactions of water molecules with SOM enhance the uptake of the following water molecules. The proposed cooperative water-SOM interactions may result from a perturbation of the SOM matrix due to a sorption of organic and water molecules where a partial disrupting of molecular contacts in SOM makes easier the following SOM-water interactions thus promoting the enhanced SOM hydration.

Borisover, Mikhail

2014-05-01

111

Lunar tidal acceleration obtained from satellite-derived ocean tide parameters  

NASA Technical Reports Server (NTRS)

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

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

1978-01-01

112

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

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

113

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

NASA Technical Reports Server (NTRS)

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.

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

2005-01-01

114

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

NASA Technical Reports Server (NTRS)

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.

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

2006-01-01

115

Simple derivation of the energy-dependent effective strength of gravitational interaction in small-angle scattering  

NASA Astrophysics Data System (ADS)

A simple derivation is given of the progression (1?2?4) of the effective strengths of the gravitational interaction in small-angle scattering, from the newtonian product of “changes”, Gm1m2, to the einsteinian strength, {2GE 1m 2}/{c 2}, for light scattered by a fixed mass, to the strength, {4GE 1E 2}/{c 4}, for two highly relativistic particles. It is noted that the “complicated” amplitude of 't Hooft is just the Glauber amplitude for a {1}/{r} potential, equal (more or less by accident) to the exact “Coulomb” amplitude of the Schrödinger equation, with ? c= {z 1z 2e 2}/{??} replaced by an appropriate gravitational parameter. The differential scattering cross section for small-angle gravitational scattering at any energy is {d? }/{dt }= {4?? 2}/{t 2}, where ? is the energy-dependent strength, given in invariant form by eq. (5).

Jackson, J. D.

1988-12-01

116

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

PubMed

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

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

117

Theoretical and experimental local reactivity parameters of 3-substituted coumarin derivatives.  

PubMed

Local reactivity descriptors, such as atomic charges, atomic electrostatic potential and atomic Fukui indices were computed for a series of 3-substituted coumarin (2-oxo-2H-1-benzopyran) derivatives, using density functional theory (DFT) and Möller-Plesset methods (MP2). The variation of those properties as a function of the substituents was compared with the variation of the measured XPS binding energies. The atomic electrostatic potentials and XPS binding energies serves as indicators of the electrophilicity of a given center within a molecule, while the atomic Fukui indices describe its degree of electronic localization, known as atomic softness. The correlation between those theoretical and experimental properties allowed us to follow the effect of electron withdrawing substituents on the electrophilicity of a given atomic center. The Fukui indices provided additional information about the softening/hardening of the center of interest due to presence of different substituents to the coumarin system. On the basis of these analysis, the 1,2-addition would be favored for 3-acetyl, 3-phosphono, and 7-diethylamino substituents, while 3-carboxyl, 3-ethoxycarbonyl, and 3-nitro substituent would favor 1,4-addition. The substituted coumarins would preferably react with soft nucleophiles at position 2 and with hard nucleophiles at position 4. PMID:25347691

Petkova, Nevena I; Nikolova, Rositca D; Kostov, Krassimir L; Mineva, Tzonka; Vayssilov, Georgi N

2014-11-20

118

Determination of orbital parameters of interacting galaxies using a genetic algorithm. Description of the method and application to artificial data  

Microsoft Academic Search

A method for determining the orbital parameters of interacting pairs of galaxies is presented and evaluated using artificial data. The method consists of a genetic algorithm which can search efficiently through the very large space of possible orbits. It is found that orbital parameters close to the actual orbital parameters of the pair can in general be found, even in

M. Wahde

1998-01-01

119

Examination of model uncertainty and parameter interaction in a global carbon cycling model (GLOCO)  

SciTech Connect

Simulation models play an important role in understanding the causes and consequences of climate change. In order to make full use of these models, it is necessary to establish the magnitude and sources of uncertainty associated with their predictions. This information can be used to achieve a better understanding of the simulated systems, to increase the reliability of model predictions, to guide field surveys and laboratory experiments, and to define realistic values that should be used in scientific, economic, and political discussions of future conditions. In this paper, a new tree-structured density estimation technique that extends the ability of Monte Carlo-based analyses to explore parameter interactions and uncertainty in complex environmental models was applied. The application of the technique is demonstrated using the GLOCO global carbon cycle model. The paper demonstrates that there are numerous distinct parameter combinations that can meet fairly stringent calibration criteria, and they are concentrated in relatively small subsets of the parameter space. These different subsets can be viewed as representing different ecological systems that achieve the same calibration or performance goals in fundamentally different ways. It is also shown that the simulated responses of these systems to future environmental change can lead to different conclusions regarding the interaction between factors affecting environmental processes, such as the growth of vegetation. Together, these results show how the tree-structured density estimation technique can be applied to gain a broader understanding of model performance and of ecosystem responses to change.

Grieb, T.M. [Tetra Tech, Inc., Lafayette, CA (United States)] [Tetra Tech, Inc., Lafayette, CA (United States); [Univ. of California, Berkeley, CA (United States). Environmental Health Sciences; Hudson, R.J.M.; Gherini, S.A. [Tetra Tech, Inc., Lafayette, CA (United States)] [Tetra Tech, Inc., Lafayette, CA (United States); Shang, N. [Rensselaer Polytechnic Inst., Troy, NY (United States)] [Rensselaer Polytechnic Inst., Troy, NY (United States); Spear, R.C. [Univ. of California, Berkeley (United States). Environmental Health Sciences] [Univ. of California, Berkeley (United States). Environmental Health Sciences; Goldstein, R.A. [Electric Power Research Inst., Palo Alto, CA (United States)] [Electric Power Research Inst., Palo Alto, CA (United States)

1999-09-01

120

Interaction of parasitism and nutrition in goats: effects on haematological parameters, correlations, and other statistical associations.  

PubMed

Weaned wether goats (n = 144) approximately 6 months of age were placed in a 2 x 3 factorial experiment to test the effects and interaction of two levels of nutrition (growth+maintenance, NUT1; and twice growth+maintenance, NUT2) and three levels of Haemonchus contortus burden (0, 500, and 2000 larvae administered every 2 weeks; W0, W500, and W2000, respectively) on packed cell volume, red blood cell count, total serum protein and leukocytes. The statistical analysis revealed clear and proportionate differences among levels of infection for all variables. A significant (P < 0.05) nutritional effect was also found associated with all the variables except leukocytes. Nutrition by worm load interactions were found for packed cell volume and leukocytes. The neutrophil/lymphocyte ratio was higher in the NUT1-infected animals, leading to the nutrition by worm load interaction for leukocytes. An analysis for the different leukocyte types revealed significant (P < 0.05) differences among infection levels for lymphocytes, while nutrition level was found to be a significant effect for basophil count and immature white cells. Several significant correlations were observed between pairs of variables. Faecal egg output could be predicted from actual worm count in three of the four necropsy periods. The clear differences observed for blood parameters were not present in production traits, suggesting that physiological thresholds may play an important role in framing the metabolic activity of biological organisms. Total serum protein was the best indicator of these effects on production parameters. PMID:1466129

Blackburn, H D; Rocha, J L; Figueiredo, E P; Berne, M E; Vieira, L S; Cavalcante, A R; Rosa, J S

1992-10-01

121

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

PubMed

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

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

122

Numerical Studies of Small Repeating Earthquakes and Their Source Parameters Using Laboratory-derived Friction Laws  

NASA Astrophysics Data System (ADS)

Small repeating earthquakes have short recurrence times and known locations, and hence they present a rare predictable opportunity for detailed observation and insights into earthquake physics. That has been exploited in the San Andreas Fault Observatory at Depth (SAFOD) drilling project. It is important to establish realistic models for their occurrence, to provide a framework for proper interpretation of SAFOD data and other studies. One of the intriguing observation about repeating earthquakes is the scaling of their repeat time T and seismic moment M0 as T\\propto M00.17 (Nadeau and Johnson, 1998). The scaling is abnormal compared to T\\propto M01/3, the typical scaling that results from a simple conceptual model of circular ruptures with stress drop independent of the seismic moment and slip proportional to the repeat time. Several explanations for the discrepancy in scaling have been proposed, including high stress drop (Nadeau and Johnson, 1998), shading asperity (Sammis and Rice, 2001), and aseismic slip (Beeler et al., 2001). Our studies show that a model based on Dieterich-Ruina rate and state friction laws reproduces the observed abnormal scaling. In our 3D model, a small patch with rate-weakening friction is surrounded by a much larger region with rate-strengthening friction. Our simulations use the 3D methodology of Liu and Lapusta (AGU, 2006) that fully resolves all aspects of seismic and aseismic behavior of the fault. For a set of laboratory-based friction parameters, we can reproduce the observed scaling simply by varying the size of the rate-weakening patch. When the patch size is smaller than the nucleation size implied by the underlying rate and state formulation, the patch has fully aseismic slip. For larger patch sizes, small repeating events start to occur, with slip rates of order of 1 m/s and sharp stress drops. The events are accompanied by significant aseismic slip on the patch, providing a physical explanation for the idea of Beeler et al. (2001). Our recent and current work pursues several directions. We have studied properties of individual small events and found that their static stress drop, averaged over the zone of seismic slip, is in the typical range, although the stress drop is quite heterogeneous in space. We will use our simulations to investigate how well the average value of stress drop on the interface corresponds to the one determined from near-field seismograms. We have found a trade-off between values of frictional parameters and plate loading rate in determining the repeat time and moment of seismic events, and we will report on our current efforts to quantify it. Simulations in 2D models, needed to study a wider range of formulations, produce the same scaling, although individual small earthquakes have much larger moment and repeat time in 2D than in 3D. Our preliminary simulations with Ruina-Dieterich version of rate and state friction have results qualitatively similar to those with Dieterich-Ruina formulation. We are also exploring models that combine rate and state friction with dynamic weakening in the form of flash heating.

Chen, T.; Lapusta, N.

2007-12-01

123

Structural evolution in Pt isotopes with the Interacting Boson Model Hamiltonian derived from the Gogny Energy Density Functional  

E-print Network

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

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

2010-10-25

124

Generalized derivation of an exact relationship linking different coefficients that characterize thermodynamic effects of preferential interactions.  

PubMed

In solutions consisting of solvent water (component '1') and two solute components ('2' and '3'), various thermodynamic effects of differences between solute-solute and solute-solvent interactions are quantitatively characterized by state functions commonly called 'preferential interaction coefficients': gamma(mu(1),mu(3)) triple bond (delta(m3)/delta(m2))(T,mu(1),mu(3)) and gamma(mu(k)) triple bond (delta(m3)/delta(m2))(T,P,mu(k)), where k = 1,2 or 3. These different derivatives are not all directly accessible to experimental determination, nor are they entirely equivalent for analyses and interpretations of thermodynamic and molecular effects of preferential interactions. Consequently, various practical and theoretical considerations arise when, for a given system, different kinds of preferential interaction coefficients have significantly different numerical values. Previously we derived the exact relationship linking all three coefficients of the type gamma(mu(k), and hence identified the physical origins of the differences between gamma(mu(1)) and gamma(mu(3)) that have been experimentally determined for each of various common biochemical solutes interacting with a protein [J. Phys. Chem. B, 106 (2002) 418-433]. Continuing our investigation of exact thermodynamic linkages among different types of preferential interaction coefficients, we present here a generalized derivation of the relationship linking gamma(mu(1),mu(3)), gamma(mu(3)) and gamma(mu(1)), with no restrictions on m(2), m(3) or any physical characteristic of either solute component (such as partial molar volume). Hence, we show that (gamma(mu(1),mu(3)) - gamma(mu(3))) is related directly to (gamma(mu(3)) - gamma(mu(1))), for which the physical determinants have been considered in detail previously, and to a factor dependent on the ratio of the partial molar volumes V3/V1. Our generalized expression also provides a basis for calculating gamma(mu(1),mu(3)), even in situations where preferential interactions could not be investigated by equilibrium dialysis. To demonstrate this applicability, we analyze isopiestic distillation data for aqueous solutions containing urea and NaCl, two small solute components that cannot be selectively dialyzed. PMID:12488023

Anderson, Charles F; Felitsky, Daniel J; Hong, Jiang; Record, M Thomas

2002-12-10

125

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

PubMed

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

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

2014-12-28

126

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

NASA Astrophysics Data System (ADS)

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.

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

2014-12-01

127

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

PubMed

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

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

2015-01-01

128

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

SciTech Connect

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.

Bentley, I. [Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556 (United States); Frauendorf, S. [Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556 (United States); ISP, Forschungszentrum Dresden-Rossendorf, Dresden (Germany)

2011-06-15

129

Chemical and Molecular Aspects on Interactions of Galanthamine and Its Derivatives with Cholinesterases.  

PubMed

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

Gulcan, H Ozan; Orhan, Ilkay Erdogan; Sener, Bilge

2014-12-01

130

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

PubMed Central

Successful high-intensity focused ultrasound (HIFU) thermal tissue ablation relies on accurate information of the tissue temperature and tissue status. Often temperature measurements are used to predict and monitor the ablation process. In this study, we conducted HIFU ablation experiments with ex vivo porcine myocardium tissue specimens to identify changes in temperature associated with tissue coagulation and bubble/cavity formation. Using infrared (IR) thermography and synchronized bright-field imaging with HIFU applied near the tissue surface, parameters derived from the spatiotemporal evolution of temperature were correlated with HIFU-induced lesion formation and overheating, of which the latter typically results in cavity generation and/or tissue dehydration. Emissivity of porcine myocardium was first measured to be 0.857 ± 0.006 (n = 3). HIFU outcomes were classified into non-ablative, normal lesion, and overheated lesion. A marked increase in the rate of temperature change during HIFU application was observed with lesion formation. A criterion using the maximum normalized second time derivative of temperature change provided 99.1% accuracy for lesion identification with a 0.05 s?1 threshold. Asymmetric temperature distribution on the tissue surface was observed to correlate with overheating and/or bubble generation. A criterion using the maximum displacement of the spatial location of the peak temperature provided 90.9% accuracy to identify overheated lesion with a 0.16 mm threshold. Spatiotemporal evolution of temperature obtained using IR imaging allowed determination of the cumulative equivalent minutes at 43 °C (CEM43) for lesion formation to be 170 min. Similar temperature characteristics indicative of lesion formation and overheating were identified for subsurface HIFU ablation. These results suggest that parameters derived from temperature changes during HIFU application are associated with irreversible changes in tissue and may provide useful information for monitoring HIFU treatment. PMID:23878517

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

2013-01-01

131

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

NASA Astrophysics Data System (ADS)

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.

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

2013-09-01

132

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

PubMed

Successful high-intensity focused ultrasound (HIFU) thermal tissue ablation relies on accurate information of the tissue temperature and tissue status. Often temperature measurements are used to predict and monitor the ablation process. In this study, we conducted HIFU ablation experiments with ex vivo porcine myocardium tissue specimens to identify changes in temperature associated with tissue coagulation and bubble/cavity formation. Using infrared (IR) thermography and synchronized bright-field imaging with HIFU applied near the tissue surface, parameters derived from the spatiotemporal evolution of temperature were correlated with HIFU-induced lesion formation and overheating, of which the latter typically results in cavity generation and/or tissue dehydration. Emissivity of porcine myocardium was first measured to be 0.857 ± 0.006 (n = 3). HIFU outcomes were classified into non-ablative, normal lesion, and overheated lesion. A marked increase in the rate of temperature change during HIFU application was observed with lesion formation. A criterion using the maximum normalized second time derivative of temperature change provided 99.1% accuracy for lesion identification with a 0.05 s(-1) threshold. Asymmetric temperature distribution on the tissue surface was observed to correlate with overheating and/or bubble generation. A criterion using the maximum displacement of the spatial location of the peak temperature provided 90.9% accuracy to identify overheated lesion with a 0.16 mm threshold. Spatiotemporal evolution of temperature obtained using IR imaging allowed determination of the cumulative equivalent minutes at 43 °C (CEM 43) for lesion formation to be 170 min. Similar temperature characteristics indicative of lesion formation and overheating were identified for subsurface HIFU ablation. These results suggest that parameters derived from temperature changes during HIFU application are associated with irreversible changes in tissue and may provide useful information for monitoring HIFU treatment. PMID:23878517

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

2013-09-01

133

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

PubMed Central

The development of novel antimicrobial agents is urgently required to curb the widespread emergence of multidrug-resistant bacteria like colistin-resistant Pseudomonas aeruginosa. We previously synthesized a series of amphiphilic neamine derivatives active against bacterial membranes, among which 3?,6-di-O-[(2?-naphthyl)propyl]neamine (3?,6-di2NP), 3?,6-di-O-[(2?-naphthyl)butyl]neamine (3?,6-di2NB), and 3?,6-di-O-nonylneamine (3?,6-diNn) showed high levels of activity and low levels of cytotoxicity (L. Zimmermann et al., J. Med. Chem. 56:7691–7705, 2013). We have now further characterized the activity of these derivatives against colistin-resistant P. aeruginosa and studied their mode of action; specifically, we characterized their ability to interact with lipopolysaccharide (LPS) and to alter the bacterial outer membrane (OM). The three amphiphilic neamine derivatives were active against clinical colistin-resistant strains (MICs, about 2 to 8 ?g/ml), The most active one (3?,6-diNn) was bactericidal at its MIC and inhibited biofilm formation at 2-fold its MIC. They cooperatively bound to LPSs, increasing the outer membrane permeability. Grafting long and linear alkyl chains (nonyl) optimized binding to LPS and outer membrane permeabilization. The effects of amphiphilic neamine derivatives on LPS micelles suggest changes in the cross-bridging of lipopolysaccharides and disordering in the hydrophobic core of the micelles. The molecular shape of the 3?,6-dialkyl neamine derivatives induced by the nature of the grafted hydrophobic moieties (naphthylalkyl instead of alkyl) and the flexibility of the hydrophobic moiety are critical for their fluidifying effect and their ability to displace cations bridging LPS. Results from this work could be exploited for the development of new amphiphilic neamine derivatives active against colistin-resistant P. aeruginosa. PMID:24867965

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

2014-01-01

134

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

PubMed

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

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

2013-11-01

135

Determination of orbital parameters of interacting galaxies using a genetic algorithm. Description of the method and application to artificial data  

E-print Network

A method for determining the orbital parameters of interacting pairs of galaxies is presented and evaluated using artificial data. The method consists of a genetic algorithm which can search efficiently through the very large space of possible orbits. It is found that, in most cases, orbital parameters close to the actual orbital parameters of the pair can be found. The method does not require information about the velocity field of the interacting system, and is able to cope with noisy data. The inner regions of the galaxies, which are difficult to model, can be neglected, and the orbital parameters can be determined using the remaining information.

M. Wahde

1997-10-24

136

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

NASA Astrophysics Data System (ADS)

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

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

2015-02-01

137

Nucleotides and nucleolipids derivatives interaction effects during multi-lamellar vesicles formation.  

PubMed

In this paper a micellar interface, constituted by the cationic surfactant CTAB, in presence of 1,2-epoxydodecane and nucleotides was used for catanionic multi-lamellar vesicles (MLVs) formation. The micellar solution of CTAB is able to disperse the 1,2 epoxydodecane in the micellar core promoting the reaction of this reagent with the nucleotide attracted by the positive surface charge of the micellar aggregates. The alkylation of AMP and UMP nucleotides leads to the synthesis of nucleolipids. The behaviour of the supramolecular structures formed depends on the starting reagents (AMP, UMP and AMP+UMP) and on the assembly capabilities of the products. In particular nucleotides and nucleotides derivatives interaction effects are evaluated during the multi-lamellar vesicles formation. NMR spectroscopy and UV-vis measurements performed on MLVs showed strong aryl interactions. Interestingly, NMR spectra revealed prevailing stacking interactions between complementary nucleolipids. The assembly of complementary nucleotides affects the course of the reaction during the MLVs formation. Moreover the MLVs supramolecular stability has been tested by means of turbidity and UV-vis measurements. In particular, an enhanced stability has been found in systems prepared with complementary nucleotides confirming that in these systems the self-assembly process is influenced by nucleolipids interactions. Furthermore by following the hypocromic effect during the micellar catalysis, we showed that even in the earlier stages of the reaction significant differences are detectable. PMID:18337067

Cuomo, Francesca; Lopez, Francesco; Angelico, Ruggero; Colafemmina, Giuseppe; Ceglie, Andrea

2008-07-15

138

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

NASA Technical Reports Server (NTRS)

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.

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

2009-01-01

139

Randomly phosphorylated polystyrene derivatives interact with RNA polymerase II transcription factors: part I.  

PubMed

Insoluble functional synthetic random copolymers are able to develop at their surfaces specific interactions with biologic components. Crosslinked phosphorylated polystyrene derivatives were previously shown to mimic DNA antigen because they interacted with anti-DNA antibodies found in the sera of systemic lupus erythematosus patients. These biospecific surfaces were postulated to be able to bind other DNA-binding proteins such as RNA polymerase II transcription factors. Indeed, these proteins play a major role in gene regulation in mammalian cells. This hypothesis was checked by adsorption and elution of HeLa cell nuclear extracts on a 72% phosphorylated resin. The composition of the eluted fractions were analyzed by electrophoresis, and the biologic activity of the transcription factors was tested using an in vitro transcription assay. The results showed that USF, TATA-binding protein (TBP), and TFIIB were specifically adsorbed on the polymer and that all eluted factors kept their biologic activity. Therefore, randomly phosphorylated polystyrene derivatives may be useful for the fractionation of RNA polymerase II transcription factors. PMID:9054526

Imbert, E; Letourneur, D; Jozefowicz, M

1997-03-15

140

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

NASA Astrophysics Data System (ADS)

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.

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

2014-12-01

141

Two-dimensional, M-mode and Doppler-derived echocardiographic parameters in sedated healthy growing female sheep.  

PubMed

Despite the fact that sheep are a widely used animal model in cardiovascular research, reference values for transthoracic echocardiography in normal growing animals are not available. Eight healthy female lambs underwent two-dimensional, M-mode and pulsed wave Doppler echocardiographic examination at 100 days of age and every three months thereafter over a 12-month period. The study was conducted under sedation with midazolam, butorphanol and constant rate infusion of intravenous propofol. Their growth phase was completed at about one year of age. All the echocardiographic parameters considered were significantly correlated with body weight and age class except for the left ventricular systolic and diastolic diameters. Functional indices were not correlated to body weight or age except for the E-point to septal separation distance (EPSS). Doppler-derived parameters were not influenced by independent variables. Transthoracic echocardiography can be considered an applicable method for cardiovascular research using a growing lamb animal model after appropriate adjustments for age and body size. PMID:23760962

Poser, H; Semplicini, L; De Benedictis, G M; Gerardi, G; Contiero, B; Maschietto, N; Valerio, E; Milanesi, O; Semplicini, A; Bernardini, D

2013-07-01

142

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

NASA Astrophysics Data System (ADS)

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.

Bonacum, Jason

2013-03-01

143

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...

144

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

PubMed Central

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

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

2011-01-01

145

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

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

146

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 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

Claridge, Ela

147

Salmonella?infected crypt?derived intestinal organoid culture system for host–bacterial interactions  

PubMed Central

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

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

2014-01-01

148

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

PubMed

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

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

2014-04-14

149

Probing protein structure and dynamics by second-derivative ultraviolet absorption analysis of cation–? interactions  

PubMed Central

We describe an alternate approach for studying protein structure using the detection of ultraviolet (UV) absorbance peak shifts of aromatic amino acid side chains induced by the presence of salts. The method is based on the hypothesis that salt cations (Li+, Na+, and Cs+) of varying sizes can differentially diffuse through protein matrices and interact with benzyl, phenyl, and indole groups through cation–? interactions. We have investigated the potential of this method to probe protein dynamics by measuring high resolution second-derivative UV spectra as a function of salt concentration for eight proteins of varying physical and chemical properties and the N-acetylated C-ethyl esterified amino acids to represent totally exposed side chains. We show that small shifts in the wavelength maxima for Phe, Tyr, and Trp in the presence of high salt concentrations can be reliably measured and that the magnitude and direction of the peak shifts are influenced by several factors, including protein size, charge, and the local environment and solvent accessibility of the aromatic groups. Evaluating the empirical UV spectral data in light of known protein structural information shows that probing cation–? interactions in proteins reveals unique information about the influence of structure on aromatic side chain spectroscopic behavior. PMID:16963649

Lucas, Laura H.; Ersoy, Baran A.; Kueltzo, Lisa A.; Joshi, Sangeeta B.; Brandau, Duane T.; Thyagarajapuram, Nagarajan; Peek, Laura J.; Middaugh, C. Russell

2006-01-01

150

Salmonella-infected crypt-derived intestinal organoid culture system for host-bacterial interactions.  

PubMed

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

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

2014-09-01

151

Key parameters in blood-surface interactions of 3D bioinspired ceramic materials.  

PubMed

Direct contact of materials with blood components may trigger numerous processes which ultimately lead to hemolysis, clot formation and recruitment of inflammatory cells. In this study, the blood-surface interactions for two inert bioinspired ceramic scaffolds obtained from natural resources; biomorphic carbon and silicon carbides (bioSiC) from different origins have been studied. The response of the blood in contact with carbon is well known, however little has been identified on the influence of their 3D porous structure. Moreover, to our knowledge, there is no reference in the literature about the hemocompatibility of biomorphic silicon carbide as a porous scaffold. The experimental results showed the surface energy to be crucial to evaluate the hemocompatibility of a material however the surface topography and material porosity are also parameters to be considered. Surface roughness modifies clot formation whereas for protein adsorption total sample porosity seems to be the key parameter to be considered for hydrophilic materials (biomorphic silicon carbides), while the size of the pores determines the hemolytic response. PMID:24907756

Díaz-Rodríguez, P; González, P; Serra, J; Landin, M

2014-08-01

152

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

PubMed

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

Belozerov, A S; Anisimov, V I

2014-09-17

153

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

NASA Astrophysics Data System (ADS)

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.

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

2014-09-01

154

Peptidelipid interactions of the -hairpin antimicrobial peptide tachyplesin and its linear derivatives from solid-state NMR  

E-print Network

Peptide­lipid interactions of the -hairpin antimicrobial peptide tachyplesin and its linear­lipid interaction of a -hairpin antimicrobial peptide tachyplesin-1 (TP-1) and its linear derivatives TP-1 and other -hairpin antimicrobial peptides are discussed in terms of their molecular structure

Hong, Mei

155

Structural determinates for apolipoprotein E-derived peptide interaction with the alpha7 nicotinic acetylcholine receptor.  

PubMed

Neuronal nicotinic acetylcholine receptor (nAChR) signaling has been implicated in a variety of normal central nervous system (CNS) functions as well as an array of neuropathologies. Previous studies have demonstrated both neurotoxic and neuroprotective actions of peptides derived from apolipoprotein E (apoE). It has been discovered that apoE-derived peptides inhibit native and recombinant alpha7-containing nAChRs, indicating a direct interaction between apoE peptides and nAChRs. To probe the structure/function interaction between alpha7 nAChRs and the apoE peptide apoE(141-148), experiments were conducted in Xenopus laevis oocytes expressing wild-type and mutated nAChRs. Mutation of Trp55 to alanine blocks apoE peptide-induced inhibition of acetylcholine (ACh)-mediated alpha7 nAChR responses. Additional mutations at Trp55 suggest that hydrophobic interactions between the receptor and apoE(141-148) are essential for inhibition of alpha7 nAChR function. A mutated apoE peptide also demonstrated decreased inhibition at alpha7-W55A nAChRs as well as activity-dependent inhibition of both wild-type alpha7 nAChRs and alpha7-W55A receptors. Finally, a three-dimensional model of the alpha7 nAChR was developed based on the recently refined Torpedo marmorata nACh receptor. A structural model is proposed for the binding of apoE(141-148) to the alpha7 nAChR where the peptide binds at the interface between two subunits, near the ACh binding site. Similar to the functional data, the computational docking suggests the importance of hydrophobic interactions between the alpha7 nAChR and the apoE peptide for inhibition of receptor function. The current data suggest a mode for apoE peptide binding that directly blocks alpha7 nAChR activity and consequently may disrupt nAChR signaling. PMID:17609418

Gay, Elaine A; Bienstock, Rachelle J; Lamb, Patricia W; Yakel, Jerrel L

2007-10-01

156

Insights into the Interactions between Maleimide Derivates and GSK3? Combining Molecular Docking and QSAR  

PubMed Central

Many protein kinase (PK) inhibitors have been reported in recent years, but only a few have been approved for clinical use. The understanding of the available molecular information using computational tools is an alternative to contribute to this process. With this in mind, we studied the binding modes of 77 maleimide derivates inside the PK glycogen synthase kinase 3 beta (GSK3?) using docking experiments. We found that the orientations that these compounds adopt inside GSK3? binding site prioritize the formation of hydrogen bond (HB) interactions between the maleimide group and the residues at the hinge region (residues Val135 and Asp133), and adopt propeller-like conformations (where the maleimide is the propeller axis and the heterocyclic substituents are two slanted blades). In addition, quantitative structure–activity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3? inhibitory activities for the studied compounds. We found a model to explain the structure–activity relationship of non-cyclic maleimide (NCM) derivatives (54 compounds). The best CoMSIA model (training set included 44 compounds) included steric, hydrophobic, and HB donor fields and had a good Q2 value of 0.539. It also predicted adequately the most active compounds contained in the test set. Furthermore, the analysis of the plots of the steric CoMSIA field describes the elements involved in the differential potency of the inhibitors that can be considered for the selection of suitable inhibitors. PMID:25010341

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

2014-01-01

157

A combined experimental and computational study of Vam3, a derivative of resveratrol, and Syk interaction.  

PubMed

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

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

2014-01-01

158

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

PubMed Central

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

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

2009-01-01

159

Betulin derivatives impair Leishmania braziliensis viability and host-parasite interaction.  

PubMed

Leishmaniasis is a public health problem in tropical and subtropical areas of the world, including Venezuela. The incidence of treatment failure and the number of cases with Leishmania-HIV co-infection underscore the importance of developing alternative, economical and effective therapies against this disease. The work presented here analyzed whether terpenoids derived from betulin are active against New World Leishmania parasites. Initially we determined the concentration that inhibits the growth of these parasites by 50% or IC50, and subsequently evaluated the chemotactic effect of four compounds with leishmanicidal activity in the sub-micromolar and micromolar range. That is, we measured the migratory capacity of Leishmania (V.) braziliensis in the presence of increasing concentrations of compounds. Finally, we evaluated their cytotoxicity against the host cell and their effect on the infectivity of L. (V.) braziliensis. The results suggest that (1) compounds 14, 17, 18, 25 and 27 are active at concentrations lower than 10?M; (2) compound 26 inhibits parasite growth with an IC50 lower than 1?M; (3) compounds 18, 26 and 27 inhibit parasite migration at pico- to nanomolar concentrations, suggesting that they impair host-parasite interaction. None of the tested compounds was cytotoxic against J774.A1 macrophages thus indicating their potential as starting points to develop compounds that might affect parasite-host cell interaction, as well as being leishmanicidal. PMID:25240731

Alcazar, Wilmer; López, Adrian Silva; Alakurtti, Sami; Tuononen, Maija-Liisa; Yli-Kauhaluoma, Jari; Ponte-Sucre, Alicia

2014-11-01

160

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

PubMed Central

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

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

2014-01-01

161

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

USGS Publications Warehouse

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.

Palandri, James L.; Kharaka, Yousif K.

2004-01-01

162

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

PubMed

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

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

2014-11-26

163

Juxtacrine and paracrine interactions of rat marrow-derived mesenchymal stem cells, muscle-derived satellite cells, and neonatal cardiomyocytes with endothelial cells in angiogenesis dynamics.  

PubMed

Research into angiogenesis has contributed to progress in the fast-moving field of regenerative medicine. Designing coculture systems is deemed a helpful method to understand the dynamic interaction of various cells involved in the angiogenesis process. We investigated the juxtacrine and paracrine interaction between 3 different cells, namely rat marrow-derived mesenchymal stem cells (rMSCs), rat muscle-derived satellite cells (rSCs), and rat neonatal cardiomyocytes (rCMs), and endothelial cells (ECs) during angiogenesis process. In vitro Matrigel angiogenesis assay was performed whereby ECs were monocultured or cocultured with rMSCs, rSCs, and rCMs or their conditioned media (CM). In addition, in vivo Matrigel plug assay for angiogenesis was conducted to assess the angiogenic potential of the rCM-, rMSC-, and rSC-derived CM. Our results demonstrated that the rMSCs, rSCs, and rCMs elongated along the EC tubules, whereas the rMSCs formed tube-like structures with sprouting tip cells, leading to improved angiogenesis in the coculture system. Moreover, the rMSC- and rSC-derived CM significantly improved angiogenesis tube formation on Matrigel, accelerated EC chemotaxis, and increased the arteriolar density, vascularization index, and vascularization flow index in the Matrigel plug in vivo. Western blotting showed that rMSCs secreted a high level of vascular endothelial growth factor, basic fibroblast growth factor, and stromal-derived factor-1-alpha. Tie2 is also shed from rMSCs. This study demonstrated that stem cells interact with ECs in the juxtacrine and paracrine manner during angiogenesis, and marrow MSCs have superior angiogenic properties. PMID:23072248

Rahbarghazi, Reza; Nassiri, Seyed Mahdi; Khazraiinia, Parvaneh; Kajbafzadeh, Abdol-Mohammad; Ahmadi, Seyed Hossein; Mohammadi, Elham; Molazem, Mohammad; Zamani-Ahmadmahmudi, Mohamad

2013-03-15

164

?12C(0+) and ?16O Potentials Derived from the SU6 Quark-Model Baryon-Baryon Interaction  

NASA Astrophysics Data System (ADS)

We derive single-hyperon potentials for light nuclei, based on the G-matrix calculations of the quark-model baryon-baryon interactions developed by the Kyoto-Niigata group. The ?12C(0+) and ?16O potentials have non-trivial oscillating behavior, reflecting strong isospin dependence of the ?N interaction; namely, attractive isospin I = 0 ?N interaction and weakly repulsive I = 1 interaction. The latter repulsive effect is largely enhanced in the intermediate region of the ?-core potential, resulting in very weak attraction at the surface region.

Fujiwara, Y.; Kohno, M.; Suzuki, Y.

2010-10-01

165

?12C(0+) and ?16O Potentials Derived from the SU6 Quark-Model Baryon-Baryon Interaction  

NASA Astrophysics Data System (ADS)

We derive single-hyperon potentials for light nuclei, based on the G-matrix calculations of the quark-model baryon-baryon interactions developed by the Kyoto-Niigata group. The ?12C(0+) and ?16O potentials have non-trivial oscillating behavior, reflecting strong isospin dependence of the ?N interaction; namely, attractive isospin I = 0 ?N interaction and weakly repulsive I = 1 interaction. The latter repulsive effect is largely enhanced in the intermediate region of the ?-core potential, resulting in very weak attraction at the surface region.

Fujiwara, Y.; Kohno, M.; Suzuki, Y.

166

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

SciTech Connect

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.

Aldaya, V.; Lopez-Ruiz, F. F.; Sanchez-Sastre, E. [Instituto de Astrofisica de Andalucia, Apartado Postal 3004, Granada 18080 (Spain); Instituto de Fisica Teorica y Computacional Carlos I, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva, Granada 18002 (Spain); Calixto, M. [Departamento de Matematica Aplicada y Estadistica, Universidad Politecnica de Cartagena, Paseo Alfonso XIII 56, 30203 Cartagena (Spain); Instituto de Fisica Teorica y Computacional Carlos I, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva, Granada 18002 (Spain)

2006-11-03

167

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

SciTech Connect

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

Ancarani, L. U. [Laboratoire de Physique Moleculaire et des Collisions, Universite Paul Verlaine-Metz, 57078 Metz (France); Gasaneo, G. [Departamento de Fisica, Universidad Nacional del Sur and Consejo Nacional de Investigaciones Cientificas y Tecnicas, 8000 Bahia Blanca, Buenos Aires (Argentina)

2008-06-15

168

Cellular interactions and biomechanical properties of a unique vascular-derived scaffold for periodontal tissue regeneration.  

PubMed

These investigations describe the development of a novel ex vivo three-dimensional scaffold derived from the human umbilical vein (HUV), and its potential as a regenerative matrix for tissue regeneration. Unique properties associated with the vascular wall have shown potential to function as a surgical barrier for guided tissue regeneration, particularly with the regeneration of periodontal tissues. HUV was isolated from umbilical cords using a semiautomated machining technology, decellularized using 1% sodium dodecyl sulfate, and then opened longitudinally to form tissue sheets. Uniaxial tensile testing, stress relaxation, and suture retention tests were performed on the acellular matrix to evaluate the HUV's biomechanical properties, followed by an evaluation of cellular interactions by seeding human gingival fibroblasts to assess adhesion, metabolic function, and proliferation on the scaffold. The scaffold's biomechanical properties were shown to display anisotropic behavior, which is attributed to the ex vivo material's composite structure. Detailed results indicated that the ultimate tensile strength of the longitudinal strips was significantly higher than that of the circumferential strips (p < 0.001). The HUV also exhibited significantly higher stress relaxation response in the longitudinal direction than in the circumferential orientation (p < 0.05). The ablumenal and lumenal surfaces of the material were also shown to differentially influence cell proliferation and metabolic activity, with both cellular functions significantly increased on the ablumenal surface (p < 0.05). Human gingival fibroblast migration into the scaffold was also influenced by the organization of extracellular matrix components, where the lumenal surface inhibits cell migration, acting as a barrier, while the ablumenal surface, which is proposed to interface with the wound site, promotes cellular invasion. These results show the HUV bioscaffold to be a promising naturally derived surgical barrier that may function well as a resorbable guided tissue regeneration membrane as well as in other clinical applications. PMID:19778172

Goktas, Selda; Pierre, Nicolas; Abe, Koki; Dmytryk, John; McFetridge, Peter S

2010-03-01

169

Best values of parameters for interacting HDE with GO IR-cutoff in Brans-Dicke cosmology  

E-print Network

We investigate the interacting holographic dark energy (HDE) with Granda-Oliveros (GO) IR-cutoff in the framework of Brans-Dicke (BD) cosmology. We obtain the equation of state (EoS) parameter of HDE, $w_D$, the effective EoS parameter $w_{\\mathrm{eff}}$, the deceleration parameter $q $ and the squared of sound speed $v_s^2$ in a flat FRW universe. We show that at late time the cosmic coincidence problem can be alleviated. Also we show that for non-interacting case, HDE can give a unified dark matter-dark energy profile in BD cosmology, except that it cannot solve the coincidence problem in the future. By studying the equation of state parameter, we see that the phantom divide may be crossed. Using the latest observational data, we calculate the best values of the parameters for interacting HDE in BD framework. Computing the deceleration parameter implies that the transition from deceleration to the acceleration phase occurred for redshift $z\\geq 0.5$. Finally, we investigate the sound stability of the model,...

Khodam-Mohammadi, A; Sheykhi, A

2014-01-01

170

Best values of parameters for interacting HDE with GO IR-cutoff in Brans-Dicke cosmology  

E-print Network

We investigate the interacting holographic dark energy (HDE) with Granda-Oliveros (GO) IR-cutoff in the framework of Brans-Dicke (BD) cosmology. We obtain the equation of state (EoS) parameter of HDE, $w_D$, the effective EoS parameter $w_{\\mathrm{eff}}$, the deceleration parameter $q $ and the squared of sound speed $v_s^2$ in a flat FRW universe. We show that at late time the cosmic coincidence problem can be alleviated. Also we show that for non-interacting case, HDE can give a unified dark matter-dark energy profile in BD cosmology, except that it cannot solve the coincidence problem in the future. By studying the equation of state parameter, we see that the phantom divide may be crossed. Using the latest observational data, we calculate the best values of the parameters for interacting HDE in BD framework. Computing the deceleration parameter implies that the transition from deceleration to the acceleration phase occurred for redshift $z\\geq 0.5$. Finally, we investigate the sound stability of the model, and find that HDE with GO cutoff in the framework of BD cosmology can lead to a stable DE-dominated universe favored by observations, provided we take $\\beta=0.44$ and $b^2<0.35$. This is in contrast to HDE model in Einstein gravity which does not lead to a stable DE dominated universe.

A. Khodam-Mohammadi; E. Karimkhani; A. Sheykhi

2014-09-09

171

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

PubMed Central

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

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

172

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

PubMed Central

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

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

2014-01-01

173

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

SciTech Connect

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.

Piron, E. [Universite Claude Bernard, Villeurbanne (France)] [Universite Claude Bernard, Villeurbanne (France); [COGEMA, Velizy-Villacoublay (France); Accominotti, M. [Hopital Edouard Heriot, Lyon (France)] [Hopital Edouard Heriot, Lyon (France); Domard, A. [Universite Claude Bernard, Villeurbanne (France)] [Universite Claude Bernard, Villeurbanne (France)

1997-03-19

174

Design and modular parallel synthesis of a MCR derived ?-helix mimetic protein–protein interaction inhibitor scaffold  

Microsoft Academic Search

A terphenyl ?-helix mimetic scaffold recognized to be capable of disrupting protein–protein interactions was structurally morphed into an easily amenable and versatile multicomponent reaction (MCR) backbone. The design, modular in-parallel library synthesis, initial cell based biological data, and preliminary in vitro screening for the disruption of the Bcl-w\\/Bak protein–protein interaction by representatives of the MCR derived scaffold are presented.

Walfrido Antuch; Sanjay Menon; Quin-Zene Chen; Yingchun Lu; Sukumar Sakamuri; Barbara Beck; Vesna Schauer-Vukašinovi?; Seema Agarwal; Sibylle Hess; Alexander Dömling

2006-01-01

175

Distinct Behaviour of the Homeodomain Derived Cell Penetrating Peptide Penetratin in Interaction with Different Phospholipids  

PubMed Central

Background Penetratin is a protein transduction domain derived from the homeoprotein Antennapedia. Thereby it is currently used as a cell penetrating peptide to introduce diverse molecules into eukaryotic cells, and it could also be involved in the cellular export of transcription factors. Moreover, it has been shown that it is able to act as an antimicrobial agent. The mechanisms involved in all these processes are quite controversial. Methodology/Principal Findings In this article, we report spectroscopic, calorimetric and biochemical data on the penetratin interaction with three different phospholipids: phosphatidylcholine (PC) and phosphatidylethanolamine (PE) to mimic respectively the outer and the inner leaflets of the eukaryotic plasma membrane and phosphatidylglycerol (PG) to mimic the bacterial membrane. We demonstrate that with PC, penetratin is able to form vesicle aggregates with no major change in membrane fluidity and presents no well defined secondary structure organization. With PE, penetratin aggregates vesicles, increases membrane rigidity and acquires an ?-helical structure. With PG membranes, penetratin does not aggregate vesicles but decreases membrane fluidity and acquires a structure with both ?-helical and ?–sheet contributions. Conclusions/Significance These data from membrane models suggest that the different penetratin actions in eukaryotic cells (membrane translocation during export and import) and on prokaryotes may result from different peptide and lipid structural arrangements. The data suggest that, for eukaryotic cell penetration, penetratin does not acquire classical secondary structure but requires a different conformation compared to that in solution. PMID:21209890

Maniti, Ofelia; Alves, Isabel; Trugnan, Germain; Ayala-Sanmartin, Jesus

2010-01-01

176

Interactions of a Platinum-Modified Perylene Derivative with the Human Telomeric G-Quadruplex  

PubMed Central

The interactions of a newly synthesized platinum-modified perylene derivative, compound 7 ([{Pt(dien)}2(?-4-S,S')](NO3)4 (dien = diethylenetriamine, 4 = N,N'-bis(1-(2-aminoethyl)-1,3-dimethylthiourea)-3,4,9,10-perylenetetracarboxylic acid diimide), with the human telomeric repeat were studied using various model oligo(deoxy)ribonucleotides to mimic the polymorphic nature of the telomeric G-quadruplex. UV/visible spectroscopy, CD spectropolarimetry, electrospray mass spectrometry (ES-MS), and isothermal titration calorimetry (ITC) were used to demonstrate that compound 7 selectively recognizes the antiparallel form of the unimolecular telomeric G-quadruplex formed by the sequence d(TTAGGG)4 (dG-24), to which it binds with a 2:1 stoichiometry and nanomolar affinity. Compared with telomeric DNA, the first binding event of compound 7 in titrations with the RNA quadruplex formed by r(UUAGGG)4 (rG-24) is an order of magnitude weaker. Compound 7 does not induce the antiparallel G-quadruplex RNA, which invariably exists in a parallel form and dimerizes in solution. Based on the cumulative experimental data, two distinct mechanisms are proposed for the recognition of G-quadruplex DNA and RNA by compound 7. Potential biomedical and biochemical applications of the platinum–perylene technology are discussed. PMID:21999566

Rao, Lu; Dworkin, Joshua D.; Nell, William E.; Bierbach, Ulrich

2012-01-01

177

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

PubMed

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

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

2014-04-25

178

Influence of the order of the constituent basis matrices on the Mueller matrix decomposition-derived polarization parameters in complex turbid media such as biological tissues  

Microsoft Academic Search

The influence of the multiplication order of the constituent basis matrices on the Mueller matrix decomposition-derived polarization parameters in complex tissue-like turbid media exhibiting simultaneous scattering and polarization effects are investigated. A polarization sensitive Monte Carlo (MC) simulation model was used to generate Mueller matrices from turbid media exhibiting simultaneous linear birefringence, optical activity and multiple scattering effects. Mueller matrix

Nirmalya Ghosh; Michael F. G. Wood; I. Alex Vitkin

2010-01-01

179

Neutral winds derived from IRI parameters and from the HWM87 wind model for the SUNDIAL campaign of September, 1986  

Microsoft Academic Search

Meridional neutral winds derived from the height of the maximum ionization of the F2-layer are compared with values from results of the HWM87 empirical neutral wind model. The time period considered in this study is the SUNDIAL-2 campaign, September 21 through October 5, 1986. Winds have been derived from measurements by a global network of ionosondes, as well as from

K. L. Miller; A. E. Hedin; P. J. Wilkinson; D. G. Torr; P. G. Richards

1990-01-01

180

Neutral winds derived from IRI parameters and from the HWM87 wind model for the sundial campaign of September, 1986  

Microsoft Academic Search

Meridional neutral winds derived from the height of the maximum ionization of the F2 layer are compared with values from results of the HWM87 empirical neutral wind model. The time period considered is the SUNDIAL-2 campaign, 21 Sept. through 5 Oct. 1986. Winds were derived from measurements by a global network of ionosondes, as well as from similar quantities generated

K. L. Miller; A. E. Hedin; P. J. Wilkinson; D. G. Torr; P. G. Richards

1990-01-01

181

Best values of parameters for interacting HDE with GO IR-cutoff in Brans-Dicke cosmology  

NASA Astrophysics Data System (ADS)

We investigate the interacting holographic dark energy (HDE) with Granda-Oliveros (GO) infrared (IR)-cutoff in the framework of Brans-Dicke (BD) cosmology. We obtain the equation of state (EoS) parameter of HDE, wD, the effective EoS parameter weff, the deceleration parameter q and the squared of sound speed vs2 in a flat Friedmann-Robertson-Walker (FRW) universe. We show that at late-time the cosmic coincidence problem can be alleviated. Also we show that for noninteracting case, HDE can give a unified dark matter-dark energy (DM-DE) profile in BD cosmology, except that it cannot solve the coincidence problem in the future. By studying the EoS parameter, we see that the phantom divide may be crossed. Using the latest observational data, we calculate the best values of the parameters for interacting HDE in BD framework. Computing the deceleration parameter implies that the transition from deceleration to the acceleration phase occurred for redshift z ? 0.5. Finally, we investigate the sound stability of the model, and find that HDE with Granda-Oliveros (GO)-cutoff in the framework of BD cosmology can lead to a stable DE-dominated universe favored by observations, provided we take ? = 0.44 and b2 < 0.35. This is in contrast to HDE model in Einstein gravity which does not lead to a stable DE-dominated universe.

Khodam-Mohammadi, A.; Karimkhani, E.; Sheykhi, A.

2014-09-01

182

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

NASA Astrophysics Data System (ADS)

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

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

2001-12-01

183

Interaction of a ?-lactam calixarene derivative with a model eukaryotic membrane affects the activity of PLA2.  

PubMed

In this research, the interaction between a membrane phospholipid, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), and a p-tert-butylcalix[4]arene derivative bearing 6-aminopenicillanic acid (Calix), conceived as a possible drug carrier, was studied. The Langmuir film balance technique was used to measure surface pressure and electrical surface potential of pure and mixed Calix/DLPC monolayers spread on water at different temperatures. Phospholipase A2 (PLA2) activity was used as well to detect the impact of the calixarene derivative on the monolayer properties. Interaction between the molecules in mixed monolayers has been described quantitatively using thermodynamic functions. Interestingly, low amounts of Calix introduce ordering in the lipid film. This effect may be analogous to that of cholesterol interacting with phospholipids. A lower activity of PLA2 observed with the Calix/DLPC films compared to pure DLPC may be related to structural modifications of the mixed systems. PMID:23201740

Korchowiec, Beata; Gorczyca, Marcelina; Ben Salem, Adel; Regnouf de Vains, Jean-Bernard; Rogalska, Ewa

2013-03-01

184

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

PubMed

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

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

2014-04-01

185

Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for protein side-chain analogues  

PubMed Central

A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being employed in further development of the POSSIM fast polarizable force field for proteins. PMID:23420678

Li, Xinbi; Ponomarev, Sergei Y.; Sa, Qina; Sigalovsky, Daniel L.; Kaminski, George A.

2013-01-01

186

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)

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.

Stephenson, J. D.

1983-01-01

187

Determination of the parameters of the potential for interaction of heavy ions from data on nuclear fission  

SciTech Connect

The Ericson statistical model has been used to extract the parameters of the potential for interaction of heavy ions from experimental data on the distribution of fragment kinetic energies for fixed values of the mass ratio in spontaneous fission of /sup 252/Cf. For nuclear fragments which are deformed in the ground state, a decrease in the inverse fusion barrier height by approx.15% is found in comparison with the barrier for spherical nuclei, and a corresponding increase is found in the effective radius constant of the interaction.

Rubchenya, V.A.; Tutin, G.A.

1978-03-01

188

Human amniotic membrane-derived stromal cells (hAMSC) interact depending on breast cancer cell type through secreted molecules.  

PubMed

Human amniotic membrane-derived stromal cells (hAMSC) are candidates for cell-based therapies. We examined the characteristics of hAMSC including the interaction between hAMSC and breast cancer cells, MCF-7, and MDA-MB-231. Human amniotic membrane-derived stromal cells showed typical MSC properties, including fibroblast-like morphology, surface antigen expression, and mesodermal differentiation. To investigate cell-cell interaction via secreted molecules, we cultured breast cancer cells in hAMSC-conditioned medium (hAMSC-CM) and analyzed their proliferation, migration, and secretome profiles. MCF-7 and MDA-MB-231 cells exposed to hAMSC-CM showed increased proliferation and migration. However, in hAMSC-CM, MCF-7 cells proliferated significantly faster than MDA-MB-231 cells. When cultured in hAMSC-CM, MCF-7 cells migrated faster than MDA-MB-231 cells. Two cell types showed different profiles of secreted factors. MCF-7 cells expressed much amounts of IL-8, GRO, and MCP-1 in hAMSC-CM. Human amniotic membrane-derived stromal cells interact with breast cancer cells through secreted molecules. Factors secreted by hAMSCs promote the proliferation and migration of MCF-7 breast cancer cells. For much safe cell-based therapies using hAMSC, it is necessary to study carefully about interaction between hAMSC and cancer cells. PMID:25441616

Kim, Sun-Hee; Bang, So Hee; Kang, So Yeong; Park, Ki Dae; Eom, Jun Ho; Oh, Il Ung; Yoo, Si Hyung; Kim, Chan-Wha; Baek, Sun Young

2014-10-22

189

Interaction de l'atome d'hydrogene avec un champ laser intense et bref a derive de frequence  

NASA Astrophysics Data System (ADS)

Nous presentons dans ce document une etude theorique de l'interaction entre l'atome d'hydrogene et un champ laser intense et bref a derive de frequence. Dans un premier temps, nous etablissons une methode basee sur les fonctions B-splines qui permet de decrire avec precision l'ensemble de la structure energetique du systeme atomique. Dans le second temps, nous developpons une approche non perturbative de type spectrale, basee sur la resolution exacte de l'equation de Schrodinger dependante du temps, pour decrire l'atome d'hydrogene en interaction avec un champ laser. Nous proposons particulierement une representation realiste d'une impulsion laser a derive de frequence. Finalement, nous etudions le processus d'ionisation au dessus du seuil de l'atome d'hydrogene soumis a une impulsion a derive de frequence. Nos resultats montrent que la derive de frequence laser permet de controler et d'optimiser le transfert de population de l'etat fondamental vers les etats electroniques intermediaires impliques dans le processus d'ionisation. Mots-cles : Atome d'hydrogene Fonctions B-splines Methode non perturbative spectrale Impulsion laser intense et breve Parametre de derive de frequence laser lonisation multiphotonique

Ba, Harouna Sileye

190

IEEE TVCG SUBMISSION DRAFT 1 ParaGlide: Interactive Parameter Space  

E-print Network

, swarms of insects, or schools of fish (see Section 3.2). The input parameters for a model in this domain of British Columbia. · S. Nabi Abdolyousefi did this work at Dept. of Applied Mathematics, SFU. She currently

Möller, Torsten

191

Tensor parameters in Skyrme and Gogny effective interactions: Trends from a ground-state-focused study  

NASA Astrophysics Data System (ADS)

Recent ground-state-focused studies of the tensor effects in the mean-field framework are our starting point. On the basis of phenomenological arguments, we indicate regions for acceptable values of the parameters that are associated with the tensor effective forces within both the Skyrme and the Gogny models. We identify acceptable signs and values of the parameters by making an adjustment on the neutron 1f spin-orbit splitting for the nuclei 40Ca, 48Ca, and 56Ni. The first nucleus is not used to adjust the tensor parameters because it is spin-saturated, but is employed to tune the spin-orbit strength. One of the main conclusions of this work is that some existing Skyrme parametrizations containing the tensor force should not be employed because the wrong sign of the tensor parameters does not lead to the correct behavior (by comparing with the experimental results). This study also allows us to better constrain the tensor parameters in the Gogny case, where much less work is published and boundaries and signs for the parameters have not been analyzed so far.

Grasso, Marcella; Anguiano, Marta

2013-11-01

192

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

PubMed Central

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

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

2014-01-01

193

Thermodynamic parameters of the interaction of Urtica dioica agglutinin with N-acetylglucosamine and its oligomers  

Microsoft Academic Search

The interaction between Urtica dioica agglutinin (UDA) and N-acetylglucosamine (GlcNAc) and its ß(1-4)-linked oligomers was studied by fluorescence titration and isothermal titration microcalorimetry. UDA possesses one significant binding site that can be measured calorimetrically. This site is composed of three subsites, each subsite accommodating one GlcNAc residue. The interaction is enthalpically driven, and the binding area of UDA is characterized

Reiko T. Lee; Hans-Joachim Gabius; Yuan C. Lee

1998-01-01

194

Determination of the Jones Matrix of an LC cell and derivation of the physical parameters of the LC molecules  

NASA Astrophysics Data System (ADS)

The wavelength-dependent Jones matrix representation of a twisted-nematic liquid crystal (TN-LC) cell contains four independent parameters. The absolute values of these parameters and two mutual sign relationships can be determined from comparatively simple transmission measurements of the TN-LC cells sandwiched between two rotatable polarizers. The physical parameters of the cell (twist angle ?, director orientation ?, birefringence ?) can be retrieved if the Jones matrix is known for more than one wavelength. We have measured the Jones matrices of the TN-LC cells of a translucent Sony LCX-016 microdisplay for six wavelengths ranging from 488nm to 1064nm and determined the physical parameters of the cell. We have also measured the Jones matrices for one wavelength for a number of applied voltages. These experimental results show that it is not sufficiently exact to calculate the Jones matrix from the known physical parameters of the cell assuming a voltage-dependent birefringence only. We attribute the deviations from the theoretical model to edge effects which are not taken into account. The direct experimental determination of the Jones matrix components is therefore preferable and permits a more accurate simulation of the TN-LC microdisplay in experimental configurations involving other polarization-dependent optical components.

Hermerschmidt, Andreas; Quiram, Stephanie; Kallmeyer, Frank; Eichler, Hans Joachim

2007-05-01

195

Bose-Einstein condensates with derivative and long-range interactions as set-ups for analog black holes  

NASA Astrophysics Data System (ADS)

General types of Bose-Einstein condensates are considered. The formation of black-hole analogues is examined for both short- and long-range interactions for arbitrary spatial dimensions greater than 2. The former case includes nonlinear derivative terms plus an inevitable external potential, while the latter one consists solely of gravitylike self-interactions for which intrinsic formation of analogue Schwarzschild-type background space-times is possible. The corresponding geometries are studied, and it is shown how they can be made stable. Their Hawking temperature is estimated, and it is found that in certain setups it can be significantly increased, thus providing better detectability.

Kühnel, Florian

2014-10-01

196

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

PubMed Central

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

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

2013-01-01

197

Azimuthally integrated HBT parameters for charged pions in nucleus-nucleus interactions versus collision energy  

E-print Network

In the paper energy dependence of space-time extent of emission region obtained from Bose - Einstein correlations is studied for charged pions in various ion collisions for all experimentally available energies. There is no dramatic change of HBT parameters with increasing of collision energy per nucleon-nucleon pair, $\\sqrt{s_{NN}}$, in domain of energies $\\sqrt{s_{NN}} \\geq 5$ GeV. Energy dependence of estimations for emission duration is almost flat for all energy domain under study within large error bars. Analytic function is suggested for smooth approximation of energy dependence of main HBT parameters. Fit curves demonstrate reasonable agreement with experimental data for most HBT parameters in energy domain $\\sqrt{s_{NN}} \\geq 5$ GeV. Estimations of some observables are obtained for energies of the LHC and FCC project.

V. A. Okorokov

2014-10-14

198

Influence of the order of the constituent basis matrices on the Mueller matrix decomposition-derived polarization parameters in complex turbid media such as biological tissues  

NASA Astrophysics Data System (ADS)

The influence of the multiplication order of the constituent basis matrices on the Mueller matrix decomposition-derived polarization parameters in complex tissue-like turbid media exhibiting simultaneous scattering and polarization effects are investigated. A polarization sensitive Monte Carlo (MC) simulation model was used to generate Mueller matrices from turbid media exhibiting simultaneous linear birefringence, optical activity and multiple scattering effects. Mueller matrix decomposition was performed with different selected multiplication orders of the constituent basis matrices, which were further analyzed to derive quantitative individual polarization medium properties. The results show that for turbid medium having weak diattenuation (differential attenuation of two orthogonal polarization states), the decomposition-derived polarization parameters are independent of the multiplication order. Importantly, the values for the extracted polarization parameters were found to be in excellent agreement with the controlled inputs, showing self-consistency in inverse decomposition analysis and successful decoupling of the individual polarization effects. These results were corroborated further by selected experimental results from phantoms having optical (scattering and polarization) properties similar to those used in the MC model. Results from tissue polarimetry confirm that the magnitude of diattenuation is generally lower compared to other polarization effects, so that the demonstrated self-consistency of the decomposition formalism with respect to the potential ambiguity of ordering of the constituent matrices should hold in biological applications.

Ghosh, Nirmalya; Wood, Michael F. G.; Vitkin, I. Alex

2010-03-01

199

Nondimensional Parameters Derived by Using Damage Tensor and Their Implications for Secondary Faulting Pattern and Branch Orientation  

NASA Astrophysics Data System (ADS)

Two nondimensional parameters associated with microcrack (damage) evolution are found to govern secondary faulting behaviors such as branch orientation. Damage tensor D and energy release rate tensor Y for damage evolution are employed here and such nondimensional parameters consist of three material parameters appearing in the framework, eta2, eta4 and Yc. The parameter eta2 represents the effect of damage amount on a constitutive relationship, while the parameter eta4 represents the effect of damage orientation on a constitutive relationship. The parameter Yc is the material yielding criterion; if an eigenvalue of Y exceeds this value, material yielding is assumed to occur. The first nondimensional parameter gamma=eta4/eta2 determines how the microcrack distribution deviates from the isotropic one, which is based on physical interpretations of the parameters eta2 and eta4. The second nondimensional parameter C is defined as C= -Yc/(eta2+eta4), which should be regarded as a nondimensional yielding criterion (eta2 and eta4 have negative values). We assume a mode III fault embedded in a damage-causing medium. If a nonlinear effect of damage evolution on the medium deformation is relatively small, these two nondimensional parameters are found to govern completely fault rock yielding (secondary faulting) behavior associated with dynamic fault tip growth. The parameter C quantitatively determines size of an area where the secondary faulting occurs; larger C produces smaller faulting areas because it becomes harder to satisfy the yielding criterion with larger C. On the other hand, gamma determines qualitative behavior of secondary faulting within such a yielded area; as described below, it governs whether fault rock pulverization or branch development occurs. First, relatively small gamma (much less than unity) values are assumed. Yielding is always isotropic fault rock pulverization in this case because damage occurs in an isotropic way and has no characteristic orientation. The pulverized area pattern obtained here is consistent with some observational studies of natural faults. We then assume relatively large values for gamma (larger than 10). Yielding is always observed as branch development in this case because damage has characteristic orientation; that is, all damages tend to show the same normal orientations. Additionally, branches perpendicular to the main fault plane are found to be expected, which is almost consistent with observations of natural faults by, e.g., Martel and Boger (1998) and Kim et al. (2003; 2004). In simulations performed for the intermediate gamma value (around unity), completely pulverized area is surrounded by branch development area; that is, both pulverization and branch development can occur simultaneously in a yielded area in this case, which may explain, e.g., combined occurrence of pulverization and branch development documented in Vermilye and Scholz (1998). While this combined secondary faulting is suggested also in Suzuki (2012a), it has now been understood systematically in terms of both gamma and C.

Suzuki, T.

2012-12-01

200

Establishing Dependences between Different Lipophilic Parameters of New Potentially Biologically Active N-Substituted-2-Phenylacetamide Derivatives by Applying Multivariate Methods.  

PubMed

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

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

2015-02-01

201

Self-Assembly of Pyridine-Modified Lipoic Acid Derivatives on Gold and Their Interaction with Thyroxine (T4)  

PubMed Central

Pyridyl derivatives of lipoic acid were prepared as ligands for the study of the interaction with thyroxine (T4). Thin self-assembled films of the ligands were prepared in 70% ethanol on gold and their interaction with T4 was studied by titration experiments in an aqueous buffer solution using Surface Plasmon Resonance (SPR). The thickness and refractive index of the ligand layers were calculated from SPR spectra recorded in two media, also allowing for surface coverage and the density of the layers to be estimated. Two ligands, a 4-pyridyl and a bis(2-hydroxyethyl) derivative of lipoic acid, were selected to investigate the feasibility for producing molecularly imprinted self-assembled layers on gold for T4. The methodology was to co-assemble T4 and the ligand onto the gold surface, elute the T4 from the layer under alkaline conditions, and study the rebinding of T4 to the layer. Multiple elution/rebinding cycles were conducted in different buffer solutions, and rebinding of T4 could be observed, with a moderate binding affinity that depended greatly on the solvent used. More optimal binding was observed in HBS buffer, and the affinity of the interaction could be slightly increased when the 4-pyridyl and bis(2-hydroxy-ethyl) derivatives of lipoic acid were combined in the imprinted layer. PMID:23389045

Albers, Willem M.; Milani, Roberto; Tappura, Kirsi; Munter, Tony; Resnati, Giuseppe; Metrangolo, Pierangelo

2013-01-01

202

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

NASA Technical Reports Server (NTRS)

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

Frederking, T. H. K.

1989-01-01

203

Learning Image-Specific Parameters for Interactive Segmentation Zhanghui Kuang1  

E-print Network

approximation scheme and the cutting plane method. Experimental results show that our method, by learning image, image synthesis, and visual effects for film making. Unfortunately, no fully automat- ic system has been support vector machines. Typically, the following assump- tions are made in learning the parameters: i

Wong, Kenneth K.Y.

204

Derivation of transfer parameters for use within the ERICA Tool and the default concentration ratios for terrestrial biota.  

PubMed

An ability to predict radionuclide activity concentrations in biota is a requirement of any method assessing the exposure of biota to ionising radiation. Within the ERICA Tool fresh weight whole-body activity concentrations in organisms are estimated using concentration ratios (the ratio of the activity concentration in the organism to the activity concentration in an environmental media). This paper describes the methodology used to derive the default terrestrial ecosystem concentration ratio database available within the ERICA Tool and provides details of the provenance of each value for terrestrial reference organisms. As the ERICA Tool considers 13 terrestrial reference organisms and the radioisotopes of 31 elements, a total of 403 concentration ratios were required for terrestrial reference organisms. Of these, 129 could be derived from literature review. The approaches taken for selecting the remaining values are described. These included, for example, assuming values for similar reference organisms and/or biogeochemically similar elements, and various simple modelling approaches. PMID:18406022

Beresford, N A; Barnett, C L; Howard, B J; Scott, W A; Brown, J E; Copplestone, D

2008-09-01

205

Neutral winds derived from IRI parameters and from the HWM87 wind model for the sundial campaign of September, 1986  

SciTech Connect

Meridional neutral winds derived from the height of the maximum ionization of the F2 layer are compared with values from results of the HWM87 empirical neutral wind model. The time period considered is the SUNDIAL-2 campaign, 21 Sept. through 5 Oct. 1986. Winds were derived from measurements by a global network of ionosondes, as well as from similar quantities generated by the International Reference Ionosphere. Global wind patterns from the three sources are similar. Differences tend to be the result of local or transient phenomena that are either too rapid to be described by the order of harmonics of the empirical models, or are the result of temporal changes not reproduced by models based on average conditions.

Miller, K.L.; Hedin, A.E.; Wilkinson, P.J.; Torr, D.G.; Richards, P.G.

1990-01-01

206

Neutral winds derived from IRI parameters and from the HWM87 wind model for the SUNDIAL campaign of September, 1986  

NASA Technical Reports Server (NTRS)

Meridional neutral winds derived from the height of the maximum ionization of the F2-layer are compared with values from results of the HWM87 empirical neutral wind model. The time period considered in this study is the SUNDIAL-2 campaign, September 21 through October 5, 1986. Winds have been derived from measurements by a global network of ionosondes, as well as from similar quantities generated by the International Reference Ionosphere. Global wind patterns from the three sources are similar. Differences tend to be the result of local or transient phenomena that are either too rapid to be described by the order of harmonics of the empirical models, or are the result of temporal changes not reproduced by models based on average conditions.

Miller, K. L.; Hedin, A. E.; Wilkinson, P. J.; Torr, D. G.; Richards, P. G.

1990-01-01

207

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

PubMed Central

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

Brito, Paula M.; Antunes, Fernando

2014-01-01

208

Mathematical model relating uniaxial compressive behavior of manufactured sand mortar to MIP-derived pore structure parameters.  

PubMed

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

Tian, Zhenghong; Bu, Jingwu

2014-01-01

209

A study of hydrogen bond of imidazole and its 4-nitro derivative by ab initio and DFT calculated NQR parameters  

NASA Astrophysics Data System (ADS)

Nuclear quadrupole resonance (NQR) parameters of 14N, 2H of N 2H groups are calculated for imidazole and 4-nitroimidazole using HF and B3LYP methods. These computations are performed on the basis of X-ray and neutron diffraction structural data which are collected at 100, 103, 123 and 293 K temperatures. In order to take into account intermolecular hydrogen bonds and the van der Waals effects, two different sizes of clusters have been considered. Results of calculation have been compared with that of a single molecule in each case. Calculations illustrate that for imidazole and 4-nitroimidazole octameric and trimeric clusters, respectively, suffice to generate results which are compatible with experimental data. Our calculated NQR parameters and X-ray data show no significant structural change for 4-nitroimidazole at 293 and 100 K.

Amini, S. K.; Hadipour, N. L.; Elmi, F.

2004-06-01

210

Two-loop correction to weak-interaction parameters due to a heavy fermion doublet  

Microsoft Academic Search

The two-loop corrections to the varrho-parameter and the vector boson mass-shifts due to a heavy fermion doublet were calculated. For very heavy (~ TeV) quarks we find improved limits on the allowed mass difference within a doublet. The limit on the top quark mass (300 GeV) is unaffected. For a degenerate doublet there is a Higgs mass dependent limit on

J. J. van der Bij; F. Hoogeveen

1987-01-01

211

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

NASA Astrophysics Data System (ADS)

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.

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

2014-08-01

212

Analytic derivative couplings for spin-flip configuration interaction singles and spin-flip time-dependent density functional theory.  

PubMed

We revisit the calculation of analytic derivative couplings for configuration interaction singles (CIS), and derive and implement these couplings for its spin-flip variant for the first time. Our algorithm is closely related to the CIS analytic energy gradient algorithm and should be straightforward to implement in any quantum chemistry code that has CIS analytic energy gradients. The additional cost of evaluating the derivative couplings is small in comparison to the cost of evaluating the gradients for the two electronic states in question. Incorporation of an exchange-correlation term provides an ad hoc extension of this formalism to time-dependent density functional theory within the Tamm-Dancoff approximation, without the need to invoke quadratic response theory or evaluate third derivatives of the exchange-correlation functional. Application to several different conical intersections in ethylene demonstrates that minimum-energy crossing points along conical seams can be located at substantially reduced cost when analytic derivative couplings are employed, as compared to use of a branching-plane updating algorithm that does not require these couplings. Application to H3 near its D(3h) geometry demonstrates that correct topology is obtained in the vicinity of a conical intersection involving a degenerate ground state. PMID:25134548

Zhang, Xing; Herbert, John M

2014-08-14

213

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

PubMed Central

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

2011-01-01

214

Relationship between lipophilicities of 1,4-dihydropyridine derivatives and pharmacokinetic interaction strengths with grapefruit juice.  

PubMed

It is well known fact that the strengths of drug interactions with grapefruit juice (GFJ) differ greatly depending on the 1,4-dihydropyridine calcium channel antagonist (DHP) used. However, there are no available data on the relationship between interactions with GFJ and its physicochemical attributes. Therefore we endeavored to study the correlation between calculated logP values, indicating lipophilicity, from chemical structures of DHPs as well as water diffusion, molecular volume, molecular polarization, molecular density, refractive index, topologic polar surface area, and calculated molar refractivity. Thirteen forms of DHP, amlodipine, azelnidipine, benidipine, cilnidipine, efonidipine, felodipine, manidipine, nicardipine, nifedipine, nimodipine, nisoldipine, nitrendipine, and pranidipine were analyzed due to clinical trials performed with GFJ and these agents. The pharmacokinetic interaction strengths were defined in common logarithmic values of increasing ratios of area under the plasma concentration-time curve (AUC) with GFJ intake compared with controls. Physicochemical properties including three categories of predicted logP values were calculated from the structures of DHPs and their estimated relationship with the interactions. As a result, the logP values indicated significant positive correlations with the interaction strengths. This finding suggests that lipophilicity is an important factor in the strengths of pharmacokinetic interactions of DHPs with GFJ intake. PMID:18176062

Uesawa, Yoshihiro; Mohri, Kiminori

2008-01-01

215

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

SciTech Connect

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

Gormley, R.J.; Link, D.D.; Baltrus, J.P.; Zandhuis, P.H.

2008-01-01

216

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

SciTech Connect

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.

Gormley, R.J.; Link, D.D.; Baltrus, J.P.; Zandhuis, P.H.

2009-01-01

217

Self-assembly of pyrene derivatives on Au(111): substituent effects on intermolecular interactions.  

PubMed

The adsorption behaviour as well as the influence of bromine substituents on the formation of highly-ordered two-dimensional structures of pyrene derivatives on Au(111) are studied by a combination of scanning tunnelling microscopy (STM) and density functional theory (DFT) calculations. PMID:24905327

Pham, Tuan Anh; Song, Fei; Nguyen, Manh-Thuong; Stöhr, Meike

2014-11-25

218

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

SciTech Connect

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.

Nelson, T.A.

1983-12-01

219

Deriving land surface parameters from three different vegetated sites with the ELBARA 1.4-GHz passive microwave radiometer  

NASA Astrophysics Data System (ADS)

A methodology was recently developed to estimate the land surface parameters soil moisture, soil temperature and vegetation optical depth on a global scale by using passive microwave remote sensing. This methodology is general, in a way that it does not require any field observations of soil moisture or canopy biophysical properties for calibration purposes, and can be used with microwave observations at different wavelengths. However, several algorithms in this approach are somewhat empirical, and the vegetation component in this methodology is still difficult to understand and interpret. A follow up field experiment was planned for April 2003 to address some of these issues. The experiment was conducted at a controlled meteorological field site in Wageningen (The Netherlands). Three different plots, a bare soil, a soil with short grass (reference site), and a site with growing grass vegetation were selected. Several hydro-meteorological parameters were monitored extensively at each site, including the radiobrightness temperatures from the ELBARA 1.4 GHz passive microwave radiometer. This paper gives a description of this field experiment and will demonstrate several effects of vegetation on the radiobrightness temperature.

De Jeu, Richard A. M.; Holmes, Thomas; Owe, Manfred

2004-02-01

220

Effect of Biologically Active Substances Derived from Hydrobionts of the Pacific Ocean on Parameters of Lipid Metabolism during Experimental Hypercholesterolemia.  

PubMed

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

Kuznetsova, T A; Kryzhanovskii, S P; Bogdanovich, L N; Besednova, N N

2014-12-01

221

Triazole-linked phenyl derivatives: redox mechanisms and in situ electrochemical evaluation of interaction with dsDNA.  

PubMed

The redox mechanism of two trisubstituted triazole-linked phenyl derivatives (CL41 and CL42) and a disubstituted triazole-linked phenyl derivative (CL2r50) were studied using cyclic, differential pulse and square wave voltammetry at a glassy carbon electrode. The CL41, CL42 and CL2r50 oxidation is a complex, pH-dependent irreversible process involving the formation of electroactive products that undergo two consecutive reversible oxidation reactions. The DNA interaction with CL41, CL42 and CL2r50 was investigated by differential pulse voltammetry using the dsDNA-electrochemical biosensor and in DNA/trisubstituted triazole incubated solutions. All three trisubstituted triazole-linked phenyl derivatives interacted with dsDNA causing morphological and oxidative damage to the dsDNA structure in a time-dependent manner. The DNA-electrochemical biosensor enabled the detection of oxidative damage to DNA following the occurrence of the 8-oxoGua and/or 2,8-oxoAde oxidation peaks. PMID:25194950

Pontinha, A Dora R; Lombardo, Caterina M; Neidle, Stephen; Oliveira-Brett, Ana Maria

2015-02-01

222

Frequency-Dependent Selection and the Maintenance of Genetic Variation: Exploring the Parameter Space of the Multiallelic Pairwise Interaction Model  

PubMed Central

When individuals' fitnesses depend on the genetic composition of the population in which they are found, selection is then frequency dependent. Frequency-dependent selection (FDS) is often invoked as a heuristic explanation for the maintenance of large numbers of alleles at a locus. The pairwise interaction model is a general model of FDS via intraspecific competition at the genotypic level. Here we use a parameter-space approach to investigate the full potential for the maintenance of multiallelic equilibria under the pairwise interaction model. We find that FDS maintains full polymorphism more often than classic constant-selection models and produces more skewed equilibrium allele frequencies. Fitness sets with some degree of rare advantage maintained full polymorphism most often, but a wide variety of nonobvious fitness patterns were also found to have positive potential for polymorphism. An example is put forth suggesting possible explanations for multiallelic polymorphisms maintained despite positive FDS on individual alleles. PMID:17483410

Trotter, Meredith V.; Spencer, Hamish G.

2007-01-01

223

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

NASA Astrophysics Data System (ADS)

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

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

224

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

PubMed Central

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

Forchheimer, Daniel; Haviland, David B

2014-01-01

225

Derivation of the Interacting Boson Model from mean-field theory  

NASA Astrophysics Data System (ADS)

A Hamiltonian of the interacting boson model (IBM) is determined from the mean- eld theory with nuclear energy density functionals (EDFs). The multinucleon dynamics of the surface deformation is simulated in terms of the boson degrees of freedom. The interaction strengths of the IBM Hamiltonian are determined so that the potential energy surfaces (PESs) of a given EDF with quadrupole degrees of freedom is compared with the corresponding PES of IBM. A fermion-to-boson mapping for a rotational nucleus is discussed. Some examples resulting from the present spectroscopic calculations are shown for neutron-rich Pt, Os and W isotopes.

Nomura, Kosuke

2013-09-01

226

Interaction of some thiouracil derivatives with horseradish peroxidase by difference spectroscopy  

NASA Astrophysics Data System (ADS)

Interactions of horseradish peroxidase with propylthiouracil, thiouracil and benzylthiouracil change its absorption spectrum due to perturbation in the region of the heme group of the protein on drug-binding. In the case of propylthiouracil, the interaction might take place near the tryptophan group. In this report, binding of the uracils to the peroxidase was characterized by difference spectroscopy. Propylthiouracil and thiouracil were the most strongly bound of these uracil drugs. The presence of the thiol group in the uracil molecule together with a suitable molecular size seem to be involved in relative strong binding between the enzyme and these compounds.

de Aspuru, Eduardo Ochoa; Lourdes Zatón, Ana M.

1997-07-01

227

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

PubMed

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

Ghahremanpour, Mohammad Mehdi; Sardari, Soroush

2015-03-01

228

Plasma parameters and electromagnetic forces induced by the magneto hydro dynamic interaction in a hypersonic argon flow experiment  

SciTech Connect

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.

Cristofolini, Andrea; Neretti, Gabriele; Borghi, Carlo A. [Department of Electrical Engineering, University of Bologna, Viale Risorgimento 2, 40136 Bologna (Italy)

2012-08-01

229

Direct Interaction between Scaffolding Proteins RACK1 and 14-3-3? Regulates Brain-derived Neurotrophic Factor (BDNF) Transcription*  

PubMed Central

RACK1 is a scaffolding protein that spatially and temporally regulates numerous signaling cascades. We previously found that activation of the cAMP signaling pathway induces the translocation of RACK1 to the nucleus. We further showed that nuclear RACK1 is required to promote the transcription of the brain-derived neurotrophic factor (BDNF). Here, we set out to elucidate the mechanism underlying cAMP-dependent RACK1 nuclear translocation and BDNF transcription. We identified the scaffolding protein 14-3-3? as a direct binding partner of RACK1. Moreover, we found that 14-3-3? was necessary for the cAMP-dependent translocation of RACK1 to the nucleus. We further observed that the disruption of RACK1/14-3-3? interaction with a peptide derived from the RACK1/14-3-3? binding site or shRNA-mediated 14-3-3? knockdown inhibited cAMP induction of BDNF transcription. Together, these data reveal that the function of nuclear RACK1 is mediated through its interaction with 14-3-3?. As RACK1 and 14-3-3? are two multifunctional scaffolding proteins that coordinate a wide variety of signaling events, their interaction is likely to regulate other essential cellular functions. PMID:22069327

Neasta, Jérémie; Kiely, Patrick A.; He, Dao-Yao; Adams, David R.; O'Connor, Rosemary; Ron, Dorit

2012-01-01

230

?-decay and fusion phenomena in heavy ion collisions using nucleon-nucleon interactions derived from relativistic mean-field theory  

NASA Astrophysics Data System (ADS)

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.) ?-decay and low-energy fusion reactions. In this paper, using PCM, we deduce empirically the ? preformation probability P0?(emp) from experimental data on a few g.s. ? decays in the trans-lead region. For fusion reactions, two projectile-target systems C12+Pb208 and O16+Pb208 are selected for calculating the barrier energies as well positions, fusion cross sections (?fus), and fusion barrier distribution [D(Ec.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 ?-decay studies the values of P0?(emp)(R3Y) are similar to those of P0?(emp)(M3Y). Further, both NN interactions give similar ?fus values using the Wong formula specifically when the R3Y NN interaction calculated ?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(Ec.m.) are also quite similar for both choices of NN interaction.

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

2011-06-01

231

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

NASA Astrophysics Data System (ADS)

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

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

2013-06-01

232

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

PubMed Central

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

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

2014-01-01

233

Training and Deriving Precalculus Relations: A Small-Group, Web-Interactive Approach  

ERIC Educational Resources Information Center

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…

McGinty, Jenny; Ninness, Chris; McCuller, Glen; Rumph, Robin; Goodwin, Andrea; Kelso, Ginger; Lopez, Angie; Kelly, Elizabeth

2012-01-01

234

Pseudomonas aeruginosa-Candida albicans Interactions: Localization and Fungal Toxicity of a Phenazine Derivative  

Microsoft Academic Search

Phenazines are redox-active small molecules that play significant roles in the interactions between pseudo- monads and diverse eukaryotes, including fungi. When Pseudomonas aeruginosa and Candida albicans were cocultured on solid medium, a red pigmentation developed that was dependent on P. aeruginosa phenazine biosynthetic genes. Through a genetic screen in combination with biochemical experiments, it was found that a P. aeruginosa-produced

Jane Gibson; Arpana Sood; Deborah A. Hogan

2009-01-01

235

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

E-print Network

Modeling host interactions with hepatitis B virus using primary and induced pluripotent stem cell and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065; b of Hepatitis C, Weill Cornell Medical College, New York, NY 10065; and f Broad Institute of MIT and Harvard

Bhatia, Sangeeta

236

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

NASA Astrophysics Data System (ADS)

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.

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

2013-09-01

237

Formation of intermolecular crosslinks by the actinocin derivatives with DNA in interaction under conditions of semidilute solution  

NASA Astrophysics Data System (ADS)

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.

Osinnikova, D. N.; Moroshkina, E. B.

2014-12-01

238

Investigating the interaction of McN-A-343 with the M 2 muscarinic receptor using its nitrogen mustard derivative  

Microsoft Academic Search

We investigated whether the aziridinium ion formed from a nitrogen mustard derivative (4-[(2-bromoethyl)methyl-amino]-2-butynyl N-(3-chlorophenyl)carbamate; BR384) structurally related to McN-A-343 (4-(trimethyl-amino)-2-butynyl N-(3-chlorophenyl)carbamate) interacts allosterically or orthosterically with the M2 muscarinic receptor. Chinese hamster ovary cells expressing the human M2 muscarinic receptor were incubated with the aziridinium ion of BR384 in combination with McN-A-343 or other known orthosteric and allosteric ligands for

Hinako Suga; Frederick J. Ehlert

2010-01-01

239

Synergy between optical and microwave remote sensing to derive soil and vegetation parameters from MAC Europe 1991 Experiment  

NASA Technical Reports Server (NTRS)

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.

Taconet, O.; Benallegue, M.; Vidal, A.; Vidal-Madjar, D.; Prevot, L.; Normand, M.

1993-01-01

240

Interacting holographic dark energy with variable deceleration parameter and accreting black holes in Bianchi type-V universe  

NASA Astrophysics Data System (ADS)

In this paper, we have considered the spatially homogeneous and anisotropic Bianchi type-V space time filled with two interacting fluids; dark matter and a hypothetical isotropic fluid as the holographic dark energy components. To obtain an exact solution of the Einstein's field equations, we used the assumption of time dependent deceleration parameter. We have investigated geometric and kinematic properties of the model. It is observed that the anisotropy parameter of the universe approaches to zero and the universe achieve flatness for large cosmic time. We have shown that this expanding solution is stable against the perturbation with respect to anisotropic spatial directions. We have also studied the evolution of the mass of a black hole embedded in a universe which interacts with a combination of dark matter and dark energy, considering that in the vicinity of the black hole the metric is of Schwarzschild type. We found that the black hole mass increases with the evolution of the universe, and on later epochs the increase in mass stops as dark energy accretion takes over. The results are found to be consistent with recent cosmological observations.

Sarkar, Sanjay

2014-07-01

241

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

NASA Astrophysics Data System (ADS)

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/?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 En?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.

Fujiwara, Y.; Fukukawa, K.

2010-05-01

242

Repeated forced swimming impairs prepulse inhibition and alters brain-derived neurotrophic factor and astroglial parameters in rats.  

PubMed

Glutamate perturbations and altered neurotrophin levels have been strongly associated with the neurobiology of neuropsychiatric disorders. Environmental stress is a risk factor for mood disorders, disrupting glutamatergic activity in astrocytes in addition to cognitive behaviours. Despite the negative impact of stress-induced neuropsychiatric disorders on public health, the molecular mechanisms underlying the response of the brain to stress has yet to be fully elucidated. Exposure to repeated swimming has proven useful for evaluating the loss of cognitive function after pharmacological and behavioural interventions, but its effect on glutamate function has yet to be fully explored. In the present study, rats previously exposed to repeated forced swimming were evaluated using the novel object recognition test, object location test and prepulse inhibition (PPI) test. In addition, quantification of brain-derived neurotrophic factor (BDNF) mRNA expression and protein levels, glutamate uptake, glutathione, S100B, GluN1 subunit of N-methyl-D-aspartate receptor and calmodulin were evaluated in the frontal cortex and hippocampus after various swimming time points. We found that swimming stress selectively impaired PPI but did not affect memory recognition. Swimming stress altered the frontal cortical and hippocampal BDNF expression and the activity of hippocampal astrocytes by reducing hippocampal glutamate uptake and enhancing glutathione content in a time-dependent manner. In conclusion, these data support the assumption that astrocytes may regulate the activity of brain structures related to cognition in a manner that alters complex behaviours. Moreover, they provide new insight regarding the dynamics immediately after an aversive experience, such as after behavioural despair induction, and suggest that forced swimming can be employed to study altered glutamatergic activity and PPI disruption in rodents. PMID:25444867

Borsoi, Milene; Antonio, Camila Boque; Müller, Liz Girardi; Viana, Alice Fialho; Hertzfeldt, Vivian; Lunardi, Paula Santana; Zanotto, Caroline; Nardin, Patrícia; Ravazzolo, Ana Paula; Rates, Stela Maris Kuze; Gonçalves, Carlos-Alberto

2015-01-01

243

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

E-print Network

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.

Giovanni Noselli; Antonio DeSimone

2014-08-26

244

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

PubMed Central

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

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

2013-01-01

245

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

PubMed

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

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

2015-01-01

246

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

PubMed

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

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

2014-04-01

247

Synthesis and antimitotic and tubulin interaction profiles of novel pinacol derivatives of podophyllotoxins.  

PubMed

Several pinacol derivatives of podophyllotoxins bearing different side chains and functions at C-7 were synthesized through reductive cross-coupling of podophyllotoxone and several aldehydes and ketones. While possessing a hydroxylated chain at C-7, the compounds retained their respective hydroxyl group with either the 7? (podo) or 7? (epipodo) configuration. Along with pinacols, some C-7 alkylidene and C-7 alkyl derivatives were also prepared. Cytotoxicities against neoplastic cells followed by cell cycle arrest and cellular microtubule disruption were evaluated and mechanistically characterized through tubulin polymerization inhibition and assays of binding to the colchicine site. Compounds of the epipodopinacol (7?-OH) series behaved similarly to podophyllotoxin in all the assays and proved to be the most potent inhibitors. Significantly, 7?-isopropyl-7-deoxypodophyllotoxin (20), without any hydroxyl function, appeared as a promising lead compound for a novel type of tubulin polymerization inhibitors. Experimental results were in overall agreement with modeling and docking studies performed on representative compounds of each series. PMID:22607205

Abad, Andrés; López-Pérez, José L; del Olmo, Esther; García-Fernández, Luis F; Francesch, Andrés; Trigili, Chiara; Barasoain, Isabel; Andreu, José M; Díaz, J Fernando; San Feliciano, Arturo

2012-08-01

248

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

NASA Astrophysics Data System (ADS)

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

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

2014-11-01

249

Forecasting the Dst index during corotating interaction region events using synthesized solar wind parameters  

NASA Astrophysics Data System (ADS)

Observations from SOHO, STEREO, and ACE during the declining phase of the solar cycle toward the deep minimum in 2008 are analyzed to establish the timing of corotating interaction region (CIR) activity. This analysis is then employed to synthesize signals of the z component of the interplanetary magnetic field (IMF) Bz, solar wind radial velocity vx, and solar wind proton density Np at 1 AU. The synthesized signals are used as a substitute for ACE measurements to represent solar wind forcing due to coronal hole driven CIR events occurring during multiple Bartel rotations (BR 2381 to BR 2393). The signals drive a low-order physics-based model of the magnetosphere called WINDMI, one of whose outputs is the ground-based measurement of the Dst index. Estimating the arrival of CIR events for future rotations using ACE and SOHO data during BR 2381 produced what we refer to as an uncalibrated yearly forecast. We next generated a video-calibrated estimate of the arrival times of CIR events in addition to information from BR 2381 using SOHO and STEREO images of the Sun in order to produce a simulated 3.5 day ahead forecast of possible geomagnetic activity. The time of arrival of CIR events is taken to be the travel time of density compressions as seen in a noninertial frame according to a radial solar wind speed of 500 km/s and a distance of 1 AU. We were able to forecast the timing of CIR-induced geomagnetic activity to within 12 h for 17 out of 28 events by using the expected recurrence of the events through multiple Bartel rotations together with SOHO and STEREO coronal hole sightings made 3.5 days before every event. The uncertainty in the IMF Bz led to a forecast of levels of geomagnetic activity on an ensemble basis, yielding a distribution of different possible Dst signatures. We used a 10-sample ensemble and a 50-sample ensemble to obtain typical representations of geomagnetic activity. Depending on the periodicity and intensity of fluctuations in Bz, we obtained higher or lower levels of activity and shorter or longer times for the recovery of the Dst to quiet levels.

Andriyas, T.; Spencer, E.; Raj, A.; Sojka, J.; Mays, M. L.

2012-03-01

250

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

SciTech Connect

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.

Lin Nan [Division of Hepatology, Third Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou City 510630, Guangdong Province (China)], E-mail: linnancn@gmail.com; Tang Zhaofeng; Deng Meihai; Zhong Yuesi; Lin Jizong [Division of Hepatology, Third Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou City 510630, Guangdong Province (China); Yang Xuhui; Xiang Peng [Center for Stem Cell Biology and Tissue Engineering, Sun Yat-Sen University, Guangzhou City, Guangdong Province (China); Xu Ruiyun [Division of Hepatology, Third Hospital of Sun Yat-Sen University, Tianhe Road 600, Guangzhou City 510630, Guangdong Province (China)

2008-07-18

251

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

PubMed

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

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

2011-02-01

252

A theoretical investigation of the interaction between substituted carbonyl derivatives and water: open or cyclic complexes?  

PubMed

The structures and binding energies of complexes between substituted carbonyl bases and water are the B3LYP/6-311++G(d,p) computational level. The calculations also include the proton affinity (PA) of the O of the C=O group, the deprotonation enthalpies (DPE) of the CH bonds along a natural bond orbital analysis. The calculations reveal that stable open C=O···H(w) O(w) as well as cyclic CH···O(w)H(w) ···O=C complexes are formed. The binding energies for the open complexes are linearly related to the PAs, whereas the binding energies for the cyclic complexes depend on both the PA and DPE. Different indicators of hydrogen bonds strength such as electron charge density, intramolecular and intermolecular hyperconjugation energy, occupation of orbitals, and charge transfer show significant differences between open and cyclic complexes. The contraction of the CH bond of the formyl group and the corresponding blue shift of the ?(CH) vibration are explained by the classical trans lone pair effect. In contrast, the elongation or contraction of the CH(3) group involved in the interaction with water results from the variation of the orbital interaction energies from the ?(CH) bonding orbital to the ?* and ?* antibonding orbitals of the C=O group. The resulting blue or red shifts of the ?(CH(3)) vibrations are calculated in the partially deuterated isotopomers. PMID:22344933

Chandra, Asit K; Zeegers-Huyskens, Thérèse

2012-04-30

253

Effective interaction parameter of linear/star polymer blends and comparison with that of linear/linear and star/star blends  

E-print Network

Effective interaction parameter of linear/star polymer blends and comparison with that of linear/linear and star/star blends P. E. Theodorakis and A. Avgeropoulos Department of Materials Science and Engineering a detailed study of the microscopic parameters, which control the miscibility in binary linear/star polymer

Theodorakis, Panagiotis E.

254

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

Microsoft Academic Search

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

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

2007-01-01

255

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

PubMed

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

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

2014-09-01

256

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

NASA Astrophysics Data System (ADS)

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

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

2010-04-01

257

Combining intracellular selection with protein-fragment complementation to derive A? interacting peptides.  

PubMed

Aggregation of the ?-amyloid (A?) peptide into toxic oligomers is considered the primary event in the pathogenesis of Alzheimer's disease. Previously generated peptides and mimetics designed to bind to amyloid fibrils have encountered problems in solubility, protease susceptibility and the population of small soluble toxic oligomers. We present a new method that opens the possibility of deriving new amyloid inhibitors. The intracellular protein-fragment complementation assay (PCA) approach uses a semi-rational design approach to generate peptides capable of binding to A?. Peptide libraries are based on A? regions responsible for instigating amyloidosis, with screening and selection occurring entirely inside Escherichia coli. Successfully selected peptides must therefore bind A? and recombine an essential enzyme while permitting bacterial cell survival. No assumptions are made regarding the mechanism of action for selected binders. Biophysical characterisation demonstrates that binding induces a noticeable reduction in amyloid. Therefore, this amyloid-PCA approach may offer a new pathway for the design of effective inhibitors against the formation of amyloid in general. PMID:23708321

Acerra, Nicola; Kad, Neil M; Mason, Jody M

2013-07-01

258

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

PubMed

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

Dvo?ák, Zden?k; Novotná, Aneta; Van?o, Ján; Trávní?ek, Zden?k

2013-12-01

259

Target dependence of clan model parameter in 84 Kr 36 - Emulsion interactions at 1 GeV per nucleon  

NASA Astrophysics Data System (ADS)

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.

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

2014-09-01

260

Drug-delivery study and estimation of polymer-solvent interaction parameter for bisacrylate ester-modified Pluronic hydrogels.  

PubMed

In this study, Pluronic F127 hydrogels were characterised as an injectable system for the controlled release of drugs with variable molecular weights (FITC-Dextran at 70 and 40 kDa). In addition, the polymer-solvent interaction parameter (chi) was successfully estimated. Pluronic hydrogels (10-25 wt.%) were redox cured and their swelling behaviour investigated in PBS (pH 7.45) at 37 degrees C. After swelling to equilibrium, the hydrogels were compressed and the rubber-elasticity theory was applied to evaluate chi. Tensile tests proved the hydrogels were elastic and their chi values ranged between 0.50 and 0.53. The full drug load could be delivered over a period of approximately 15 h suggesting that redox cured Pluronic F127 hydrogels can function as injectable systems for controlled and sustained release of macromolecules. PMID:18550304

Mawad, Damia; Foster, John L J R; Lauto, Antonio

2008-08-01

261

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

PubMed Central

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

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

262

Tensor interaction limit derived from the ?-?-?[over ¯] correlation in trapped 8Li ions.  

PubMed

A measurement of the ?-?-?[over ¯] angular correlation in the Gamow-Teller decay (8)Li?(8)Be(*)+?[over ¯]+?, (8)Be(*)??+? has been performed using ions confined in a linear Paul trap surrounded by silicon detectors. The energy difference spectrum of the ? particles emitted along and opposite the direction of the ? particle is consistent with the standard model prediction and places a limit of 3.1% (95.5% confidence level) on any tensor contribution to the decay. From this result, the amplitude of any tensor component C(T) relative to that of the dominant axial-vector component C(A) of the electroweak interaction is limited to |C(T)/C(A)|<0.18 (95.5% confidence level). This experimental approach is facilitated by several favorable features of the (8)Li ? decay and has different systematic effects than the previous ?-?[over ¯] correlation results for a pure Gamow-Teller transition obtained from studying (6)He ? decay. PMID:23496705

Li, G; Segel, R; Scielzo, N D; Bertone, P F; Buchinger, F; Caldwell, S; Chaudhuri, A; Clark, J A; Crawford, J E; Deibel, C M; Fallis, J; Gulick, S; Gwinner, G; Lascar, D; Levand, A F; Pedretti, M; Savard, G; Sharma, K S; Sternberg, M G; Sun, T; Van Schelt, J; Yee, R M; Zabransky, B J

2013-03-01

263

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

PubMed Central

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

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

2012-01-01

264

Toxicological interactions between the mycotoxins deoxynivalenol, nivalenol and their acetylated derivatives in intestinal epithelial cells.  

PubMed

In case of mycotoxin contaminations, food and feedstuff are usually contaminated by more than one toxin. However toxicological data concerning the effects of mycotoxin combinations are sparse. The intestinal epithelium is the first barrier against food contaminants and this constantly renewing organ is particularly sensitive to mycotoxins. The aim of this study was to investigate the effects of deoxynivalenol (DON) and four other type B trichothecenes (TCTB), 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON), nivalenol (NIV) and fusarenon-X (FX) alone or in combination on intestinal epithelial cells. Proliferating, non-transformed IPEC-1 cells were exposed to increasing doses of TCTB, alone or in binary mixtures and mycotoxin-induced cytotoxicity was measured with MTT test. The toxicological interactions were assessed using the isobologram-Combination index method. The five tested mycotoxins and their mixtures had a dose-dependent effect on the proliferating enterocytes. DON-NIV, DON-15-ADON and 15-ADON-3-ADON combinations were synergistic, with magnitude of synergy for 10 % cytotoxicity ranging from 2 to 7. The association between DON and 3-ADON also demonstrated a synergy but only at high doses, at lower doses antagonism was noted. Additivity was observed between NIV and FX, and antagonism between DON and FX. These results indicate that the simultaneous presence of mycotoxins in food commodities and diet may be more toxic than predicted from the mycotoxins alone. This synergy should be taken into account considering the frequent co-occurrence of TCTB in the diet. PMID:25033990

Alassane-Kpembi, Imourana; Puel, Olivier; Oswald, Isabelle P

2014-07-18

265

Interactions between rod-like cellulose nanocrystals and xylan derivatives: A light scattering study  

NASA Astrophysics Data System (ADS)

Interactions between rod-like cellulose nanocrystals and 2-hydroxypropyl-trimethylammonium (HPMA) xylan were investigated by polarized (DLS) and depolarized dynamic light scattering (DDLS). Cellulose nanocrystals were prepared by the controlled hydrolysis of black spruce pulp. Binary rod-like cellulose nanocrystal/water and ternary HPMA xylan/rod-like cellulose nanocrystal/water systems with different concentrations of cellulose nanocrystals were probed. Translational and rotational diffusion coefficients of cellulose nanocrystals in water are (4.8 ± 0.4) x 10-8 cm^2s-1 and (526 ± 20) s-1, respectively, and calculated lengths and diameters for nanocrystals are comparable to those of cellulose whiskers from cotton. At high cellulose nanocrystal concentrations, DDLS studies in ternary systems provide translational and rotational diffusion coefficients. However, at low cellulose nanocrystal concentrations, DDLS studies of ternary systems do not yield rotational diffusion coefficients. This behavior is attributed to bridging between polymer chains that causes non-linear deviation on standard decay rate (?) versus scattering vector magnitude (q^2) plots.

Sim, Jae Hyun; Schwikal, Katrin; Heinze, Thomas; Dong, Shuping; Roman, Maren; Esker, Alan

2009-03-01

266

[Effect of amiloride and its derivative dichlorobenzamil on guinea pig atria: interaction with other inotropic mechanisms].  

PubMed

The inotropic and chronotropic effects of Amiloride (AMI) and Dichloro-benzamil Amiloride (DBC-AMI) were studied on the guinea pig isolated atria, also, the interaction between these drugs and Beta-methyl-Digoxin (BM-DIGO), epinephrine and low extracellular potassium (1 mM). AMI (10(-3) M) has a negative chronotropic and positive inotropic effects, not dependent on the autonomic system. DCB-AMI has a bimodal effect on the contractile force: increases it at low concentrations but causes a decrease at concentrations higher than 10(-6) M. The effect of AMI on the sinus frequency is unchanged by BM-DIGO. AMI (10(-3) M) decreases the inotropic effect of BM-DIGO and increases the toxic concentration of this drug on isolated tissues. The dose-response curve to epinephrine was not changed by AMI. Similar results were obtained using DCB-AMI (2 x 10(-7) M). The positive inotropic effect obtained by low extracellular potassium (1 mM) was not altered by AMI. The activity of the Mg(++)-dependent, Na+/K+ ATPase measured in the microsomal fraction obtained from guinea pig heart was diminished (10%) by AMI (10(-3) M). The drug did not affect the inhibition of the enzyme induced by ouabain. In conclusion, our experiments show multiple effects of AMI and DCB-AMI on the guinea pig heart. The inhibition of the Na+/Ca++ exchange explains them only partially. A slow channel blocking effect appears fundamental to interpret our results. PMID:10513038

Padrón-Nieves, M; Alfonso, C; Lamanna, V; Pérez-González, M

1999-01-01

267

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

268

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

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

Nasel, Christian; Kalcher, Klaudius; Boubela, Roland; Moser, Ewald

2014-01-01

269

Can radiobiological parameters derived from squamous cell carcinoma of the head and neck be used to predict local control in anal cancer treated with chemoradiation?  

PubMed Central

Objectives Parameters have been derived in head and neck cancer to account for the additional biological effective dose provided by synchronous chemotherapy. The purpose of this study was to establish whether such parameters could be used to predict local control differences in anal cancer. Methods In anal cancer two randomised trials of radiotherapy vs chemoradiotherapy and two trials randomising between different synchronous chemotherapy regimens were identified. To predict differences in local control between the arms of the first two studies, a global value of 9.3 Gy for the chemotherapy biologically effective dose was employed. For the last two trials, values specific to differing chemotherapy schedules were derived. These values were added to the calculated biological effective dose for the radiotherapy component in order to predict local control outcomes in anal cancer trials. Results The predicted difference in local control using the global value of 9.3 Gy for the addition of synchronous chemotherapy in the trials of radiotherapy vs radiotherapy and synchronous chemotherapy was 24.6% compared with the observed difference of 21.4%. Using schedule-specific values for the contribution of chemotherapy, the predicted differences in local control in the two trials of differing synchronous chemotherapy schedules were 7.2% and 12% compared with the observed 18% and 0%. Conclusion The methods initially proposed require modification to result in adequate prediction. If the decreased cisplatin dose intensity employed in anal cancer is modelled, more satisfactory predictions for such trials can be achieved. Advances in knowledge This revised modelling may be hypothesis generating. PMID:23239699

Pettit, L; Meade, S; Sanghera, P; Glaholm, J; Geh, J I; Hartley, A

2013-01-01

270

Aromatic interactions in asymmetric catalysis: control of enantioselectivity in Diels-Alder reactions catalysed by camphor-derived hydrazides.  

PubMed

Density functional theory calculations (M06-2X//B3LYP) have been performed to determine the factors responsible for enantioselectivity in Diels–Alder reactions catalysed by two series of camphor-derived amines. Hydrazides 2 and sulfonylhydrazides 3 catalyze the reaction of cyclopentadiene with cinnamaldehyde to give the same enantiomer of cycloadduct. The calculations reveal that the two classes of catalysts control enantioselectivity by opposite mechanisms. Hydrazides 2 favour addition to the bottom face of a trans iminium cation, while sulfonylhydrazides 3 favour addition to the top face of a cis iminium ion. In the transition state for cycloadditions catalysed by 2, a stabilising CH–? interaction between the diene and a benzyl substituent ? to the iminium nitrogen accelerates the reaction and enhances the enantioselectivity. The facial selectivity can be reinforced by appending onto the benzyl side-arm an ?-methyl group that sterically hinders addition to the top face. PMID:23800726

Krenske, Elizabeth H

2013-08-28

271

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

PubMed Central

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

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

272

Interactions of Fullerene (C60) and its Hydroxyl Derivatives with Lipid Bilayer: A Coarse-Grained Molecular Dynamics Simulation  

NASA Astrophysics Data System (ADS)

Coarse-grained molecular dynamic simulations were employed to study the interactions of fullerene (C60) and its hydroxyl derivatives (C60(OH)n, n = 4, 5, 6, 8, 12, and 16) with a lipid bilayer composed of dipalmitoylphosphatidylcholine molecules. It was found that the C60 moves towards the center of the bilayer and laid between central and peripheral regions of the bilayer. The potential mean force was calculated to estimate free energy profile when pulling the fullerene from its initial position to the center of the bilayer using an umbrella sampling method. Results showed that the hydrophobic region of the membrane acts as a barrier to transport a nonpolar C60 molecule through the bilayer. This makes a deep minimum in the free energy profile between the center and head regions of membrane. Various numbers of polar functional groups (-OH) were then used to make derivatives of fullerene and change the hydrophilic of the molecule. It was found that optimal number of hydroxyl groups to facilitate the transportation of C60(OH)n through the bilayer is 4.

Mohammadyani, Dariush; Modarress, Hamid; To, Alber C.; Amani, Amir

2013-12-01

273

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

PubMed

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

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

2015-05-01

274

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method.  

PubMed

Protein-RNA interactions play important roles in many biological processes. Given the high cost and technique difficulties in experimental methods, computationally predicting the binding complexes from individual protein and RNA structures is pressingly needed, in which a reliable scoring function is one of the critical components. Here, we have developed a knowledge-based scoring function, referred to as ITScore-PR, for protein-RNA binding mode prediction by using a statistical mechanics-based iterative method. The pairwise distance-dependent atomic interaction potentials of ITScore-PR were derived from experimentally determined protein-RNA complex structures. For validation, we have compared ITScore-PR with 10 other scoring methods on four diverse test sets. For bound docking, ITScore-PR achieved a success rate of up to 86% if the top prediction was considered and up to 94% if the top 10 predictions were considered, respectively. For truly unbound docking, the respective success rates of ITScore-PR were up to 24 and 46%. ITScore-PR can be used stand-alone or easily implemented in other docking programs for protein-RNA recognition. PMID:24476917

Huang, Sheng-You; Zou, Xiaoqin

2014-04-01

275

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

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.

Perkins, S.T.; Cullen, D.E. (Lawrence Livermore National Lab., CA (United States)); Seltzer, S.M. (National Inst. of Standards and Technology (NML), Gaithersburg, MD (United States). Center for Radiation Research)

1991-11-12

276

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

NASA Astrophysics Data System (ADS)

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

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

2014-09-01

277

Detection of ‘best’ positive end-expiratory pressure derived from electrical impedance tomography parameters during a decremental positive end-expiratory pressure trial  

PubMed Central

Introduction This study compares different parameters derived from electrical impedance tomography (EIT) data to define ‘best’ positive end-expiratory pressure (PEEP) during a decremental PEEP trial in mechanically-ventilated patients. ‘Best’ PEEP is regarded as minimal lung collapse and overdistention in order to prevent ventilator-induced lung injury. Methods A decremental PEEP trial (from 15 to 0 cm H2O PEEP in 4 steps) was performed in 12 post-cardiac surgery patients on the ICU. At each PEEP step, EIT measurements were performed and from this data the following were calculated: tidal impedance variation (TIV), regional compliance, ventilation surface area (VSA), center of ventilation (COV), regional ventilation delay (RVD index), global inhomogeneity (GI index), and intratidal gas distribution. From the latter parameter we developed the ITV index as a new homogeneity parameter. The EIT parameters were compared with dynamic compliance and the PaO2/FiO2 ratio. Results Dynamic compliance and the PaO2/FiO2 ratio had the highest value at 10 and 15 cm H2O PEEP, respectively. TIV, regional compliance and VSA had a maximum value at 5 cm H2O PEEP for the non-dependent lung region and a maximal value at 15 cm H2O PEEP for the dependent lung region. GI index showed the lowest value at 10 cm H2O PEEP, whereas for COV and the RVD index this was at 15 cm H2O PEEP. The intratidal gas distribution showed an equal contribution of both lung regions at a specific PEEP level in each patient. Conclusion In post-cardiac surgery patients, the ITV index was comparable with dynamic compliance to indicate ‘best’ PEEP. The ITV index can visualize the PEEP level at which ventilation of the non-dependent region is diminished, indicating overdistention. Additional studies should test whether application of this specific PEEP level leads to better outcome and also confirm these results in patients with acute respiratory distress syndrome. PMID:24887391

2014-01-01

278

Synergistic interaction of NaCl and Cd on growth and photosynthetic parameters in soybean genotypes differing in salinity tolerance.  

PubMed

The effects of salinity (50 mmol/L NaCl) and Cd (1 micromol/L CdCl(2)) as sole and combined on growth and photosynthetic parameters were studied using two soybean genotypes, Huachun 18 and NGB. The concentrations of Cd(2+), Zn(2+), Ca(2+), Mg(2+), K(+) and Na(+) were also determined in seeds and pods. Huachun 18 suffered a more serious decrease than NGB in net photosynthetic rate (P(n)) in the treatments of salinity stress alone and combined stress (NaCl+Cd), showing that it is relatively sensitive to salinity. The decrease in P(n) caused by salt stress in Huachun 18 was mainly due to the reduced total chlorophyll content and photosynthetic efficiency (the ratio of variable fluorescence to maximal fluorescence, F(v)/F(m)), whereas the decease in NGB was mainly related to reduced stomatal conductance (G(s)). The combined stress of both Na and Cd did not induce further decrease in photosynthesis and fluorescence in the two genotypes relative to salt or Cd stress alone. Greater change in the pod concentrations of Zn(2+), Ca(2+), Mg(2+), K(+) and Na(+) was detected under salt stress for Huachun 18 than for NGB. The results suggested that the interactive effect of NaCl-Cd on growth and nutrient uptake differs between the two soybean genotypes. PMID:17444602

Wei, Kang; Shamsi, Imran Haider; Zhang, Guo-ping

2007-04-01

279

Synergistic interaction of NaCl and Cd on growth and photosynthetic parameters in soybean genotypes differing in salinity tolerance*  

PubMed Central

The effects of salinity (50 mmol/L NaCl) and Cd (1 ?mol/L CdCl2) as sole and combined on growth and photosynthetic parameters were studied using two soybean genotypes, Huachun 18 and NGB. The concentrations of Cd2+, Zn2+, Ca2+, Mg2+, K+ and Na+ were also determined in seeds and pods. Huachun 18 suffered a more serious decrease than NGB in net photosynthetic rate (P n) in the treatments of salinity stress alone and combined stress (NaCl+Cd), showing that it is relatively sensitive to salinity. The decrease in P n caused by salt stress in Huachun 18 was mainly due to the reduced total chlorophyll content and photosynthetic efficiency (the ratio of variable fluorescence to maximal fluorescence, F v/F m), whereas the decease in NGB was mainly related to reduced stomatal conductance (G s). The combined stress of both Na and Cd did not induce further decrease in photosynthesis and fluorescence in the two genotypes relative to salt or Cd stress alone. Greater change in the pod concentrations of Zn2+, Ca2+, Mg2+, K+ and Na+ was detected under salt stress for Huachun 18 than for NGB. The results suggested that the interactive effect of NaCl-Cd on growth and nutrient uptake differs between the two soybean genotypes. PMID:17444602

Wei, Kang; Shamsi, Imran Haider; Zhang, Guo-ping

2007-01-01

280

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)

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.

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

2014-09-01

281

A quantitative uncertainty assessment of eruptive parameters derived from tephra deposits: the example of two large eruptions of Cotopaxi volcano, Ecuador  

NASA Astrophysics Data System (ADS)

Physical parameters of explosive eruptions are typically derived from tephra deposits. However, the characterization of a given eruption relies strongly on the quality of the dataset used, the strategy chosen to obtain and process field data and the particular model considered to derive eruptive parameters. As a result, eruptive parameters are typically affected by a certain level of uncertainty and should not be considered as absolute values. Unfortunately, such uncertainty is difficult to assess because it depends on several factors and propagates from field sampling to the application and interpretation of dispersal models. Characterization of explosive eruptions is made even more difficult when tephra deposits are poorly exposed and only medial data are available. In this paper, we present a quantitative assessment of the uncertainty associated with the characterization of tephra deposits generated by the two largest eruptions of the last 2,000 years of Cotopaxi volcano, Ecuador. In particular, we have investigated the effects of the determination of the maximum clast on the compilation of isopleth maps, and, therefore, on the characterization of plume height. We have also compared the results obtained from the application of different models for the determination of both plume height and erupted volume and for the eruption classification. Finally, we have investigated the uncertainty propagation into the calculation of mass eruption rate and eruption duration. We have found that for our case study, the determination of plume height from isopleth maps is more sensitive to the averaging techniques used to define the maximum clast than to the choice of dispersal models used (i.e. models of Carey and Sparks 1986; Pyle 1989) and that even the application of the same dispersal model can result in plume height discrepancies if different isopleth lines are used (i.e. model of Carey and Sparks 1986). However, the uncertainties associated with the determination of erupted mass, and, as a result, of the eruption duration, are larger than the uncertainties associated with the determination of plume height. Mass eruption rate is also associated with larger uncertainties than the determination of plume height because it is related to the fourth power of plume height. Eruption classification is also affected by data processing. In particular, uncertainties associated with the compilation of isopleth maps affect the eruption classification proposed by Pyle (1989), whereas the VEI classification is affected by the uncertainties resulting from the determination of erupted mass. Finally, we have found that analytical and empirical models should be used together for a more reliable characterization of explosive eruptions. In fact, explosive eruptions would be characterized better by a range of parameters instead of absolute values for erupted mass, plume height, mass eruption rate and eruption duration. A standardization of field sampling would also reduce the uncertainties associated with eruption characterization.

Biass, Sébastien; Bonadonna, Costanza

2011-01-01

282

UP Modelling System for large scale hydrology: deriving large-scale physically-based parameters for the Arkansas-Red River basin  

NASA Astrophysics Data System (ADS)

The UP modelling system has been applied to the 570,000 km2 Arkansas-Red River Basin (ARRB) as part of the UK NERC Terrestrial initiative in Global Environmental Research (TIGER). The model can be run as a stand-alone basin hydrology model or be linked to existing climate and weather forecasting models. It runs on a grid comprising 1923 UP elements, each 17km by 17km in area, and each containing five water storage compartments: one each for the snowpack, vegetation canopy, surface water, root zone and groundwater. All the main transfers and processes of the terrestrial phase of the hydrological cycle are represented, including river network routing of the runoff from the UP elements. The parameters of the ARRB model are physically-based, being derived either from fine-scale, sub-grid, data on the topography and physical properties of the soils, aquifers and vegetation of the basin, or from the results of fine-scale physically-based simulations. With the approach, the parameters account for the effects of sub-grid variations in moisture status and spatial distribution and are sensitive to changes in the fine-scale property data. This sensitivity is either absent or less directly represented in existing large-scale hydrology models, yet it plays a central role in studies of the impact of changes in climate and land-use. The ARRB model, as described here and in Kilsby et al. (1999), is a first attempt at large-scale physically-based hydrological modelling of the type outlined in the "blueprint" for the UP system (Ewen, 1997), and gives a clear, positive, indication of the nature and quality of what is currently practical with the approach.

Ewen, J.; Sloan, W. T.; Kilsby, C. G.; O'Connell, P. E.

283

Effect of tetrahydropyrimidine derivatives on protein-nucleic acids interaction. Type II restriction endonucleases as a model system.  

PubMed

2-Methyl-4-carboxy,5-hydroxy-3,4,5,6-tetrahydropyri- midine (THP(A) or hydroxyectoine) and 2-methyl,4-carboxy-3,4,5, 6-tetrahydropyrimidine (THP(B) or ectoine) are now recognized as ubiquitous bacterial osmoprotectants. To evaluate the impact of tetrahydropyrimidine derivatives (THPs) on protein-DNA interaction and on restriction-modification systems, we have examined their effect on the cleavage of plasmid DNA by 10 type II restriction endonucleases. THP(A) completely arrested the cleavage of plasmid and bacteriophage lambda DNA by EcoRI endonuclease at 0.4 mM and the oligonucleotide (d(CGCGAATTCGCG))2 at about 4.0 mM. THP(B) was 10-fold less effective than THP(A), whereas for betaine and proline, a notable inhibition was observed only at 100 mM. Similar effects of THP(A) were observed for all tested restriction endonucleases, except for SmaI and PvuII, which were inhibited only partially at 50 mM THP(A). No effect of THP(A) on the activity of DNase I, RNase A, and Taq DNA polymerase was noticed. Gel-shift assays showed that THP(A) inhibited the EcoRI-(d(CGCGAATTCGCG))2 complex formation, whereas facilitated diffusion of EcoRI along the DNA was not affected. Methylation of the carboxy group significantly decreased the activity of THPs, suggesting that their zwitterionic character is essential for the inhibition effect. Possible mechanisms of inhibition, the role of THPs in the modulation of the protein-DNA interaction, and the in vivo relevance of the observed phenomena are discussed. PMID:10066745

Malin, G; Iakobashvili, R; Lapidot, A

1999-03-12

284

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)

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.

Walter, Bernadette P.; Heimann, Martin

1999-01-01

285

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

PubMed

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

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

2014-01-01

286

Interactive Effects of Elevated CO2 Concentration and Irrigation on Photosynthetic Parameters and Yield of Maize in Northeast China  

PubMed Central

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

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

2014-01-01

287

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

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.

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

1981-11-11

288

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

PubMed

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

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

2014-11-13

289

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

PubMed

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

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

2014-01-01

290

Interaction of 4-nitroquinoline-1-oxide with indole derivatives and some related biomolecules: a study with magnetic field.  

PubMed

Laser flash photolysis and an external magnetic field have been used for the study of the interaction of 4-nitroquinoline-1-oxide (4NQO) with some indole derivatives, amino acids, tyrosine and tryptophan, and model proteins, lysozyme and bovine serum albumin. In an aprotic medium, photoinduced electron transfer (PET) from indoles to 4NQO is accompanied by proton transfer from the indole moieties irrespective of the substitution at the N-1 position. For 1,2-dimethylindole, however, proton abstraction is hindered possibly due to steric effects. In a protic medium, obviously proton transfer is possible from the medium and is the dominating reaction following PET. The effect of an external magnetic field is very small for all the systems studied. This is attributed to a competition between geminate proton abstraction by the 4NQO radical anion from the partner radical cation and escape of the 4NQO radical anion to the medium followed by proton transfer. The latter process is more predominant, and the former one, which produces a small population of geminate spin-correlated radical pairs, leads to a minor field effect. Another interesting observation is the affinity of 4NQO toward the tryptophan residues in a protein environment. It is seen that PET takes place preferably from the tryptophan residues rather than from the tyrosine residues. PMID:16640444

Dutta Choudhury, Sharmistha; Basu, Samita

2006-05-01

291

New potential antitumoral fluorescent tetracyclic thieno[3,2- b]pyridine derivatives: interaction with DNA and nanosized liposomes  

NASA Astrophysics Data System (ADS)

Fluorescence properties of two new potential antitumoral tetracyclic thieno[3,2- b]pyridine derivatives were studied in solution and in liposomes of DPPC (dipalmitoyl phosphatidylcholine), egg lecithin (phosphatidylcholine from egg yolk; Egg-PC) and DODAB (dioctadecyldimethylammonium bromide). Compound 1, pyrido[2',3':3,2]thieno[4,5- d]pyrido[1,2- a]pyrimidin-6-one, exhibits reasonably high fluorescence quantum yields in all solvents studied (0.20 ? ?F ? 0.30), while for compound 2, 3-[( p-methoxyphenyl)ethynyl]pyrido[2',3':3,2]thieno[4,5- d]pyrido[1,2- a]pyrimidin-6-one, the values are much lower (0.01 ? ?F ? 0.05). The interaction of these compounds with salmon sperm DNA was studied using spectroscopic methods, allowing the determination of intrinsic binding constants, K i = (8.7 ± 0.9) × 103 M-1 for compound 1 and K i = (5.9 ± 0.6) × 103 M-1 for 2, and binding site sizes of n = 11 ± 3 and n = 7 ± 2 base pairs, respectively. Compound 2 is the most intercalative compound in salmon sperm DNA (35%), while for compound 1 only 11% of the molecules are intercalated. Studies of incorporation of both compounds in liposomes of DPPC, Egg-PC and DODAB revealed that compound 2 is mainly located in the hydrophobic region of the lipid bilayer, while compound 1 prefers a hydrated and fluid environment.

Castanheira, Elisabete Ms; Carvalho, Maria Solange D.; Rodrigues, Ana Rita O.; Calhelha, Ricardo C.; Queiroz, Maria-João Rp

2011-05-01

292

Interactions between butterfly-shaped pulses in the inhomogeneous media  

NASA Astrophysics Data System (ADS)

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.

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

2014-10-01

293

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

NASA Astrophysics Data System (ADS)

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

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

2012-05-01

294

Chlorine Isotope Evidence for Syn-Subduction Modification of Serpentinites by Interaction with Sediment-Derived Fluid  

NASA Astrophysics Data System (ADS)

High-pressure serpentinites and rodingites and high- to ultrahigh-pressure metasedimentary rocks from the Aosta region, Italy, preserve strikingly different chlorine isotope compositions that can be used to constrain the nature of fluid-rock interactions during subduction. Serpentinites and rodingitized gabbroic dikes subducted to 70-80 km have bulk ?37Cl values between -1.6 and +0.9‰ (median= -0.5‰, n=26 plus 5 replicates; one amphibole-vein outlier at -2.9‰). Serpentinite ?37Cl values are positively correlated with Cr ± Cl contents (r2= 0.97 and 0.58) and negatively correlated with CaO (r2=0.72). BSE imaging and X-ray mapping reveal up to three generations of compositionally distinct serpentine and chlorite in single samples. The youngest generation, which is most abundant, has the lowest chlorine content. Three rodingite samples contain abundant texturally early fluid inclusions. These samples were finely crushed and leached in 18 M? H2O to extract water-soluble chlorides. The leachates, which are assumed to record the compositions of the fluid inclusions, have ?37Cl values that are 0.7-1.5‰ lower than the corresponding bulk rock values. Leachate from the outlier amph-magnesite vein is indistinguishable from the bulk value at -2.7‰. There is almost no overlap between the Cl isotope compositions of HP serp/rod samples and associated HP/UHP metasedimentary rocks. Calcmica schists, diamond-bearing Mn nodules, and impure marbles subducted to >130 km and calcmica schists and Mn crusts transported to 70-80 km have ?37Cl values between -4.5 and -1.5‰ (median= -2.7‰, n=25 plus 7 replicates; two outlier points at -0.5‰). Primary fluid inclusions in the diamondiferous samples contain carbonate- and silicate-bearing aqueous fluids with very low chloride contents (Frezzotti et al., 2011, Nature Geosci). Taken together, these data record a history of progressive modification of serpentinites and rodingites by mixing with low-?37Cl, low-Cl, high-Ca fluids during subduction and metamorphism. Serpentinites with the highest Cr contents have Cl isotopic compositions identical to those of modern seafloor serpentinites (?37Cl=0.2-0.6‰), consistent with primary serpentinization by seawater (e.g., Barnes et al. 2009, Lithos). Low-Cr serpentinites record significant interaction with a Ca-rich fluid that shifted the rocks to lower ?37Cl values and diluted the original Cr and Cl contents. The fluid was likely derived from continuous devolatilization reactions in associated low-?37Cl, calcareous metasedimentary rocks. These data have important implications for models of subduction mass transfer associated with antigorite breakdown. If serpentinites are commonly modified by interaction with metasedimentary fluids prior to antigorite dehydration, chemical signatures imparted during deserpentinization will reflect the integrated history of fluid-rock interaction in the subduction channel rather than an endmember "serpentinite signature". The data further suggest that Cl may be hydrophobic in HP/UHP carbonate-bearing aqueous fluids, resulting in generation of low-Cl fluid during metamorphic devolatilization.

Selverstone, J.; Sharp, Z. D.

2012-12-01

295

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

PubMed

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

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

2005-12-15

296

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)

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.

Susskind, Joel; Molnar, Gyula I.

2009-01-01

297

Eight salts constructed from 4-phenylthiazol-2-amine and carboxylic acid derivatives through combination of strong hydrogen bonding and weak noncovalent interactions  

NASA Astrophysics Data System (ADS)

Eight crystalline organic salts derived from 4-phenylthiazol-2-amine and carboxylic acid derivatives (2-chloronicotinic acid, 3-hydroxy-2-naphthoic acid, p-nitrobenzoic acid, 2-hydroxy-5-(phenyldiazenyl)benzoic acid, 5-nitrosalicylic acid, 5-sulfosalicylic acid, oxalic acid, and L-malic acid) were prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. In all of the salts except 6, 7, and 8, the 4-phenylthiazol-2-amine and carboxylic acid components are held together by two fused heterosynthons: a R22(7) heterosynthon and a R22(8) heterosynthon. All supramolecular architectures of the organic salts 1-8 involve extensive Nsbnd H⋯O hydrogen bonds as well as other noncovalent interactions. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. The salts displayed 2D/3D framework structure under these weak interactions.

Jin, Shouwen; Zhu, Qiaowang; Wei, ShuaiShuai; Wang, Daqi

2013-10-01

298

The long-lived triplet excited state of an elongated ketoprofen derivative and its interactions with amino acids and nucleosides.  

PubMed

The aim of the present work was to find a ketoprofen (KP) equivalent suitable for time-resolved studies on the interactions of its KP-like triplet state with biomolecules or their simple building blocks, under physiologically relevant conditions. Such a compound should fulfill the following requirements: (i) it should be soluble in aqueous media; (ii) its triplet lifetime should be longer than that of KP, ideally in the microsecond range; and (iii) its photodecarboxylation should be slow enough to avoid interference in the time-resolved studies associated with formation of photoproducts. Here, the glycine derivative of ketoprofen (KPGly) has been found to fulfill all the above requirements. In a first stage, the attention has been focused on the photophysical and photochemical properties of KPGly, and then on its excited-state interactions with key amino acids and nucleosides. In acetonitrile, the typical benzophenone-like triplet-triplet absorption (3KPGly) with lambda(max) at 520 nm and a lifetime of 5.3 micros was observed. This value is very close to that of 3KP (5.6 micros) obtained under the same conditions. In methanol, the 3KPGly features were also close to those of 3KP with detection of a short-lived triplet state that evolves to give a ketyl radical. By contrast with the behavior of KP, in deaerated aqueous solutions at pH = 7.4, the transient detected in the case of KPGly displayed two bands at lambda(max) at 330 and 520 nm, very similar to those observed in acetonitrile solution but with a lifetime of 7.5 micros at 520 nm. Hence, it was assigned to the KPGly triplet. In the case of KP, efficient decarboxylation occurs in the subnanosecond time scale, via intramolecular electron transfer. This process gives rise to a detectable carbanion intermediate (lifetime approximately 250 ns) and prevents detection of the shorter-lived 3KP signal. In a second stage, the attention has been focused on the excited-state interactions between 3KPGly and amino acids or nucleosides; for this purpose, 2'-deoxyguanosine (dGuo), thymidine (Thd), tryptophan (Trp), and tyrosine (Tyr) have been chosen as photosensitization targets. In general, efficient quenching (rate constant kq > 109 M(-1) x s(-1)) was observed; it was attributed for dGuo, Tyr, and Trp to a photochemical reaction involving initial electron transfer from the biological target to 3KPGly, followed by proton transfer from the amino acid or the nucleoside radical cation to KPGly-*. As a matter of fact, ketyl radical together with guanosinyl, tyrosinyl, or tryptophanyl radicals were detected; this supports the proposed mechanism. The results with Thd were somewhat different, as the efficient 3KPGly quenching was ascribed to oxetane formation by a Paterno Büchi photocycloaddition. PMID:17590040

Lhiaubet-Vallet, Virginie; Belmadoui, Noureddine; Climent, Maria J; Miranda, Miguel A

2007-07-19

299

In-situ surface wettability parameters of submerged in brackish water surfaces derived from captive bubble contact angle studies as indicators of surface condition level  

NASA Astrophysics Data System (ADS)

The characterization of wetting properties (by contact angles) of several undersea artificial (glass plates,) and natural (stones, sand layers, soft-bottom structures, aquatic macrophytes, sediments, and seafloor communities) solid substrata in the Baltic Sea brackish water (Gulf of Gdansk). The studies were performed under laboratory and field conditions using a novel captive bubble air-pipette computer microscope system. A set of the surface wettability parameters: the apparent surface free energy ?SV, adhesive layer film pressure ?, work of adhesion WA, and work of spreading WS were determined to quantify the wetting properties of model substrata using the contact angle hysteresis (CAH) approach. The useful technique to measure in situ the contact angle giving reproducible and accurate values of CA turned out to be a captive bubble method, for fully hydrated interfacial layers of highly hydrophilic and porous nature met at seabed (Rodrigues-Valverde et al., 2002). CA measurements revealed mostly hydrophilic nature of the studied solid material (CA < 90°) where the presence of adsorbed organic matter layer or crude oil film covering lead to surface hydrophobization (CA?, ?SV ?,WA?, WS more negative). The adhesion of biofouling was correlated both with CAH and the dispersive interaction term ?SVd of the total ?SV. Monitoring of the artificial substrata of the hydrophilic nature with a CA technique can be used to observe the development of the organisms community i.e., microfouling, and to carry out a comprehensive study of surfaces of the submerged macrophytes (Potamogeton lucens in particular). Since aquatic macrophytes can act as bio-indicators of water chemistry their surface wettability may reflect plant surface erosion and organic matter accumulation state being of particular value in biological assessment of ecosystems status.

Pogorzelski, S. J.; Mazurek, A. Z.; Szczepanska, A.

2013-06-01

300

The effect of specific solvent-solute interactions on complexation of alkali-metal cations by a lower-rim calix[4]arene amide derivative.  

PubMed

Complexation of alkali-metal cations with calix[4]arene secondary-amide derivative, 5,11,17,23-tetra(tert-butyl)-25,26,27,28-tetra(N-hexylcarbamoylmethoxy)calix[4]arene (L), in benzonitrile (PhCN) and methanol (MeOH) was studied by means of microcalorimetry, UV and NMR spectroscopies, and in the solid state by X-ray crystallography. The inclusion of solvent molecules (including acetonitrile, MeCN) in the calixarene hydrophobic cavity was also investigated. The classical molecular dynamics (MD) simulations of the systems studied were carried out. By combining the results obtained using the mentioned experimental and computational techniques, an attempt was made to get an as detailed insight into the complexation reactions as possible. The thermodynamic parameters, that is, equilibrium constants, reaction Gibbs energies, enthalpies, and entropies, of the investigated processes were determined and discussed. The stability constants of the 1:1 (metal:ligand) complexes measured by different methods were in very good agreement. Solution Gibbs energies of the ligand and its complexes with Na(+) and K(+) in methanol and acetonitrile were determined. It was established that from the thermodynamic point of view, apart from cation solvation, the most important reason for the huge difference in the stability of these complexes in the two solvents lay in the fact that the transfer of complex species from MeOH to MeCN was quite favorable. That could be at least partly explained by a more exergonic inclusion of the solvent molecule in the complexed calixarene cone in MeCN as compared to MeOH, which was supported by MD simulations. Molecular and crystal structures of the lithium cation complex of L with the benzonitrile molecule bound in the hydrophobic calixarene cavity were determined by single-crystal X-ray diffraction. As far as we are aware, for the first time the alkali-metal cation was found to be coordinated by the solvent nitrile group in a calixarene adduct. According to the results of MD simulations, the probability of such orientation of the benzonitrile molecule included in the ligand cone was by far the largest in the case of LiL(+) complex. Because of the favorable PhCN-Li(+) interaction, L was proven to have the highest affinity toward the lithium ion in benzonitrile, which was not the case in the other solvents examined (in acetonitrile, sodium complex was the most stable, whereas in methanol, complexation of lithium was not even observed). That could serve as a remarkable example showing the importance of specific solvent-solute interactions in determining the equilibrium in solution. PMID:24144364

Horvat, Gordan; Stilinovi?, Vladimir; Kaitner, Branko; Frkanec, Leo; Tomiši?, Vladislav

2013-11-01

301

The influence of soil organic carbon on interactions between microbial parameters and metal concentrations at a long-term contaminated site.  

PubMed

The effects of lead, zinc, cadmium, arsenic and copper deposits on soil microbial parameters were investigated at a site exposed to contamination for over 200years. Soil samples were collected in triplicates at 121 sites differing in contamination and soil organic carbon (SOC). Microbial biomass, respiration, dehydrogenase activity and metabolic quotient were determined and correlated with total and extractable metal concentrations in soil. The goal was to analyze complex interactions between toxic metals and microbial parameters by assessing the effect of soil organic carbon in the relationships. The effect of SOC was significant in all interactions and changed the correlations between microbial parameters and metal fractions from negative to positive. In some cases, the effect of SOC was combined with that of clay and soil pH. In the final analysis, dehydrogenase activity was negatively correlated to total metal concentrations and acetic acid extractable metals, respiration and metabolic quotient were to ammonium nitrate extractable metals. Dehydrogenase activity was the most sensitive microbial parameter correlating most frequently with contamination. Total and extractable zinc was most often correlated with microbial parameters. The large data set enabled robust explanation of discrepancies in organic matter functioning occurring frequently in analyzing of contaminated soil processes. PMID:25260167

Muhlbachova, G; Sagova-Mareckova, M; Omelka, M; Szakova, J; Tlustos, P

2015-01-01

302

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

SciTech Connect

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.

Berbís, M. Álvaro [Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid (Spain)] [Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid (Spain); André, Sabine [Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539 Munich (Germany)] [Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539 Munich (Germany); Cañada, F. Javier [Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid (Spain)] [Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid (Spain); Pipkorn, Rüdiger [Central Peptide Synthesis Unit, German Cancer Research Center, 69120 Heidelberg (Germany)] [Central Peptide Synthesis Unit, German Cancer Research Center, 69120 Heidelberg (Germany); Ippel, Hans [Department of Biochemistry, CARIM, University of Maastricht, Maastricht (Netherlands) [Department of Biochemistry, CARIM, University of Maastricht, Maastricht (Netherlands); Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Mayo, Kevin H. [Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 (United States)] [Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Kübler, Dieter [Biomolecular Interactions, German Cancer Research Center, 69120 Heidelberg (Germany)] [Biomolecular Interactions, German Cancer Research Center, 69120 Heidelberg (Germany); Gabius, Hans-Joachim [Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539 Munich (Germany)] [Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539 Munich (Germany); Jiménez-Barbero, Jesús, E-mail: jjbarbero@cib.csic.es [Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid (Spain)] [Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid (Spain)

2014-01-03

303

Ethers and esters derived from apocynin avoid the interaction between p47phox and p22phox subunits of NADPH oxidase: evaluation in vitro and in silico  

PubMed Central

NOX (NADPH oxidase) plays an important role during several pathologies because it produces the superoxide anion (O2•?), which reacts with NO (nitric oxide), diminishing its vasodilator effect. Although different isoforms of NOX are expressed in ECs (endothelial cells) of blood vessels, the NOX2 isoform has been considered the principal therapeutic target for vascular diseases because it can be up-regulated by inhibiting the interaction between its p47phox (cytosolic protein) and p22phox (transmembrane protein) subunits. In this research, two ethers, 4-(4-acetyl-2-methoxy-phenoxy)-acetic acid (1) and 4-(4-acetyl-2-methoxy-phenoxy)-butyric acid (2) and two esters, pentanedioic acid mono-(4-acetyl-2-methoxy-phenyl) ester (3) and heptanedioic acid mono-(4-acetyl-2-methoxy-phenyl) ester (4), which are apocynin derivatives were designed, synthesized and evaluated as NOX inhibitors by quantifying O2•? production using EPR (electron paramagnetic resonance) measurements. In addition, the antioxidant activity of apocynin and its derivatives were determined. A docking study was used to identify the interactions between the NOX2?s p47phox subunit and apocynin or its derivatives. The results showed that all of the compounds exhibit inhibitory activity on NOX, being 4 the best derivative. However, neither apocynin nor its derivatives were free radical scavengers. On the other hand, the in silico studies demonstrated that the apocynin and its derivatives were recognized by the polybasic SH3A and SH3B domains, which are regions of p47phox that interact with p22phox. Therefore this experimental and theoretical study suggests that compound 4 could prevent the formation of the complex between p47phox and p22phox without needing to be activated by MPO (myeloperoxidase), this being an advantage over apocynin. PMID:23802190

Macías-Pérez, Martha Edith; Martínez-Ramos, Federico; Padilla-Martínez, Itzia Irene; Correa-Basurto, José; Kispert, Lowell; Mendieta-Wejebe, Jessica Elena; Rosales-Hernández, Martha Cecilia

2013-01-01

304

Comparisons of at sensor radiance estimated with measured size distributions of aerosol and that with size distributions estimated from Junge parameter derived from Angstrome exponent through optical depth measurements  

Microsoft Academic Search

At sensor radiance estimated with measured size distributions of aerosol is compared to that with size distributions estimated from Junge parameter derived from Angstrome exponent through optical depth measurements. Relatively large and heavy areolemeter which allows measurement of direct, aureole and diffuse solar irradiance is required for estimation of size distribution as well as refractive index of aerosol. Therefore, AERONET

Kohei Arai

2010-01-01

305

Features of parameters of gamma-ray families formed from AA-interactions at superhigh energies above 1016 eV  

NASA Astrophysics Data System (ADS)

Different lateral and energetic characteristics of gamma-ray families produced in nucleus-nucleus (AA) interactions of primary cosmic rays (PCR) are studied. Primary mass composition analysis performed on the basis of "Pamir" Collaboration X-ray emulsion chambers (XREC) data by using of selection criteria of gamma-ray families originating from AA-interactions above 10 PeV. Experimental data are compared with results of MC0 algorithm based on quark-gluon string model (QGSM). Among seven considered variables, only two lateral parameters, R1E and ?, are not described by the MC0 model.

Yuldashbaev, T. S.; Nuritdinov, Kh

2013-02-01

306

Membrane Surface-Associated Helices Promote Lipid Interactions and Cellular Uptake of Human Calcitonin-Derived Cell Penetrating Peptides  

PubMed Central

hCT(9-32) is a human calcitonin (hCT)-derived cell-penetrating peptide that has been shown to translocate the plasma membrane of mammalian cells. It has been suggested as a cellular carrier for drugs, green fluorescent protein, and plasmid DNA. Because of its temperature-dependent cellular translocation resulting in punctuated cytoplasmatic distribution, its uptake is likely to follow an endocytic pathway. To gain insight into the molecular orientation of hCT(9-32) when interacting with lipid models, and to learn more about its mode of action, various biophysical techniques from liposome partitioning to high-resolution NMR spectroscopy were utilized. Moreover, to establish the role of individual residues for the topology of its association with the lipid membrane, two mutants of hCT(9-32), i.e., W30-hCT(9-32) and A23-hCT(9-32), were also investigated. Although unstructured in aqueous solution, hCT(9-32) adopted two short helical stretches when bound to dodecylphosphocholine micelles, extending from Thr10 to Asn17 and from Gln24 to Val29. A23-hCT(9-32), in which the helix-breaking Pro23 was replaced by Ala, displayed a continuous ?-helix extending from residue 12 to 26. Probing with the spin label 5-doxylstearate revealed that association with dodecylphosphocholine micelles was such that the helix engaged in parallel orientation to the micelle surface. Moreover, the Gly to Trp exchange in W30-hCT(9-32) resulted in a more stable anchoring of the C-terminal segment close to the interface, as reflected by a twofold increase in the partition coefficient in liposomes. Interestingly, tighter binding to model membranes was associated with an increase in the in vitro uptake in human cervix epithelial andenocarcinoma cell line cells. Liposome leakage studies excluded pore formation, and the punctuated fluorescence pattern of internalized peptide indicated vesicular localization and, in conclusion, strongly suggested an endocytic pathway of translocation. PMID:16183886

Herbig, Michael E.; Weller, Kathrin; Krauss, Ulrike; Beck-Sickinger, Annette G.; Merkle, Hans P.; Zerbe, Oliver

2005-01-01

307

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

SciTech Connect

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.

Huang, Bor-Ren [Department of Neurosurgery, Buddhist Tzu Chi General Hospital, Taichung Branch, Taichung, Taiwan (China); Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan (China); Tsai, Cheng-Fang [Department of Biotechnology, Asia University, Taichung, Taiwan (China); Lin, Hsiao-Yun [Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan (China); Tseng, Wen-Pei [Graduate Institute of Sports and Health, National Changhua University of Education, Changhua County, Taiwan (China); Huang, Shiang-Suo [Department of Pharmacology and Institute of Medicine, College of Medicine, Chung Shan Medical University, Taiwan (China); Wu, Chi-Rei [Graduate Institute of Chinese Pharmaceutical Sciences, College of Pharmacy, China Medical University, Taiwan (China); Lin, Chingju [Department of Physiology, School of Medicine, China Medical University, Taichung, Taiwan (China); Yeh, Wei-Lan [Cancer Research Center, Department of Medical Research, Changhua Christian Hospital, Changhua, Taiwan (China); Lu, Dah-Yuu, E-mail: dahyuu@mail.cmu.edu.tw [Graduate Institute of Neural and Cognitive Sciences, China Medical University, Taichung, Taiwan (China)

2013-05-15

308

Vortex chains due to nonpairwise interactions and field-induced phase transitions between states with different broken symmetry in superconductors with competing order parameters  

NASA Astrophysics Data System (ADS)

We study superconductors with two order components and phase separation driven by intercomponent density-density interaction, focusing on the phase where only one condensate has nonzero ground-state density and a competing order parameter exists only in vortex cores. We demonstrate there that multibody intervortex interactions can be strongly nonpairwise, leading to some unusual vortex patterns in an external field, such as vortex pairs and vortex chains. We demonstrate that in an external magnetic field such a system undergoes a field-driven phase transition from (broken) U (1 ) to (broken) U (1 )×U (1 ) symmetries when a subdominant order parameter in the vortex cores acquires global coherence. Observation of these characteristic ordering patterns in surface probes may signal the presence of a subdominant condensate in the vortex core.

Garaud, Julien; Babaev, Egor

2015-01-01

309

Prediction of time-dependent CYP3A4 drug–drug interactions by physiologically based pharmacokinetic modelling: Impact of inactivation parameters and enzyme turnover  

Microsoft Academic Search

Predicting the magnitude of time-dependent metabolic drug–drug (mDDIs) interactions involving cytochrome P-450 3A4 (CYP3A4) from in vitro data requires accurate knowledge of the inactivation parameters of the inhibitor (KI, kinact) and of the turnover of the enzyme (kdeg) in both the gut and the liver. We have predicted the magnitude of mDDIs observed in 29 in vivo studies involving six

K. Rowland Yeo; R. L. Walsky; M. Jamei; A. Rostami-Hodjegan; G. T. Tucker

2011-01-01

310

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)

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.

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

2011-04-01

311

Interacting generalized ghost polytropic gas model of dark energy with a specific Hubble parameter in LRS Bianchi type-II universe  

NASA Astrophysics Data System (ADS)

We study a spatially homogeneous and anisotropic universe where dark energy interacts with dark matter. To solve the Einstein's field equations, we consider a variation law of Hubble parameter which exhibits a transition of the universe from decelerating phase to the present accelerating phase. It is seen that the model of the universe approaches isotropy under suitable condition and the coincidence parameter is found to be an increasing function of time. We discuss the physical and geometrical properties of the universe which are found to be consistent with recent observation. Moreover, we examine a correspondence between the generalized ghost dark energy and polytropic gas model of dark energy. This correspondence allows us to reconstruct the potential and the dynamics for the scalar field of the polytropic gas which describes the accelerated expansion of the universe. We also investigate the statefinder parameters to characterize different phases of the evolution of the universe.

Rahman, M. Azizur; Ansari, M.

2014-12-01

312

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

E-print Network

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

Toronto, University of

313

Determination of Preferential Interaction Parameters by Multicomponent Diffusion. Applications to Poly(ethylene glycol)-Salt-Water Ternary Mixtures  

E-print Network

interaction coef- ficients have been determined for several protein-osmolyte aqueous solutions.3 These studies compact proteins. Moreover, we observe that the PEG preferential hydration significantly decreases as salt of macromolecules in aqueous solution is perturbed by the presence of osmolytes such as salts and small organic

Annunziata, Onofrio

314

Design and Synthesis of Chalcone Derivatives as Inhibitors of the Ferredoxin - Ferredoxin-NADP+ Reductase Interaction of Plasmodium falciparum: Pursuing New Antimalarial Agents.  

PubMed

Some chalcones have been designed and synthesized using Claisen-Schmidt reactions as inhibitors of the ferredoxin and ferredoxin-NADP+ reductase interaction to pursue a new selective antimalaria agent. The synthesized compounds exhibited inhibition interactions between PfFd-PfFNR in the range of 10.94%-50%. The three strongest inhibition activities were shown by (E)-1-(4-aminophenyl)-3-(4-methoxyphenyl)prop-2-en-1-one (50%), (E)-1-(4-aminophenyl)-3-(2,4-dimethoxyphenyl)prop-2-en-1-one (38.16%), and (E)-1-(4-aminophenyl)-3-(2,3-dimethoxyphenyl)prop-2-en-1-one (31.58%). From the docking experiments we established that the amino group of the methoxyamino chlacone derivatives plays an important role in the inhibition activity by electrostatic interaction through salt bridges and that it forms more stable and better affinity complexes with FNR than with Fd. PMID:25532844

Suwito, Hery; Jumina; Mustofa; Pudjiastuti, Pratiwi; Fanani, Much Zaenal; Kimata-Ariga, Yoko; Katahira, Ritsuko; Kawakami, Toru; Fujiwara, Toshimichi; Hase, Toshiharu; Sirat, Hasnah Mohd; Puspaningsih, Ni Nyoman Tri

2014-01-01

315

Investigation and correlation of physical stability, dissolution behaviour and interaction parameter of amorphous solid dispersions of telmisartan: a drug development perspective.  

PubMed

The aim of this study was to investigate if amorphous solid dispersions of telmisartan, prepared in presence of different polymers, exhibit different structural and thermodynamic characteristics and whether these differences can be correlated to their physical stability (time to crystallisation) and dissolution behaviour. Amorphous samples were prepared by melt quenching. The resulting amorphous materials were characterised using X-ray diffraction, Raman spectroscopy and differential scanning calorimetry. All freshly prepared samples were completely X-ray amorphous (with a halo being the only feature in the diffractograms). The shape of the halos in the diffractograms varied suggesting structural variations in the near order of the molecules between the different amorphous solid dispersions (ASDs). Principal component analysis of the Raman spectra of the various ASD revealed that the samples clustered in the scores plot, again suggesting structural differences due to the presence of different drug-polymer interaction. The ranking of the samples with respect to physical stability and interaction parameter was: ASD of telmisartan:eudragit>ASD of telmisartan:soluplus>ASD of telmisartan:HPMC>ASD of telmisartan:PVP>amorphous telmisartan. The interaction parameter, calculated by using the Flory Huggins theory, showed a good correlation with the experimentally determined stability whereas a weak correlation was found with dissolution behaviour of different ASD. This study showed that correlation of physical stability and dissolution behaviour with calculated interaction parameter is possible for the same amorphous systems prepared by using different polymers. This could aid in selecting the most appropriate polymer for the development of optimised formulations containing amorphous drugs. It can be concluded that ASD prepared by using different polymers have different structural and thermal properties. These differences affect the physical stability and dissolution profiles of the amorphous solids. Thus, choosing the right polymer for preparing ASD is critical for producing materials with desired dissolution profiles and enhanced stability. PMID:23684913

Dukeck, R; Sieger, P; Karmwar, P

2013-07-16

316

An Anilinoquinazoline Derivative Inhibits Tumor Growth through Interaction with hCAP-G2, a Subunit of Condensin II  

PubMed Central

We screened 46 novel anilinoquinazoline derivatives for activity to inhibit proliferation of a panel of human cancer cell lines. Among them, Q15 showed potent in vitro growth-inhibitory activity towards cancer cell lines derived from colorectal cancer, lung cancer and multiple myeloma. It also showed antitumor activity towards multiple myeloma KMS34 tumor xenografts in lcr/scid mice in vivo. Unlike the known anilinoquinazoline derivative gefitinib, Q15 did not inhibit cytokine-mediated intracellular tyrosine phosphorylation. Using our mRNA display technology, we identified hCAP-G2, a subunit of condensin II complex, which is regarded as a key player in mitotic chromosome condensation, as a Q15 binding partner. Immunofluorescence study indicated that Q15 compromises normal segregation of chromosomes, and therefore might induce apoptosis. Thus, our results indicate that hCAP-G2 is a novel therapeutic target for development of drugs active against currently intractable neoplasms. PMID:23028663

Kimura, Hironobu; Genma, Hiroaki; Takashima, Hideaki; Tokunaga, Mayuko; Ono, Takao; Hirano, Tatsuya; Du, Wenlin; Yamada, Taketo; Doi, Nobuhide; Iijima, Shiro; Hattori, Yutaka; Yanagawa, Hiroshi

2012-01-01

317

Interacting effects of diet and environmental temperature on biochemical parameters in the liver of Leuciscus idus melanotus (Cyprinidae: Teleostei)  

Microsoft Academic Search

One year old golden ide (Leuciscus idus melanotus) were starved for 2 weeks at 20°C (time zero) and then they were fed either freeze-dried mosquito larvae (natural diet) or a commercial fish chow (artificial diet) at an ambient temperature of 14°C and 20°C, respectively. Growth parameters and biochemical data in the liver were measured at time zero and after 3

Johannes Rafael I; Thomas Braunbeck

1988-01-01

318

Modulation and Interaction of Immune-Associated Parameters with Antioxidant in the Immunocytes of Crab Scylla paramamosain Challenged with Lipopolysaccharides  

PubMed Central

Invertebrates are dependent on cellular and humoral immune defences against microbial infection. Scylla paramamosain is an important commercial species, but the fundamental knowledge on its immune defense related to the antioxidant and immune-associated reactions is still lacking. The study was to differentiate the responses of immune-associated parameters of haemolymph components in S. paramamosain when challenged with bacterial lipopolysaccharides (LPSs). The immunostimulating effects of LPS in crab by triggering various immune parameters (phagocytosis, lysozyme, antibacterial activity, phenoloxidase, and the generation of superoxide and nitric oxide) were investigated. Results showed that the generation of free radicals, phenoloxidase, lysozyme and antibacterial activities was significantly increased through the exposure periods. Conversely, total hemocyte count and lysosomal membrane stability decreased significantly as the exposure period extended to 96?h. The relationship between the antioxidant enzymes and immune reactions due to LPS was highly significant. In addition, ROS production was positively correlated with antioxidant showing immediate response of antioxidant defense to the oxyradicals generated. Overall, the study indicated that nonspecific immune components in hemocytes of crab showed active response to the LPS stimulation, and their responses suggested that many immune-associated parameters could be modulated and interrelated with the influence of antioxidants in crustaceans. PMID:21716691

Gopalakrishnan, Singaram; Chen, Fang-Yi; Thilagam, Harikrishnan; Qiao, Kun; Xu, Wan-Fang; Wang, Ke-Jian

2011-01-01

319

Interaction of fisetin with human serum albumin by fluorescence, circular dichroism spectroscopy and DFT calculations: binding parameters and conformational changes  

Microsoft Academic Search

The interaction between fisetin, an antioxidant and neuroprotective flavonoid, and human serum albumin (HSA) is investigated by means of fluorescence (steady-state, synchronous, time-resolved) and circular dichroism (CD) spectroscopy. The formation of a 1:1 complex with a constant of about 105M?1 was evidenced. Förster's resonance energy transfer and competitive binding with site markers warfarin and ibuprofen were considered and discussed. Changes

Iulia Matei; Sorana Ionescu; Mihaela Hillebrand

2011-01-01

320

Exploration of the African green monkey as a preclinical pharmacokinetic model: oral pharmacokinetic parameters and drug-drug interactions.  

PubMed

African green monkeys (vervets) have been proposed as an alternate species that might allow improved access and provide high-quality pharmacokinetic results comparable with other primates. However, no oral data are available in vervets to evaluate cross-species predictive performance. Therefore, this study was conducted to evaluate the use of the vervet to predict human oral pharmacokinetics and drug interactions. Oral pharmacokinetic studies were conducted in the vervet for eight compounds: phenytoin, moxifloxacin, erythromycin, lidocaine, propranolol, ciprofloxacin, metroprolol, and prednisolone. To assess drug-drug interactions, co-administration experiments were conducted with ketoconazole and either propranolol or erythromycin. In general, the vervet provided similar predictivity for human oral exposure as cynomolgus or rhesus monkeys. In all non-human primates, human exposure to phenytoin would be over-predicted, and erythromycin, lidocaine, and propranolol under-predicted, with good predictivity for the other compounds studied. Furthermore, in the vervet, ketoconazole co-administration resulted in a six-fold increase in exposure to erythromycin, demonstrating proof of concept for drug-drug interaction screening. These data support further exploration of the vervet as an alternate primate species for use in preclinical pharmacokinetic screening. PMID:19280525

Ward, K W; Coon, D J; Magiera, D; Bhadresa, S; Struharik, M; Lawrence, M S

2009-03-01

321

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

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.

Sanz, E.; Voss, C.I.

2006-01-01

322

Interaction  

NSDL National Science Digital Library

Set values for the initial position, velocity, and mass of the two particles, and click on the button "Initialize Animation" to play the animation using your specified values. Note, if m or v are too large, the particles may actually pass through one another which will seem a little strange. Note: the interaction between the particles is a "non-contact" interaction, much like the electrostatic force on two charges. Mathematically, it is actually a Hooke's law interaction.

Christian, Wolfgang; Belloni, Mario

2008-02-19

323

Differentiating antimicrobial peptides interacting with lipid bilayer: Molecular signatures derived from quartz crystal microbalance with dissipation monitoring.  

PubMed

Many antimicrobial peptides (AMPs) kill bacteria by disrupting the lipid bilayer structure of their inner membrane. However, there is only limited quantitative information in the literature to differentiate between AMPs of differing molecular properties, in terms of how they interact with the membrane. In this study, we have used quartz crystal microbalance with dissipation monitoring (QCM-D) to probe the interactions between a supported bilayer membrane of egg phosphatidylcholine (egg PC) and four structurally different AMPs: alamethicin, chrysophsin-3, indolicidin, and sheep myeloid antimicrobial peptide (SMAP-29). Multiple signatures from the QCM-D measurements were extracted, differentiating the AMPs, that provide information on peptide addition to and lipid removal from the membrane, the dynamics of peptide-membrane interactions and the rates at which the peptide actions are initiated. The mechanistic variations in peptide action were related to the fundamental structural properties of the peptides including the hydrophobicity, hydrophobic moment, and the probability of ?-helical secondary structures. PMID:25307196

Wang, Kathleen F; Nagarajan, Ramanathan; Camesano, Terri A

2015-01-01

324

Microstructural Parameters of Bone Evaluated Using HR-pQCT Correlate with the DXA-Derived Cortical Index and the Trabecular Bone Score in a Cohort of Randomly Selected Premenopausal Women  

PubMed Central

Background Areal bone mineral density is predictive for fracture risk. Microstructural bone parameters evaluated at the appendicular skeleton by high-resolution peripheral quantitative computed tomography (HR-pQCT) display differences between healthy patients and fracture patients. With the simple geometry of the cortex at the distal tibial diaphysis, a cortical index of the tibia combining material and mechanical properties correlated highly with bone strength ex vivo. The trabecular bone score derived from the scan of the lumbar spine by dual-energy X-ray absorptiometry (DXA) correlated ex vivo with the micro architectural parameters. It is unknown if these microstructural correlations could be made in healthy premenopausal women. Methods Randomly selected women between 20–40 years of age were examined by DXA and HR-pQCT at the standard regions of interest and at customized sub regions to focus on cortical and trabecular parameters of strength separately. For cortical strength, at the distal tibia the volumetric cortical index was calculated directly from HR-pQCT and the areal cortical index was derived from the DXA scan using a Canny threshold-based tool. For trabecular strength, the trabecular bone score was calculated based on the DXA scan of the lumbar spine and was compared with the corresponding parameters derived from the HR-pQCT measurements at radius and tibia. Results Seventy-two healthy women were included (average age 33.8 years, average BMI 23.2 kg/m2). The areal cortical index correlated highly with the volumetric cortical index at the distal tibia (R ?=? 0.798). The trabecular bone score correlated moderately with the microstructural parameters of the trabecular bone. Conclusion This study in randomly selected premenopausal women demonstrated that microstructural parameters of the bone evaluated by HR-pQCT correlated with the DXA derived parameters of skeletal regions containing predominantly cortical or cancellous bone. Whether these indexes are suitable for better predictions of the fracture risk deserves further investigation. PMID:24551194

Popp, Albrecht W.; Buffat, Helene; Eberli, Ursula; Lippuner, Kurt; Ernst, Manuela; Richards, R. Geoff; Stadelmann, Vincent A.; Windolf, Markus

2014-01-01

325

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

SciTech Connect

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.

Du Li [Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); Zhao Yaxue [School of Pharmacy, East China University of Science and Technology, Shanghai 200237 (China); Chen, Jing [Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); Yang Liumeng; Zheng Yongtang [Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223 (China); Tang Yun [School of Pharmacy, East China University of Science and Technology, Shanghai 200237 (China)], E-mail: ytang234@ecust.edu.cn; Shen Xu [Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); School of Pharmacy, East China University of Science and Technology, Shanghai 200237 (China)], E-mail: xshen@mail.shcnc.ac.cn; Jiang Hualiang [Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); School of Pharmacy, East China University of Science and Technology, Shanghai 200237 (China)

2008-10-10

326

Technical Note: Calculation of standard errors of estimates of genetic parameters with the multiple-trait derivative-free restricted maximal likelihood programs  

Technology Transfer Automated Retrieval System (TEKTRAN)

The MTDFREML (Boldman et al., 1995) set of programs was written to handle partially missing data in an expedient manner. When estimating (co)variance components and genetic parameters for multiple trait models, the programs have not been able to estimate standard errors of those estimates for multi...

327

Productivity, Respiration, and Light-Response Parameters of World Grassland and1 Agro-Ecosystems Derived From Flux-Tower Measurements2  

E-print Network

Productivity, Respiration, and Light-Response Parameters of World Grassland and1 Agro in the exponential equation for respiration temperature dependence (°C)-1 8 L ­ leaf area index (m2 m-2 )9 Lmax ­ daytime ecosystem respiration rate (mg CO2 m-2 s-1 )16 Rd ­ daytime ecosystem respiration (mg CO2 m-2 s-1

Boyer, Edmond

328

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

Microsoft Academic Search

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

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

2002-01-01

329

Precopulatory sexual interaction in an arctiid moth ( Utetheisa ornatrix ): Role of a pheromone derived from dietary alkaloids  

Microsoft Academic Search

Males of Utetheisa ornatrix have a pair of brushlike glandular structures, the coremata, which they evert from the abdomen during close-range precopulatory interaction with the female. Males experimentally deprived of coremata are less acceptable to females. The principal chemical associated with the coremata, identified as a pyrrolizine (hydroxydanaidal), has a proven pheromonal role: males raised under conditions where they fail

William E. Conner; Thomas Eisner; Robert K. Vander Meer; Angel Guerrero; Jerrold Meinwald

1981-01-01

330

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

SciTech Connect

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.

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

331

Interaction of amiloride and one of its derivatives with Vpu from HIV-1: a molecular dynamics simulation  

E-print Network

Societies. Key words: Viral ion channel; Vpu; HIV-1; Molecular dynamics simulation; Drug^protein interaction-loop helix-helix/turn motif. Such models can be used in molecular dynamics simulations to investigate procedure with short molecular dynamics (MD) simulations. The initial inter-helical distance was set to 0

Fischer, Wolfgang

332

A Screening Assay Based on Host-Pathogen Interaction Models Identifies a Set of Novel Antifungal Benzimidazole Derivatives?  

PubMed Central

Fungal infections are a serious health problem in clinics, especially in the immune-compromised patient. Disease ranges from widespread superficial infections like vulvovaginal infections to life-threatening systemic candidiasis. Especially for systemic mycoses, only a limited arsenal of antifungals is available. The most commonly used classes of antifungal compounds used include azoles, polyenes, and echinocandins. Due to emerging resistance to standard therapy, significant side effects, and high costs for several antifungals, there is a medical need for new antifungals in the clinic and general practice. In order to expand the arsenal of compounds with antifungal activities, we screened a compound library including more than 35,000 individual compounds derived from organic synthesis as well as combinatorial compound collections representing mixtures of compounds for antimycotic activity. In total, more than 100,000 compounds were screened using a new type of activity-selectivity assay, analyzing both the antifungal activity and the compatibility with human cells at the same time. One promising hit, an (S)-2-aminoalkyl benzimidazole derivative, was developed among a series of lead compounds showing potent antifungal activity. (S)-2-(1-Aminoisobutyl)-1-(3-chlorobenzyl) benzimidazole showed the highest antifungal activity and the best compatibility with human cells in several cell culture models and against a number of clinical isolates of several species of pathogenic Candida yeasts. Transcriptional profiling indicates that the newly discovered compound is a potential inhibitor of the ergosterol pathway, in contrast to other benzimidazole derivatives, which target microtubules. PMID:21746957

Burger-Kentischer, Anke; Finkelmeier, Doris; Keller, Petra; Bauer, Jörg; Eickhoff, Holger; Kleymann, Gerald; Abu Rayyan, Walid; Singh, Anurag; Schröppel, Klaus; Lemuth, Karin; Wiesmüller, Karl-Heinz; Rupp, Steffen

2011-01-01

333

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

PubMed

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

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

2015-01-01

334

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

PubMed Central

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

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

2015-01-01

335

Order Parameter Interaction at Interfaces and Domain Walls in a BiFeO3 Thin Film  

NASA Astrophysics Data System (ADS)

Atomic scale studies of the different structural, electronic, and chemical order parameters at domain walls and interfaces are vital for optimization and design of the ferroelectric-based thin film devices. In this study, we use quantitative scanning transmission electron microscopy (STEM) combined with electron energy loss spectroscopy to study atomic-scale phenomena in a multiferroic thin film heterostructures of BiFeO3 (BFO) epitaxially grown on (La,Sr)MnO3 (LSMO) layer on a SrTiO3 (STO) substrate. We find that charged and uncharged domain walls, as well as interfaces to domain of different polarity, have distinct structural signatures. Charged domain walls are associated with local lattice expansion, suggesting segregation of oxygen vacancies; uncharged domain walls show increased Debye-Waller factors for Bi, suggesting structural frustration. At the LSMO/BFO interface, downward polarization direction is associated with change in local valence state of near-interface Mn cations and lattice expansion.

Kim, Young-Min; Oxley, Mark; Morozovska, Anna; Eliseev, Eugene; Yu, Pu; Chu, Ying-Hao; Ramesh, Ramamoorthy; Pennycook, Stephen; Kalinin, Sergei; Borisevich, Albina

2013-03-01

336

Synthesis, characterization, spectroscopic and thermodynamic studies of charge transfer interaction of a new water-soluble cobalt(II) Schiff base complex with imidazole derivatives  

NASA Astrophysics Data System (ADS)

The water-soluble cobalt(II) tetradentate Schiff base complex [Co(II)L](ClO 4) 2, L: ( N, N'-bis{5-[(triphenylphosphonium)-methyl]salicylidine}- o-phenylenediamineperchlorate has been synthesized and characterized. This complex forms charge transfer (CT) complexes with imidazole and 1-methylimidazole. The formation constant, molar absorptivity ( ?'), and thermodynamic parameters for charge transfer complexes formation of cobalt(II) Schiff base complexes with imidazole derivatives were determined by using UV-vis spectrophotometric method in aqueous solutions at constant ionic strength ( I = 0.2 mol dm -3 KNO 3) at pH 6.0 and various temperatures between 292 and 315 K.

Boghaei, Davar M.; Askarizadeh, Elham; Bezaatpour, Abolfazl

2008-02-01

337

Oil droplet interaction with suspended sediment in the seawater column: influence of physical parameters and chemical dispersants.  

PubMed

The interaction of dispersed oil droplets with large diameter suspended particulate materials (SPM) has been little studied. In the current study, particle size, oil characteristics and chemical dispersant significantly influence the adsorption of oil droplets to SPM in seawater. Sediments with a smaller particulate size (clay) approaching that of the oil droplets (2-20 ?m) adsorbed more oil per gram than sediments with large particle size (sand). Heavier, more polar oils with a high asphaltene content adsorbed more efficiently to SPM than lighter, less polar oils. A decrease in the smaller, more water soluble oil components in the sediment adsorbed oil was observed for all oil types. Addition of chemical dispersant decreased the adsorption of oil droplets to suspended carbonate sand in an exponential-like manner. No change in the relative distribution of compounds adsorbed to the sediment was observed, indicating dispersants do not alter the dissolution of compounds from oil droplets. PMID:24257650

Sørensen, Lisbet; Melbye, Alf G; Booth, Andy M

2014-01-15

338

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

PubMed

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

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

2015-03-01

339

Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms.  

PubMed Central

The three-dimensional structures of D-Phe-Pro-Arg-chloromethyl ketone-inhibited thrombin in complex with Tyr-63-sulfated hirudin (ternary complex) and of thrombin in complex with the bifunctional inhibitor D-Phe-Pro-Arg-Pro-(Gly)4-hirudin (CGP 50,856, binary complex) have been determined by X-ray crystallography in crystal forms different from those described by Skrzypczak-Jankun et al. (Skrzypczak-Jankun, E., Carperos, V.E., Ravichandran, K.G., & Tulinsky, A., 1991, J. Mol. Biol. 221, 1379-1393). In both complexes, the interactions of the C-terminal hirudin segments of the inhibitors binding to the fibrinogen-binding exosite of thrombin are clearly established, including residues 60-64, which are disordered in the earlier crystal form. The interactions of the sulfate group of Tyr-63 in the ternary complex structure explain why natural sulfated hirudin binds with a 10-fold lower K(i) than the desulfated recombinant material. In this new crystal form, the autolysis loop of thrombin (residues 146-150), which is disordered in the earlier crystal form, is ordered due to crystal contacts. Interactions between the C-terminal fragment of hirudin and thrombin are not influenced by crystal contacts in this new crystal form, in contrast to the earlier form. In the bifunctional inhibitor-thrombin complex, the peptide bond between Arg-Pro (P1-P1') seems to be cleaved. PMID:8251938

Priestle, J. P.; Rahuel, J.; Rink, H.; Tones, M.; Grütter, M. G.

1993-01-01

340

Assessment of the sensitivity of core/shell parameters derived using the single-particle soot photometer to density and refractive index  

NASA Astrophysics Data System (ADS)

Black carbon (BC) is the dominant absorbing aerosol in the atmosphere, and plays an important role in climate and human health. The optical properties and cloud condensation nuclei (CCN) activity of soot depend on the amounts (both relative and absolute) of BC and nonrefractory material in the particles. Mixing between these two components is often considered using a core/shell coated sphere morphology. The Single Particle Soot Photometer (SP2) is the premier instrument for reporting distributions of both core size and coating thickness. Most studies combine the SP2's incandescence and scattering data to report coating properties, but there is variation in the assumed density and refractive index of the core that are used in these calculations. In this study we explore the sensitivity of the reported coatings to these parameters. An assessment of the coating properties of freshly-emitted, thermodenuded ambient particles demonstrated that a core density of 1.8 g cm-3 and refractive index n = (2.26-1.26i) were the most appropriate to use with ambient soot in the Los Angeles area. Using these parameters generated a distribution of shell/core ratio of 1.04 ± 0.21, corresponding to an absolute coating thickness distribution of 1.7 ± 17.5 nm. This demonstrates that using this technique the SP2 can accurately determine the mixing state (externally or internally mixed) of ambient soot, but with limited precision. Using other core parameters resulted in an offset in the coating distribution, but similar precision. For comparison, using the core parameters that resulted in the thickest coatings (on the same particles as before) generated a distribution of shell/core ratio of 1.40 ± 0.19, corresponding to an absolute coating thickness distribution of 30.3 ± 14.9 nm. Relative changes in coatings associated with secondary aerosol condensation were captured regardless of the assumed core parameters. These results must be taken into account when comparing BC coatings measured using this technique, or if using these data for optical or CCN activity calculations.

Taylor, J. W.; Allan, J. D.; Liu, D.; Flynn, M.; Weber, R.; Zhang, X.; Lefer, B. L.; Grossberg, N.; Flynn, J.; Coe, H.

2014-06-01

341

N-terminal ?-strand swapping in a consensus-derived alternative scaffold driven by stabilizing hydrophobic interactions.  

PubMed

The crystal structure of an N-terminal ?-strand-swapped consensus-derived tenascin FN3 alternative scaffold has been determined. A comparison with the unswapped structure reveals that the side chain of residue F88 orients differently and packs more tightly with the hydrophobic core of the domain. Dimer formation also results in the burial of a hydrophobic patch on the surface of the domain. Thus, it appears that tighter packing of F88 in the hydrophobic core and burial of surface hydrophobicity provide the driving forces for the N-terminal ?-strand swapping, leading to the formation of a stable compact dimer. PMID:24464739

Luo, Jinquan; Teplyakov, Alexey; Obmolova, Galina; Malia, Thomas J; Chan, Winnie; Jacobs, Steven A; O'Neil, Karyn T; Gilliland, Gary L

2014-07-01

342

Thermodynamic analysis of the impact of the surfactant-protein interactions on the molecular parameters and surface behavior of food proteins.  

PubMed

This paper reports on the thermodynamics of the interactions between surfactants (anionic, CITREM, SSL; nonionic, PGE; zwitterionic, phospholipids) and food proteins (sodium caseinate, legumin) depending on the chemical structure and molecular state (individual molecules, micelles) of the surfactants and the molecular parameters (conformation, molar mass, charge) of the proteins under changes of pH in the range from 7.2 to 5.0 and temperature from 293 to 323 K. The marked effect of the protein-surfactant interactions on the molecular parameters (the weight-average molar mass, the gyration and hydrodynamic radii) and the thermodynamic affinity of the proteins for an aqueous medium were determined by a combination of static and dynamic laser light scattering. Thermodynamically justified schematic sketches of the molecular mechanisms of the complex formation between like-charged proteins and surfactants have been proposed. In response to the complex formation between the proteins and the surfactants, the more stable and fine foams have been detected generally. PMID:16398504

Semenova, Maria G; Belyakova, Larisa E; Polikarpov, Yurii N; Il'in, Michael M; Istarova, Tatyana A; Anokhina, Maria S; Tsapkina, Elena N

2006-01-01

343

Interaction between storm surges and tides in shallow waters  

Microsoft Academic Search

The interaction between astronomical tides and storm surges in two different water bodies, namely the St. Lawrence estuary and the Suez Canal, is studied using simple analytical theories. Two parameters were derived that are of fundamental importance to this interaction. Based on the values of these parameters one should be able to determine with which state of the tide (rising,

T. S. Murty

1981-01-01

344

Virtual-screening targeting Human Immunodeficiency Virus type 1 integrase-lens epithelium-derived growth factor/p75 interaction for drug development.  

PubMed

Abstract Three integrase (IN) inhibitors have been approved by FDA for clinical treatment of Human Immunodeficiency Virus (HIV) infection. This stimulates more researchers to focus their studies on this target for anti-HIV drug development. Three steps regarding of IN activity have been validated for inhibitor discovery: strand transfer, 3'-terminal processing, and IN-lens epithelium-derived growth factor (LEDGF)/p75 interaction. Among them, IN-LEDGF/p75 interaction is a new target validated in recent years. Emergence of drug-resistant virus strains makes this target appealing to pharmacologists. Compared with the traditional screening methods such as AlphaScreen and cell-based screening developed for IN inhibitor discovery, virtual screening is a powerful technique in modern drug discovery. Here we summarized the recent advances of virtual-screening targeting IN-LEDFG/p75 interaction. The combined application of virtual screening and experiments in drug discovery against IN-LEDFG/p75 interaction sheds light on anti-HIV research and drug discovery. PMID:25230778

Gu, Wan-Gang; Liu, Bai-Nan; Yuan, Jun-Fa

2015-02-01

345

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

SciTech Connect

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.

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

1983-09-01

346

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)

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.

Reif, Maria M.; Hünenberger, Philippe H.

2011-04-01

347

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.  

PubMed

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. Hu?nenberger, J. Chem. Phys. 124, 224501 (2006); M. M. Reif and P. H. Hu?nenberger, 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); 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)(?)[H(+)] = -1100, -1075 or -1050 kJ mol(-1), resulting in three sets L, M, and H for the SPC water model and three sets L(E), M(E), and H(E) for the SPC/E water model (alternative sets can easily be interpolated to intermediate ?G(hyd)(?)[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)(?)[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)(?)[H(+)] close to -1100 kJ·mol(-1). PMID:21495739

Reif, Maria M; Hünenberger, Philippe H

2011-04-14

348

Interaction of a cholera toxin derivative containing a reduced number of receptor binding sites with intact cells in culture.  

PubMed

Hybrid CTB (hCTB), having only one or two functional binding sites, has been constructed from two chemically inactivated derivatives of CTB. One inactive derivative consisted of CTB formylated in the lone Trp-88 of each beta-chain (fCTB), whereas the other inactive derivative consisted of CTB specifically succinylated in three amino groups located in or near the receptor binding site (sssCTB). hCTB, fCTB and sssCTB were able to reassociate with CTA and form the corresponding holotoxins hCT, fCT and sssCT as measured by gel filtration chromatography. In contrast to fCT and sssCT, hCT could increase the cAMP content of intact Vero cells in a time- and dose-dependent way: concentrations as low as a few nanograms of hCT per milliliter caused a significant increase in the intracellular cAMP level. The maximal cAMP level induced by hCT (1 microgram/ml) was, however, more than 2-fold lower than that elicited by its native counterpart. At saturating ligand concentrations and at 37 degrees C, the lag periods and rates of CT and hCT induced cAMP accumulation were essentially the same. Treatment of Vero and HeLa cells with GM1 did not affect their difference in response to CT and hCT. When Vero cells treated with hCT were incubated for longer periods of time, a further slow accumulation of cAMP occurred until after about 20 h cAMP levels of cells exposed to CT or hCT were essentially the same. In contrast to Vero and HeLa cells, human skin fibroblasts exhibited an almost identical response to CT as well as to hCT. Acidotropic agents such as chloroquine and monensin affected the CT and hCT induced increase in cAMP content of Vero cells, fibroblasts and GM1 treated Hela cells in a similar way. The results are consistent with the view that CT receptor recognition domains are shared between adjacent beta-chains, that pentavalent binding appears not to be essential for cytotoxicity and that in the cell types studied intracellular processing of CT, hCT is involved. PMID:8086502

De Wolf, M J; Dams, E; Dierick, W S

1994-09-01

349

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)

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.

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

2013-12-01

350

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

NASA Astrophysics Data System (ADS)

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.

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

2015-02-01

351

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

PubMed

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. PMID:25218220

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

2015-02-25

352

New triorganotin (IV) derivatives of dipeptides as models for metal-protein interactions: Synthesis, structural characterization and biological studies  

NASA Astrophysics Data System (ADS)

New non-electrolytic triorganotin(IV) derivatives of dipeptides with general formulae R 3Sn(HL), where R = Ph and HL = monoanion of glycylisoleucine (H 2L-1), valylvaline (H 2L-2), alanylvaline (H 2L-3), leucylalanine (H 2L-4), leucylleucine (H 2L-5); R = n-Bu and HL = monoanion of glycylisoleucine (H 2L-1) and leucylalanine (H 2L-4); and R = Me and HL = monoanion of leucylalanine (H 2L-4) have been synthesized and characterized on the basis of infrared, multinuclear 1H, 13C and 119Sn NMR and 119Sn Mössbauer spectroscopic studies. These investigations suggest that all the ligands in R 3Sn(HL) act as monoanionic bidentates coordinating through the COO - and NH 2 groups. The 119Sn Mössbauer studies, together with the NMR data, indicate that, for these polymeric derivatives, the polyhedron around tin in R 3Sn(HL) is a trigonal-bipyramid with the three organic groups in the equatorial positions, while the axial positions are occupied by a carboxylic oxygen and the amino nitrogen atom from the adjacent molecule. The anti-inflammatory and cardiovascular activities and toxicity of all these compounds have been determined. Four of the complexes have also been screened against some of the chosen bacterial and fungal strains. The Ph 3Sn(IV) compounds exhibit better anti-inflammatory and cardiovascular activities in comparison to the Me 3Sn(IV) and n-Bu 3Sn(IV) analogues. n-Bu 3Sn(Gly-Ile) and Ph 3Sn(Ala-Val) exhibit good antibacterial activity against all the chosen strains.

Nath, Mala; Pokharia, Sandeep; Eng, George; Song, Xueqing; Kumar, Ashok

2006-01-01

353

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

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

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

1994-08-01

354

Superbasicity of silylene derivatives achieved via non-covalent intramolecular cation···? interactions and exploited as molecular containers for CO2.  

PubMed

We have reported for the first time designed silylene superbases involving intramolecular H(+)···? interaction using density functional theory (DFT) calculations. The non-covalent interactions augment the proton affinity values by 13 kcal mol?1 in the designed superbase (1) compared to the acyclic silylene, [:Si(NMe2)2]. These divalent Si(II) compounds can act as powerful neutral organic superbases in gas and solvent phases. The DFT calculations performed at the B3LYP/6-311+G**//B3LYP/6-31+G* level of theory showed that the gas phase proton affinity of the paracyclophane based silylene superbase (8) reaches up to ~271.0 kcal mol(?1), which is the highest in paracyclophane Si(II) compounds. In tetrahydrofuran solvent medium, the calculated proton affinity of 8 was found to be 301.4 kcal mol(?1). The paracyclophane-based silylene systems are used for binding with small alkali metal ions. The calculated results showed that these systems selectively bind to lithium ions over sodium ions due to the small size of lithium ions which is well fitted in the space between the silicon atom and the phenyl ring. Furthermore, we have used the lithiated silylene 1 and 9 (which exhibits bis-protonation) for gas storage (CO and CO2). The calculated results showed both the lithiated silylene 1 and 9 bind preferentially to CO2 than CO. The calculated gravimetric density of CO2 is found to be 26.97 wt% for 9-Li2–(CO2)4. The energy decomposition analysis (EDA) has been performed to investigate the role of various contributing factors to the total binding strength of the CO2 or CO molecules with lithiated silylene superbases. EDA reveals that the electrostatic energy and polarization energy are the major driving force for higher total interaction energy of the lithiated-silylene–CO2 complex than the lithiated-silylene–CO complex. The lithiated silylene systems showed a higher binding energy with CO2 than the previously reported imidazopyridamine at the same level of theory. These results suggest that the lithiated silylene systems can be used as a more efficient CO2 storage material than the aforementioned system. The calculated desorption energies per CO2 and CO (?EDE) also indicate the recyclable property of the materials. PMID:24830460

Biswas, Abul Kalam; Lo, Rabindranath; Si, Mrinal Kanti; Ganguly, Bishwajit

2014-06-28

355

Images of Gravitational and Magnetic Phenomena Derived from Two-dimensional Back-projection Doppler Tomography of Interacting Binary Stars  

NASA Astrophysics Data System (ADS)

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.

Richards, Mercedes T.; Cocking, Alexander S.; Fisher, John G.; Conover, Marshall J.

2014-11-01

356

The progression of muscle fatigue during exercise estimation with the aid of high-frequency component parameters derived from ensemble empirical mode decomposition.  

PubMed

Muscle fatigue is often monitored via the median frequency derived from the surface electromyography (sEMG) power spectrum during isometric contractions. The power spectrum of sEMG shifting toward lower frequencies can be used to quantify the electromanifestation of muscle fatigue. The dynamic sEMG belongs to a nonstationary signal, which will be affected by the electrode moving, the shift of the muscle, and the change of innervation zone. The goal of this study is to find a more sensitive and stable method in order to sense the progression of muscle fatigue in the local muscle during exercise in healthy people. Five male and five female volunteers participated. Each subject was asked to run on a multifunctional pedaled elliptical trainer for about 30 min, twice a week, and was recorded a total of six times. Three decomposed methods, discrete wavelet transform (DWT), empirical mode decomposition (EMD), and ensemble EMD (EEMD), were used to sense the progression of muscle fatigue. They compared with each other. Although the highest frequency components of sEMG by DWT, EMD, and EEMD have the better performance to sense the progression of muscle fatigue than the raw sEMG, the EEMD has the best performance to reduce nonstationary characteristics and noise of the dynamic sEMG. PMID:25192574

Liu, Shing-Hong; Chang, Kang-Ming; Cheng, Da-Chuan

2014-09-01

357

Synthesis, Characterization, DNA Interaction, and Antitumor Activities of La (III) Complex with Schiff Base Ligand Derived from Kaempferol and Diethylenetriamine  

PubMed Central

A novel La (III) complex, [LaL(H2O)3]NO3·3H2O, with Schiff base ligand L derived from kaempferol and diethylenetriamine, has been synthesized and characterized by elemental analysis, IR, UV-visible, 1H NMR, thermogravimetric analysis, and molar conductance measurements. The fluorescence spectra, circular dichroism spectra, and viscosity measurements and gel electrophoresis experiments indicated that the ligand L and La (III) complex could bind to CT-DNA presumably via intercalative mode and the La (III) complex showed a stronger ability to bind and cleave DNA than the ligand L alone. The binding constants (Kb) were evaluated from fluorescence data and the values ranged from 0.454 to 0.659 × 105 L mol?1 and 1.71 to 17.3 × 105 L mol?1 for the ligand L and La (III) complex, respectively, in the temperature range of 298–310?K. It was also found that the fluorescence quenching mechanism of EB-DNA by ligand L and La (III) complex was a static quenching process. In comparison to free ligand L, La (III) complex exhibited enhanced cytotoxic activities against tested tumor cell lines HL-60 and HepG-2, which may correlate with the enhanced DNA binding and cleaving abilities of the La (III) complex. PMID:25371657

Wang, Qin; Huang, Yu; Zhang, Jin-Sheng; Yang, Xin-Bin

2014-01-01

358

Investigations on the interactions of ?phage-derived peptides against the SrtA mechanism in Bacillus anthracis.  

PubMed

Bacillus anthracis is a well-known bioweapon pathogen, which coordinates the expression of its virulence factors in response to a specific environmental signal by its protein architecture. Absences of sortase signal functioning may fail to assemble the surface linked proteins and so B. anthracis cannot sustain an infection with host cells. Targeting the signaling mechanism of B. anthracis can be achieved by inhibition of SrtA enzyme through ?phage-derived plyG. The lysin enzyme plyG is experimentally proven as bacteriolytic agent, specifically kill's B. anthracis by inhibiting the SrtA. Here, we have screened the peptides from ?phage lysin, and these peptides are having the ability as LPXTG competitive inhibitors. In comparison to the activator peptide LPXTG binding motif, ?phage lysin based inhibitor peptides are having much supremacy towards binding of SrtA. Finally, peptide structures extracted from PlyG are free from toxic, allergic abilities and also have the ability to terminate the signal transduction mechanism in B. anthracis. PMID:24264995

Selvaraj, Chandrabose; Singh, Poonam; Singh, Sanjeev Kumar

2014-02-01

359

Protein-specific force field derived from the fragment molecular orbital method can improve protein-ligand binding interactions.  

PubMed

Accurate computational estimate of the protein-ligand binding affinity is of central importance in rational drug design. To improve accuracy of the molecular mechanics (MM) force field (FF) for protein-ligand simulations, we use a protein-specific FF derived by the fragment molecular orbital (FMO) method and by the restrained electrostatic potential (RESP) method. Applying this FMO-RESP method to two proteins, dodecin, and lysozyme, we found that protein-specific partial charges tend to differ more significantly from the standard AMBER charges for isolated charged atoms. We did not see the dependence of partial charges on the secondary structure. Computing the binding affinities of dodecin with five ligands by MM PBSA protocol with the FMO-RESP charge set as well as with the standard AMBER charges, we found that the former gives better correlation with experimental affinities than the latter. While, for lysozyme with five ligands, both charge sets gave similar and relatively accurate estimates of binding affinities. PMID:23420697

Chang, Le; Ishikawa, Takeshi; Kuwata, Kazuo; Takada, Shoji

2013-05-30

360

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)

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.

Palchik, V.

2014-11-01

361

Atmospheric parameters in a subtropical cloud regime transition derived by AIRS+MODIS - observed statistical variability compared to ERA-Interim  

NASA Astrophysics Data System (ADS)

Cloud occurrence, microphysical and optical properties and atmospheric profiles within a subtropical cloud regime transition in the northeastern Pacific Ocean are obtained from a synergistic combination of the Atmospheric Infrared Sounder (AIRS) and the MODerate resolution Imaging Spectroradiometer (MODIS). The observed cloud parameters and atmospheric thermodynamic profile retrievals are binned by cloud type and analyzed based on their probability density functions (PDFs). Comparison of the PDFs to data from the European Center for Medium Range Weather Forecasting Re-analysis (ERA-Interim) shows a strong difference in the occurrence of the different cloud types compared to clear sky. An increasing non-Gaussian behavior is observed in cloud optical thickness (?c), effective radius (re) and cloud top temperature (Tc) distributions from Stratocumulus to Trade Cumulus, while decreasing values of lower tropospheric stability are seen. However, variations in the mean, width and shape of the distributions are found. The AIRS potential temperature (?) and water vapor (q) profiles in the presence of varying marine boundary layer (MBL) cloud types show overall similarities to the ERA-Interim in the mean profiles, but differences arise in the higher moments at some altitudes. The differences between the PDFs from AIRS+MODIS and ERA-Interim make it possible to pinpoint systematic errors in both systems and helps to understand joint PDFs of cloud properties and coincident thermodynamic profiles from satellite observations.

Schreier, M. M.; Kahn, B. H.; Sušelj, K.; Karlsson, J.; Ou, S. C.; Yue, Q.; Nasiri, S. L.

2013-09-01

362

Atmospheric parameters in a subtropical cloud regime transition derived by AIRS and MODIS: observed statistical variability compared to ERA-Interim  

NASA Astrophysics Data System (ADS)

Cloud occurrence, microphysical and optical properties, and atmospheric profiles within a subtropical cloud regime transition in the northeastern Pacific Ocean are obtained from a synergistic combination of the Atmospheric Infrared Sounder (AIRS) and the MODerate resolution Imaging Spectroradiometer (MODIS). The observed cloud parameters and atmospheric thermodynamic profile retrievals are binned by cloud type and analyzed based on their probability density functions (PDFs). Comparison of the PDFs to data from the European Centre for Medium Range Weather Forecasting reanalysis (ERA-Interim) shows a strong difference in the occurrence of the different cloud types compared to clear sky. An increasing non-Gaussian behavior is observed in cloud optical thickness (?c), effective radius (re) and cloud-top temperature (Tc) distributions from stratocumulus to trade cumulus, while decreasing values of lower-tropospheric stability are seen. However, variations in the mean, width and shape of the distributions are found. The AIRS potential temperature (?) and water vapor (q) profiles in the presence of varying marine boundary layer (MBL) cloud types show overall similarities to the ERA-Interim in the mean profiles, but differences arise in the higher moments at some altitudes. The differences between the PDFs from AIRS+MODIS and ERA-Interim make it possible to pinpoint systematic errors in both systems and help to understand joint PDFs of cloud properties and coincident thermodynamic profiles from satellite observations.

Schreier, M. M.; Kahn, B. H.; Sušelj, K.; Karlsson, J.; Ou, S. C.; Yue, Q.; Nasiri, S. L.

2014-04-01

363

Dynamic extremes of voice in the light of time domain parameters extracted from the amplitude features of glottal flow and its derivative.  

PubMed

In the first part of the study, the subjects (4 females, 4 males) produced sustained breathy, normal and pressed types of phonation. The maximum AC flow (f(ac)) and the negative peak amplitude (d(min)) of the first derivative of the glottal flow were extracted from glottal volume velocity waveforms estimated by inverse filtering. The ratio between f(ac) and d(min) (amplitude quotient, AQ), which gives an estimate of the closing time of the glottal flow, and its normalised version (NAQ) were computed. The NAQ values correlated strongly with the closing quotient of glottal flow. In the second part of the study, the aim was to investigate the dynamic extremes of the human voice in terms of F(0), SPL, f(ac), d(min), AQ and NAQ as well as the intraoral pressure (p) used for subglottal pressure estimation. Eleven normal subjects (5 females, 6 males) participated in this experiment. The subjects started with the production of soft phonation (approximately 55 dB at 40 cm) and increased their vocal intensity at 5-dB steps up to the level of 105 dB. At the analysis stage, the voice samples were divided into three categories: soft (<70 dB), normal (70-90 dB) and loud (>90 dB). In soft and normal phonation, intensity change was correlated with changes in the shape of the glottal flow waveform, whereas the loud voice samples showed a large increase in F(0) and p values. At the loudest extreme, d(min) approached its maximum and AQ its minimum values and NAQ started to rise. In terms of the NAQ values of stressed syllables, the type of phonation was breathy in the soft intensity category, whereas in the normal and loud intensity categories it was within the range of the pressed type of phonation of sustained phonation samples. PMID:12077506

Vilkman, Erkki; Alku, Paavo; Vintturi, Juha

2002-01-01

364

A Multi-parameter In Vitro Screen in Human Stem Cell-Derived Cardiomyocytes Identifies Ponatinib-Induced Structural and Functional Cardiac Toxicity.  

PubMed

Ponatinib, a multi-targeted TKI and potent pan-ABL inhibitor, approved for the treatment of Ph + ALL and CML, was temporarily withdrawn from the U.S. market due to severe vascular adverse events. Cardiac-specific toxicities including myocardial infarction, severe congestive heart failure, and cardiac arrhythmias have also been shown with ponatinib. Targeted oncology agents such as ponatinib have transformed cancer treatment but often induce toxicity due to inhibition of survival pathways shared by both cancer and cardiac cells. These toxicities are often missed by the standard preclinical toxicity assessment methods, which include human Ether-à-go-go-related gene (hERG) and animal toxicity testing. In this study, we show that a multiparameter in vitro toxicity screening approach using human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) accurately predicted the cardiac toxicity potential of ponatinib. This in vitro model evaluated ponatinib's effect on the overall cell health, mitochondrial stress, and function of hiPSC-CM and also provided mechanistic insight into the signaling pathways and cellular structures altered with treatment. We show here that ponatinib rapidly inhibits prosurvival signaling pathways, induces structural cardiac toxicity (as shown by actin cytoskeleton damage, mitochondrial stress, cell death, and troponin secretion), and disrupts cardiac cell beating. Most of these effects occurred at doses between 10× and 50× ponatinib's Cmax, a dose range shown to be relevant for accurate prediction of in vivo toxicity. Together these studies show that a comprehensive in vitro screening tool in a more relevant human cardiac cell model can improve the detection of cardiac toxicity with targeted oncology agents such as ponatinib. PMID:25304212

Talbert, Dominique R; Doherty, Kimberly R; Trusk, Patricia B; Moran, Diarmuid M; Shell, Scott A; Bacus, Sarah

2015-01-01

365

Interactions of the sponge-derived antimitotic tripeptide hemiasterlin with tubulin: comparison with dolastatin 10 and cryptophycin 1.  

PubMed

The sponge-derived antimitotic tripeptide hemiasterlin was previously shown to inhibit tubulin polymerization. We have now demonstrated that hemiasterlin resembles most other antimitotic peptides in noncompetitively inhibiting the binding of vinblastine to tubulin (apparent K(i) value, 7.0 microM), competitively inhibiting the binding of dolastatin 10 to tubulin (apparent K(i) value, 2.0 microM), stabilizing the colchicine binding activity of tubulin, inhibiting nucleotide exchange on beta-tubulin, and inducing the formation of tubulin oligomers that are stable to gel filtration in the absence of free drug, even at low drug concentrations. The tubulin oligomerization reaction induced by hemiasterlin was compared to the reactions induced by dolastatin 10 and cryptophycin 1. Like dolastatin 10, hemiasterlin induced formation of a tubulin aggregate that had the morphological appearance primarily of ring-like structures with a diameter of about 40 nm, while the morphology of the cryptophycin 1 aggregate consisted primarily of smaller rings (diameter about 30 nm). However, the hemiasterlin aggregate differed from the dolastatin 10 aggregate in that its formation was not associated with turbidity development, and the morphology of the hemiasterlin aggregate (as opposed to the dolastatin 10 aggregate) did not change greatly when microtubule-associated proteins were present (tight coils and pinwheels are observed with dolastatin 10 but not with hemiasterlin or cryptophycin 1). Opacification of tubulin-dolastatin 10 mixtures was inhibited by hemiasterlin at 22 degrees C and stimulated at 0 degrees C, while cryptophycin 1 was inhibitory at both reaction temperatures. PMID:10572005

Bai, R; Durso, N A; Sackett, D L; Hamel, E

1999-10-26

366

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

PubMed

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

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

367

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

PubMed

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

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

368

Comparative Molecular Field Analysis of fenoterol derivatives interacting with an agonist-stabilized form of the ?2-adrenergic receptor  

PubMed Central

The ?2-adrenergic receptor (?2-AR) agonist [3H]-(R,R?)-methoxyfenoterol was employed as the marker ligand in displacement studies measuring the binding affinities (Ki values) of the stereoisomers of a series of 4?-methoxyfenoterol analogs in which the length of the alkyl substituent at ?? position was varied from 0 to 3 carbon atoms. The binding affinities of the compounds were additionally determined using the inverse agonist [3H]-CGP-12177 as the marker ligand and the ability of the compounds to stimulate cAMP accumulation, measured as EC50 values, were determined in HEK293 cells expressing the ?2-AR. The data indicate that the highest binding affinities and functional activities were produced by methyl and ethyl substituents at the ?? position. The results also indicate that the Ki values obtained using [3H]-(R,R?)-methoxyfenoterol as the marker ligand modeled the EC50 values obtained from cAMP stimulation better than the data obtained using [3H]-CGP-12177 as the marker ligand. The data from this study was combined with data from previous studies and processed using the Comparative Molecular Field Analysis approach to produce a CoMFA model reflecting the binding to the ?2-AR conformation probed by [3H]-(R,R?)-4?-methoxyfenoterol. The CoMFA model of the agonist-stabilized ?2-AR suggests that the binding of the fenoterol analogs to an agonist-stabilized conformation of the ?2-AR is governed to a greater extend by steric effects than binding to the [3H]-CGP-12177-stabilized conformation(s) in which electrostatic interactions play a more predominate role. PMID:24326276

Plazinska, Anita; Pajak, Karolina; Rutkowska, Ewelina; Jimenez, Lucita; Kozocas, Joseph; Koolpe, Gary; Tanga, Mary; Toll, Lawrence; Wainer, Irving W.; Jozwiak, Krzysztof

2014-01-01

369

Comparative molecular field analysis of fenoterol derivatives interacting with an agonist-stabilized form of the ??-adrenergic receptor.  

PubMed

The ??-adrenergic receptor (??-AR) agonist [(3)H]-(R,R')-methoxyfenoterol was employed as the marker ligand in displacement studies measuring the binding affinities (Ki values) of the stereoisomers of a series of 4'-methoxyfenoterol analogs in which the length of the alkyl substituent at ?' position was varied from 0 to 3 carbon atoms. The binding affinities of the compounds were additionally determined using the inverse agonist [(3)H]-CGP-12177 as the marker ligand and the ability of the compounds to stimulate cAMP accumulation, measured as EC?? values, were determined in HEK293 cells expressing the ??-AR. The data indicate that the highest binding affinities and functional activities were produced by methyl and ethyl substituents at the ?' position. The results also indicate that the Ki values obtained using [(3)H]-(R,R')-methoxyfenoterol as the marker ligand modeled the EC?? values obtained from cAMP stimulation better than the data obtained using [(3)H]-CGP-12177 as the marker ligand. The data from this study was combined with data from previous studies and processed using the Comparative Molecular Field Analysis approach to produce a CoMFA model reflecting the binding to the ??-AR conformation probed by [(3)H]-(R,R')-4'-methoxyfenoterol. The CoMFA model of the agonist-stabilized ??-AR suggests that the binding of the fenoterol analogs to an agonist-stabilized conformation of the ??-AR is governed to a greater extend by steric effects than binding to the [(3)H]-CGP-12177-stabilized conformation(s) in which electrostatic interactions play a more predominate role. PMID:24326276

Plazinska, Anita; Pajak, Karolina; Rutkowska, Ewelina; Jimenez, Lucita; Kozocas, Joseph; Koolpe, Gary; Tanga, Mary; Toll, Lawrence; Wainer, Irving W; Jozwiak, Krzysztof

2014-01-01

370

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

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.

Bloomsburg, G.; Finnie, J.; Horn, D.; King, B.; Liou, J. [Idaho Univ., Moscow, ID (United States)

1993-05-01

371

Exploring the full parameter space for an interacting dark energy model with recent observations including redshift-space distortions: Application of the parametrized post-Friedmann approach  

NASA Astrophysics Data System (ADS)

Dark energy can modify the dynamics of dark matter if there exists a direct interaction between them. Thus, a measurement of the structure growth, e.g., redshift-space distortions (RSDs), can provide a powerful tool to constrain the interacting dark energy (IDE) models. For the widely studied Q =3 ? H ?de model, previous works showed that only a very small coupling [? ˜O (10-3) ] can survive in current RSD data. However, all of these analyses had to assume w >-1 and ? >0 due to the existence of the large-scale instability in the IDE scenario. In our recent work [Phys. Rev. D 90, 063005 (2014)], we successfully solved this large-scale instability problem by establishing a parametrized post-Friedmann framework for the IDE scenario. So we, for the first time, have the ability to explore the full parameter space of the IDE models. In this work, we re-examine the observational constraints on the Q =3 ? H ?de model within the parametrized post-Friedmann framework. By using the Planck data, the baryon acoustic oscillation data, the JLA sample of supernovae, and the Hubble constant measurement, we get ? =-0.01 0-0.033+0.037 (1 ? ). The fit result becomes ? =-0.014 8-0.0089+0.0100 (1 ? ) once we further incorporate the RSD data in the analysis. The error of ? is substantially reduced with the help of the RSD data. Compared with the previous results, our results show that a negative ? is favored by current observations, and a relatively larger interaction rate is permitted by current RSD data.

Li, Yun-He; Zhang, Jing-Fei; Zhang, Xin

2014-12-01

372

Using visible and near-infrared diffuse reflectance spectroscopy for predicting soil properties based on regression with peaks parameters as derived from continuum-removed spectra  

NASA Astrophysics Data System (ADS)

Visible and near-infrared diffuse reflectance spectroscopy (VNIR-DRS) provides a rapid and inexpensive tool for simultaneous prediction of a variety of soil properties. Usually, some sophisticated multivariate mathematical or statistical methods are employed in order to extract the required information from the raw spectra measurement. For this purpose especially the Partial least squares regression (PLSR) and Support vector machines (SVM) are the most frequently used. These methods generally benefit from the complexity with which the soil spectra are treated. But it is interesting that also techniques that focus only on a single spectral feature, such as a simple linear regression with selected continuum-removed spectra (CRS) characteristic (e.g. peak depth), can often provide competitive results. Therefore, we decided to enhance the potential of CRS taking into account all possible CRS peak parameters (area, width and depth) and develop a comprehensive methodology based on multiple linear regression approach. The eight considered soil properties were oxidizable carbon content (Cox), exchangeable (pHex) and active soil pH (pHa), particle and bulk density, CaCO3 content, crystalline and amorphous (Fed) and amorphous Fe (Feox) forms. In four cases (pHa, bulk density, Fed and Feox), of which two (Fed and Feox) were predicted reliably accurately (0.50 < R2cv < 0.80) and the other two (pHa and bulk density) only poorly (R2cv < 0.50), we obtained slightly better results than with PLSR and SVM. In one case (pHex) we achieved a significantly higher, although just reliable, accuracy (R2cv = 0.601) than with PLSR and SVM (R2cv = 0.448 and 0.442, resp.). But most interestingly, in the case of particle density, the presented approach outperformed the PLSR and SVM dramatically offering a fairly accurate prediction (R2cv = 0.827) against two failures (R2cv = 0.034 and 0.121 for PLSR and SVM, resp.). In last two cases (Cox and CaCO3) a slightly worse results were achieved then with PLSR and SVM with overall fairly accurate prediction (R2cv > 0.80). Acknowledgment: Authors acknowledge the financial support of the Ministry of Agriculture of the Czech Republic (grant No. QJ1230319).

Vasat, Radim; Klement, Ales; Jaksik, Ondrej; Kodesova, Radka; Drabek, Ondrej; Boruvka, Lubos

2014-05-01

373

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

PubMed

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

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

2007-06-21

374

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)

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.

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

2014-12-01

375

Recognition of O6-benzyl-2?-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction  

PubMed Central

The 2?-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O6-benzyl-2?-deoxyguanosine nucleoside (O6-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O6-Bn-dG and dG in DNA. The structure of the modified Dickerson–Drew dodecamer (DDD) in which guanine at position G4 has been replaced by O6-Bn-dG and cytosine C9 has been replaced with dPer to form the modified O6-Bn-dG:dPer (DDD-XY) duplex [5?-d(C1G2C3X4A5A6T7T8Y9G10C11G12)-3?]2 (X = O6-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O6-Bn-dG to intercalate between Per and thymine of the 3?-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O6-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C9 is replaced with dPer to form the dG:dPer (DDD-GY) [5?-d(C1G2C3G4A5A6T7T8Y9G10C11G12)-3?]2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine. PMID:23748954

Kowal, Ewa A.; Lad, Rahul R.; Pallan, Pradeep S.; Dhummakupt, Elizabeth; Wawrzak, Zdzislaw; Egli, Martin; Sturla, Shana J.; Stone, Michael P.

2013-01-01

376

Temporospatial gene expression of Prx1 and Prx2 is involved in morphogenesis of cranial placode-derived tissues through epithelio-mesenchymal interaction during rat embryogenesis.  

PubMed

Paired-related homeobox transcription factors, PRX1 and PRX2, are verified to play essential roles in limb, heart and craniofacial development by analyses of knockout animals. Their gene expression in the embryonic primordia derived from the mesoderm and neural crest is confirmed by in situ hybridization. Nevertheless, a detailed localization of PRX1 and PRX2 was not carried out because of a lack of specific antibodies for each factor. We have previously confirmed the presence of PRX proteins in rat embryonic pituitary by using an antibody that recognizes both PRX1 and PRX2. However, the pituitary originates in the cranial placodes, not the mesoderm or neural crest. In this study, we analyze the temporospatial distribution of PRX1 and PRX2 with novel antibodies specific for each factor, together with a stem/progenitor marker SOX2 (sex-determining region Y-box 2) in the primordia formed by epithelio-mesenchymal interaction. We observe immunoreactive signals of both PRX proteins in rat embryo, showing a similar pattern to that obtained by in situ hybridization. In early embryogenesis, PRX proteins are not co-localized with SOX2 but PRX2 and/or PRX1-positive cells are present in the border or periphery of SOX2-positive primordia originating in the cranial placode. During advanced embryogenesis, either PRX2-positive cells become condensed in the border of SOX2-positive cells or PRX1 and/or PRX2 become co-localized with SOX2. Our results suggest that PRX proteins, especially PRX2, play a role in the morphogenesis of the primordial tissues formed by the epithelio-mesenchymal interaction and that neural crest cells contribute to the morphogenesis of tissues derived from the cranial placode. PMID:23644741

Higuchi, Masashi; Kato, Takako; Chen, Mo; Yako, Hideji; Yoshida, Saishu; Kanno, Naoko; Kato, Yukio

2013-07-01

377

Prioritization of active antimalarials using structural interaction profile of Plasmodium falciparum enoyl-acyl carrier protein reductase (PfENR)-triclosan derivatives.  

PubMed

An empirical relationship between the experimental inhibitory activities of triclosan derivatives and its computationally predicted Plasmodium falciparum enoyl-acyl carrier protein (ACP) reductase (PfENR) dock poses was developed to model activities of known antimalarials. A statistical model was developed using 57 triclosan derivatives with significant measures (r = 0.849, q(2) = 0.619, s = 0.481) and applied on structurally related and structurally diverse external datasets. A substructure-based search on ChEMBL malaria dataset (280 compounds) yielded only two molecules with significant docking energy, whereas eight active antimalarials (EC50 < 100 nM, tested on 3D7 strain) with better predicted activities (pIC50 ~ 7) from Open Access Malaria Box (400 compounds) were prioritized. Further, calculations on the structurally diverse rhodanine molecules (known PfENR inhibitors) distinguished actives (experimental IC50 = 0.035 ?M; predicted pIC50 = 6.568) and inactives (experimental IC50 = 50 ?M; predicted pIC50 = -4.078), which showed that antimalarials possessing dock poses similar to experimental interaction profiles can be used as leads to test experimentally on enzyme assays. PMID:25567142

Kumar, S P; George, L B; Jasrai, Y T; Pandya, H A

2015-01-01

378

Interactions of Neuropathogenic Escherichia coli K1 (RS218) and Its Derivatives Lacking Genomic Islands with Phagocytic Acanthamoeba castellanii and Nonphagocytic Brain Endothelial Cells  

PubMed Central

Here we determined the role of various genomic islands in E. coli K1 interactions with phagocytic A. castellanii and nonphagocytic brain microvascular endothelial cells. The findings revealed that the genomic islands deletion mutants of RS218 related to toxins (peptide toxin, ?-hemolysin), adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin), protein secretion system (T1SS for hemolysin), invasins (IbeA, CNF1), metabolism (D-serine catabolism, dihydroxyacetone, glycerol, and glyoxylate metabolism) showed reduced interactions with both A. castellanii and brain microvascular endothelial cells. Interestingly, the deletion of RS218-derived genomic island 21 containing adhesins (P fimbriae, F17-like fimbriae, nonfimbrial adhesins, Hek, and hemagglutinin), protein secretion system (T1SS for hemolysin), invasins (CNF1), metabolism (D-serine catabolism) abolished E. coli K1-mediated HBMEC cytotoxicity in a CNF1-independent manner. Therefore, the characterization of these genomic islands should reveal mechanisms of evolutionary gain for E. coli K1 pathogenicity. PMID:24818136

Yousuf, Farzana Abubakar; Yousuf, Zuhair; Iqbal, Junaid; Siddiqui, Ruqaiyyah; Khan, Hafsa; Khan, Naveed Ahmed

2014-01-01

379

Genetic parameters and investigation of genotype × environment interactions in Nellore × Hereford crossbred for resistance to cattle ticks in different regions of Brazil.  

PubMed

Data from 6,156 Nellore × Hereford crossbred cattle, distributed in 18 herds located in the Brazilian states of Mato Grosso do Sul (MS), São Paulo (SP), Paraná (PR) and Rio Grande do Sul (RS), were analysed in order to investigate genetic variation for resistance to the cattle tick through the estimation of variance components and genetic parameters for counting ticks (Rhipicephalus (Boophilus) microplus) in natural infestation, and also a possible genotype × environment interaction. The tick count data (CC) were transformed to log10(CC?+?1) and grouped into two regions, defined by cluster analysis and analysed using the method of restricted maximum likelihood. The statistical model included the additive genetic effect as random and fixed effects of the contemporary group (CG) and genetic group (GG) as classificatory and the age of the animal at the time of counting (linear effect) and individual heterozygosity (linear effect, ranging from 0 to 1) as covariates. In the studied regions, the effect of heterosis found was inversely proportional; in other words, the count of ticks decreased with the increase of heterozygosity. The observed heritability estimation for resistance to tick infestation were 0.12?±?0.04 and 0.11?±?0.04 for groups A (RS and south PR) and B (MS, SP and north PR), respectively. The results of this study suggest that selection for animals resistant to ticks would be possible using the tick count to estimate the genetic value of animals, but with a slow genetic progress. The genetic correlation for tick count between the two groups (A and B) was 0.84?±?0.27 and genotype × environment interaction for this trait was not observed in the studied population. PMID:25108748

Ayres, D R; Pereira, R J; Boligon, A A; Baldi, F; Roso, V M; Albuquerque, L G

2015-02-01

380

Trypano-PPI: a web server for prediction of unique targets in trypanosome proteome by using electrostatic parameters of protein-protein interactions.  

PubMed

Trypanosoma brucei causes African trypanosomiasis in humans (HAT or African sleeping sickness) and Nagana in cattle. The disease threatens over 60 million people and uncounted numbers of cattle in 36 countries of sub-Saharan Africa and has a devastating impact on human health and the economy. On the other hand, Trypanosoma cruzi is responsible in South America for Chagas disease, which can cause acute illness and death, especially in young children. In this context, the discovery of novel drug targets in Trypanosome proteome is a major focus for the scientific community. Recently, many researchers have spent important efforts on the study of protein-protein interactions (PPIs) in pathogen Trypanosome species concluding that the low sequence identities between some parasite proteins and their human host render these PPIs as highly promising drug targets. To the best of our knowledge, there are no general models to predict Unique PPIs in Trypanosome (TPPIs). On the other hand, the 3D structure of an increasing number of Trypanosome proteins is reported in databases. In this regard, the introduction of a new model to predict TPPIs from the 3D structure of proteins involved in PPI is very important. For this purpose, we introduced new protein-protein complex invariants based on the Markov average electrostatic potential xi(k)(R(i)) for amino acids located in different regions (R(i)) of i-th protein and placed at a distance k one from each other. We calculated more than 30 different types of parameters for 7866 pairs of proteins (1023 TPPIs and 6823 non-TPPIs) from more than 20 organisms, including parasites and human or cattle hosts. We found a very simple linear model that predicts above 90% of TPPIs and non-TPPIs both in training and independent test subsets using only two parameters. The parameters were (d)xi(k)(s) = |xi(k)(s(1)) - xi(k)(s(2))|, the absolute difference between the xi(k)(s(i)) values on the surface of the two proteins of the pairs. We also tested nonlinear ANN models for comparison purposes but the linear model gives the best results. We implemented this predictor in the web server named TrypanoPPI freely available to public at http://miaja.tic.udc.es/Bio-AIMS/TrypanoPPI.php. This is the first model that predicts how unique a protein-protein complex in Trypanosome proteome is with respect to other parasites and hosts, opening new opportunities for antitrypanosome drug target discovery. PMID:19947655

Rodriguez-Soca, Yamilet; Munteanu, Cristian R; Dorado, Julián; Pazos, Alejandro; Prado-Prado, Francisco J; González-Díaz, Humberto

2010-02-01

381

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

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.

Sato, H.; Sugiyama, Y.; Sawada, Y.; Iga, T.; Sakamoto, S.; Fuwa, T.; Hanano, M. (Univ. of Tokyo (Japan))

1988-11-01

382

Transposase-Derived Proteins FHY3/FAR1 Interact with PHYTOCHROME-INTERACTING FACTOR1 to Regulate Chlorophyll Biosynthesis by Modulating HEMB1 during Deetiolation in Arabidopsis[W  

PubMed Central

Successful chlorophyll biosynthesis during initial light exposure is critical for plant survival and growth, as excess accumulation of chlorophyll precursors in darkness can cause photooxidative damage to cells. Therefore, efficient mechanisms have evolved to precisely regulate chlorophyll biosynthesis in plants. Here, we identify FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED IMPAIRED RESPONSE1 (FAR1), two transposase-derived transcription factors, as positive regulators of chlorophyll biosynthesis in Arabidopsis thaliana. We show that null mutations in FHY3 and FAR1 cause reduced protochlorophyllide (a precursor of chlorophyll) levels in darkness and less photobleaching in the light. We find that FHY3 directly binds to the promoter and activates expression of HEMB1, which encodes 5-aminolevulinic acid dehydratase in the chlorophyll biosynthetic pathway. We reveal that PHYTOCHROME-INTERACTING FACTOR1 physically interacts with the DNA binding domain of FHY3, thereby par