Sample records for field scf method

  1. Hybrid particle-field molecular dynamics simulation for polyelectrolyte systems.

    PubMed

    Zhu, You-Liang; Lu, Zhong-Yuan; Milano, Giuseppe; Shi, An-Chang; Sun, Zhao-Yan

    2016-04-14

    To achieve simulations on large spatial and temporal scales with high molecular chemical specificity, a hybrid particle-field method was proposed recently. This method is developed by combining molecular dynamics and self-consistent field theory (MD-SCF). The MD-SCF method has been validated by successfully predicting the experimentally observable properties of several systems. Here we propose an efficient scheme for the inclusion of electrostatic interactions in the MD-SCF framework. In this scheme, charged molecules are interacting with the external fields that are self-consistently determined from the charge densities. This method is validated by comparing the structural properties of polyelectrolytes in solution obtained from the MD-SCF and particle-based simulations. Moreover, taking PMMA-b-PEO and LiCF3SO3 as examples, the enhancement of immiscibility between the ion-dissolving block and the inert block by doping lithium salts into the copolymer is examined by using the MD-SCF method. By employing GPU-acceleration, the high performance of the MD-SCF method with explicit treatment of electrostatics facilitates the simulation study of many problems involving polyelectrolytes.

  2. σ-SCF: A direct energy-targeting method to mean-field excited states

    NASA Astrophysics Data System (ADS)

    Ye, Hong-Zhou; Welborn, Matthew; Ricke, Nathan D.; Van Voorhis, Troy

    2017-12-01

    The mean-field solutions of electronic excited states are much less accessible than ground state (e.g., Hartree-Fock) solutions. Energy-based optimization methods for excited states, like Δ-SCF (self-consistent field), tend to fall into the lowest solution consistent with a given symmetry—a problem known as "variational collapse." In this work, we combine the ideas of direct energy-targeting and variance-based optimization in order to describe excited states at the mean-field level. The resulting method, σ-SCF, has several advantages. First, it allows one to target any desired excited state by specifying a single parameter: a guess of the energy of that state. It can therefore, in principle, find all excited states. Second, it avoids variational collapse by using a variance-based, unconstrained local minimization. As a consequence, all states—ground or excited—are treated on an equal footing. Third, it provides an alternate approach to locate Δ-SCF solutions that are otherwise hardly accessible by the usual non-aufbau configuration initial guess. We present results for this new method for small atoms (He, Be) and molecules (H2, HF). We find that σ-SCF is very effective at locating excited states, including individual, high energy excitations within a dense manifold of excited states. Like all single determinant methods, σ-SCF shows prominent spin-symmetry breaking for open shell states and our results suggest that this method could be further improved with spin projection.

  3. σ-SCF: A direct energy-targeting method to mean-field excited states.

    PubMed

    Ye, Hong-Zhou; Welborn, Matthew; Ricke, Nathan D; Van Voorhis, Troy

    2017-12-07

    The mean-field solutions of electronic excited states are much less accessible than ground state (e.g., Hartree-Fock) solutions. Energy-based optimization methods for excited states, like Δ-SCF (self-consistent field), tend to fall into the lowest solution consistent with a given symmetry-a problem known as "variational collapse." In this work, we combine the ideas of direct energy-targeting and variance-based optimization in order to describe excited states at the mean-field level. The resulting method, σ-SCF, has several advantages. First, it allows one to target any desired excited state by specifying a single parameter: a guess of the energy of that state. It can therefore, in principle, find all excited states. Second, it avoids variational collapse by using a variance-based, unconstrained local minimization. As a consequence, all states-ground or excited-are treated on an equal footing. Third, it provides an alternate approach to locate Δ-SCF solutions that are otherwise hardly accessible by the usual non-aufbau configuration initial guess. We present results for this new method for small atoms (He, Be) and molecules (H 2 , HF). We find that σ-SCF is very effective at locating excited states, including individual, high energy excitations within a dense manifold of excited states. Like all single determinant methods, σ-SCF shows prominent spin-symmetry breaking for open shell states and our results suggest that this method could be further improved with spin projection.

  4. Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics.

    PubMed

    Sevink, G J A; Schmid, F; Kawakatsu, T; Milano, G

    2017-02-22

    We have extended an existing hybrid MD-SCF simulation technique that employs a coarsening step to enhance the computational efficiency of evaluating non-bonded particle interactions. This technique is conceptually equivalent to the single chain in mean-field (SCMF) method in polymer physics, in the sense that non-bonded interactions are derived from the non-ideal chemical potential in self-consistent field (SCF) theory, after a particle-to-field projection. In contrast to SCMF, however, MD-SCF evolves particle coordinates by the usual Newton's equation of motion. Since collisions are seriously affected by the softening of non-bonded interactions that originates from their evaluation at the coarser continuum level, we have devised a way to reinsert the effect of collisions on the structural evolution. Merging MD-SCF with multi-particle collision dynamics (MPCD), we mimic particle collisions at the level of computational cells and at the same time properly account for the momentum transfer that is important for a realistic system evolution. The resulting hybrid MD-SCF/MPCD method was validated for a particular coarse-grained model of phospholipids in aqueous solution, against reference full-particle simulations and the original MD-SCF model. We additionally implemented and tested an alternative and more isotropic finite difference gradient. Our results show that efficiency is improved by merging MD-SCF with MPCD, as properly accounting for hydrodynamic interactions considerably speeds up the phase separation dynamics, with negligible additional computational costs compared to efficient MD-SCF. This new method enables realistic simulations of large-scale systems that are needed to investigate the applications of self-assembled structures of lipids in nanotechnologies.

  5. A Least-Squares Commutator in the Iterative Subspace Method for Accelerating Self-Consistent Field Convergence.

    PubMed

    Li, Haichen; Yaron, David J

    2016-11-08

    A least-squares commutator in the iterative subspace (LCIIS) approach is explored for accelerating self-consistent field (SCF) calculations. LCIIS is similar to direct inversion of the iterative subspace (DIIS) methods in that the next iterate of the density matrix is obtained as a linear combination of past iterates. However, whereas DIIS methods find the linear combination by minimizing a sum of error vectors, LCIIS minimizes the Frobenius norm of the commutator between the density matrix and the Fock matrix. This minimization leads to a quartic problem that can be solved iteratively through a constrained Newton's method. The relationship between LCIIS and DIIS is discussed. Numerical experiments suggest that LCIIS leads to faster convergence than other SCF convergence accelerating methods in a statistically significant sense, and in a number of cases LCIIS leads to stable SCF solutions that are not found by other methods. The computational cost involved in solving the quartic minimization problem is small compared to the typical cost of SCF iterations and the approach is easily integrated into existing codes. LCIIS can therefore serve as a powerful addition to SCF convergence accelerating methods in computational quantum chemistry packages.

  6. Local time distribution of the SSC-associated HF-Doppler frequency shifts

    NASA Technical Reports Server (NTRS)

    Kikuchi, T.; Sugiuchi, H.; Ishimine, T.

    1985-01-01

    The HF-Doppler frequency shift observed at the storm's sudden commencement is composed of a frequency increase (+) and decrease (-), and classified into four types, SCF(+ -), SCF(- +), SCF(+) and SCF(-). Since the latter two types are special cases of the former two types, two different kinds of electrical field exist in the F region and cause the ExB drift motion of plasma. HUANG (1976) interpreted the frequency increase of SCF(+ -) as due to the westward induction electric field proportional to delta H/ delta t and the succeeding frequency decrease due to the eastward conduction electric field which produces ionospheric currents responsible for the magnetic increase on the ground. In spite of his success in interpreting the SCF(+ -), some other interpretations are needed for the explanation of the whole set of SCF's, particularly SCF(- +). Local time distributions of the SCF's are derived from 41 SCF's which are observed on the HF standard signal (JJY) as received in Okinawa (path length =1600 km) and Kokubunji (60 km). It is shown that the SCF(+ -) appears mainly during the day, whereas the SCF(- +) is observed during the night. The results indicate that the preliminary frequency shift (+) of SCF(+ -) and (-) of SCF(- +) is caused by a westward electric field in the dayside hemisphere, while by an eastward electric field in the nightside hemisphere. The main frequency shift (-) of SCF(+ -) and (+) of SCF(- +) is caused by the reversed electric field. Consequently, the preliminary frequency shift is caused by the dusk-to-dawn electric field, while the main frequency shift by the dawn-to-dusk electric field.

  7. σ -SCF: A Direct Energy-targeting Method To Mean-field Excited States

    NASA Astrophysics Data System (ADS)

    Ye, Hongzhou; Welborn, Matthew; Ricke, Nathan; van Voorhis, Troy

    The mean-field solutions of electronic excited states are much less accessible than ground state (e.g. Hartree-Fock) solutions. Energy-based optimization methods for excited states, like Δ-SCF, tend to fall into the lowest solution consistent with a given symmetry - a problem known as ``variational collapse''. In this work, we combine the ideas of direct energy-targeting and variance-based optimization in order to describe excited states at the mean-field level. The resulting method, σ-SCF, has several advantages. First, it allows one to target any desired excited state by specifying a single parameter: a guess of the energy of that state. It can therefore, in principle, find all excited states. Second, it avoids variational collapse by using a variance-based, unconstrained local minimization. As a consequence, all states - ground or excited - are treated on an equal footing. Third, it provides an alternate approach to locate Δ-SCF solutions that are otherwise hardly accessible by the usual non-aufbau configuration initial guess. We present results for this new method for small atoms (He, Be) and molecules (H2, HF). This work was funded by a Grant from NSF (CHE-1464804).

  8. An analytical derivation of MC-SCF vibrational wave functions for the quantum dynamical simulation of multiple proton transfer reactions: Initial application to protonated water chains

    NASA Astrophysics Data System (ADS)

    Drukker, Karen; Hammes-Schiffer, Sharon

    1997-07-01

    This paper presents an analytical derivation of a multiconfigurational self-consistent-field (MC-SCF) solution of the time-independent Schrödinger equation for nuclear motion (i.e. vibrational modes). This variational MC-SCF method is designed for the mixed quantum/classical molecular dynamics simulation of multiple proton transfer reactions, where the transferring protons are treated quantum mechanically while the remaining degrees of freedom are treated classically. This paper presents a proof that the Hellmann-Feynman forces on the classical degrees of freedom are identical to the exact forces (i.e. the Pulay corrections vanish) when this MC-SCF method is used with an appropriate choice of basis functions. This new MC-SCF method is applied to multiple proton transfer in a protonated chain of three hydrogen-bonded water molecules. The ground state and the first three excited state energies and the ground state forces agree well with full configuration interaction calculations. Sample trajectories are obtained using adiabatic molecular dynamics methods, and nonadiabatic effects are found to be insignificant for these sample trajectories. The accuracy of the excited states will enable this MC-SCF method to be used in conjunction with nonadiabatic molecular dynamics methods. This application differs from previous work in that it is a real-time quantum dynamical nonequilibrium simulation of multiple proton transfer in a chain of water molecules.

  9. An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Albaugh, Alex; Demerdash, Omar; Head-Gordon, Teresa, E-mail: thg@berkeley.edu

    2015-11-07

    We have adapted a hybrid extended Lagrangian self-consistent field (EL/SCF) approach, developed for time reversible Born Oppenheimer molecular dynamics for quantum electronic degrees of freedom, to the problem of classical polarization. In this context, the initial guess for the mutual induction calculation is treated by auxiliary induced dipole variables evolved via a time-reversible velocity Verlet scheme. However, we find numerical instability, which is manifested as an accumulation in the auxiliary velocity variables, that in turn results in an unacceptable increase in the number of SCF cycles to meet even loose convergence tolerances for the real induced dipoles over the coursemore » of a 1 ns trajectory of the AMOEBA14 water model. By diagnosing the numerical instability as a problem of resonances that corrupt the dynamics, we introduce a simple thermostating scheme, illustrated using Berendsen weak coupling and Nose-Hoover chain thermostats, applied to the auxiliary dipole velocities. We find that the inertial EL/SCF (iEL/SCF) method provides superior energy conservation with less stringent convergence thresholds and a correspondingly small number of SCF cycles, to reproduce all properties of the polarization model in the NVT and NVE ensembles accurately. Our iEL/SCF approach is a clear improvement over standard SCF approaches to classical mutual induction calculations and would be worth investigating for application to ab initio molecular dynamics as well.« less

  10. On the extension of the MCSCF/CI method

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C., Jr.; Nelin, C. J.; Komornicki, A.

    1984-01-01

    Research conducted during this period was focused on two main areas: (1) bonding in transition metal oxides; and (2) adsorption of CO on Al and Ni. In both of these theoretical studies a major interest was to obtain a better understanding of the nature of the bonding in transition metal containing systems. The studies used self consistent field (SCF), multi-configuration self cosistent field (MCSCF) and configuration interaction (CI) methods in the treatment of the transition metal oxides and only the SCF method in the adsorption studies. The reports of three principle investigators who contributed to this work during the tenure of the project are presented along with associated published papers.

  11. Probabilistic Simulation of Stress Concentration in Composite Laminates

    NASA Technical Reports Server (NTRS)

    Chamis, C. C.; Murthy, P. L. N.; Liaw, D. G.

    1994-01-01

    A computational methodology is described to probabilistically simulate the stress concentration factors (SCF's) in composite laminates. This new approach consists of coupling probabilistic composite mechanics with probabilistic finite element structural analysis. The composite mechanics is used to probabilistically describe all the uncertainties inherent in composite material properties, whereas the finite element is used to probabilistically describe the uncertainties associated with methods to experimentally evaluate SCF's, such as loads, geometry, and supports. The effectiveness of the methodology is demonstrated by using is to simulate the SCF's in three different composite laminates. Simulated results match experimental data for probability density and for cumulative distribution functions. The sensitivity factors indicate that the SCF's are influenced by local stiffness variables, by load eccentricities, and by initial stress fields.

  12. First and second energy derivative analyses for open-shell self-consistent field wavefunctions

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Yukio; Schaefer, Henry F., III; Frenking, Gernot

    A study of first and second derivatives of the orbital, electronic, nuclear and total energies for the self-consistent field (SCF) wavefunction has been applied to general open-shell SCF systems. The diagonal elements of the Lagrangian matrix for the general open-shell SCF wavefunction are adapted as the 'oŕbital' energies. The first and second derivatives of the orbital energies in terms of the normal coordinates are determined via the finite difference method, while those of the electronic, nuclear and total energies are obtained by analytical techniques. Using three low lying states of the CH2 and H2CO molecules as examples, it is demonstrated that the derivatives of the SCF energetic quantities with respect to the normal coordinates provide useful chemical information concerning the respective molecular structures and reactivities. The conventional concept of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) has been extended to the molecular vibrational motion, and the terminology of vibrationally active MOs (va-MOs), va-HOMO and va-LUMO has been introduced for each normal coordinate. The energy derivative analysis method may be used as a powerful semi-quantitative modelin understanding and interpreting various chemical phenomena.

  13. Self-consistent field for fragmented quantum mechanical model of large molecular systems.

    PubMed

    Jin, Yingdi; Su, Neil Qiang; Xu, Xin; Hu, Hao

    2016-01-30

    Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter-fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block-wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods. © 2015 Wiley Periodicals, Inc.

  14. [Effects of controlled-release fertilizers on summer maize grain yield, field ammonia volatilization, and fertilizer nitrogen use efficiency].

    PubMed

    Zhao, Bin; Dong, Shu-Ting; Wang, Kong-Jun; Zhang, Ji-Wang; Liu, Peng

    2009-11-01

    A field experiment with colophony-coated fertilizer (CRF) and sulfur-coated fertilizer (SCF) showed that under the same application rates of N, P and K, applying CRF and SCF increased the summer maize grain yield by 13.15% and 14.15%, respectively, compared to the application of common compound fertilizer CCF. When the applied amount of CRF and SCF was decreased by 25%, the yield increment was 9.69% and 10.04%, respectively; and when the applied amount of CRF and SCF was decreased by 50%, the yield had less difference with that under CCF application. The field ammonia volatilization rate in treatments CRF and SCF increased slowly, with a peak appeared 7 days later than that in treatment CCF, and the total amount of ammonia volatilization in treatments CRF and SCF was ranged from 0.78 kg N x hm(-2) to 4.43 kg N x hm(-2), with a decrement of 51.34%-91.34% compared to that in treatment CCF. The fertilizer nitrogen use efficiency and agronomic nitrogen use efficiency of CRF and SCF were also significantly higher than those of CCF.

  15. Supercritical Fluid Technologies to Fabricate Proliposomes.

    PubMed

    Falconer, James R; Svirskis, Darren; Adil, Ali A; Wu, Zimei

    2015-01-01

    Proliposomes are stable drug carrier systems designed to form liposomes upon addition of an aqueous phase. In this review, current trends in the use of supercritical fluid (SCF) technologies to prepare proliposomes are discussed. SCF methods are used in pharmaceutical research and industry to address limitations associated with conventional methods of pro/liposome fabrication. The SCF solvent methods of proliposome preparation are eco-friendly (known as green technology) and, along with the SCF anti-solvent methods, could be advantageous over conventional methods; enabling better design of particle morphology (size and shape). The major hurdles of SCF methods include poor scalability to industrial manufacturing which may result in variable particle characteristics. In the case of SCF anti-solvent methods, another hurdle is the reliance on organic solvents. However, the amount of solvent required is typically less than that used by the conventional methods. Another hurdle is that most of the SCF methods used have complicated manufacturing processes, although once the setup has been completed, SCF technologies offer a single-step process in the preparation of proliposomes compared to the multiple steps required by many other methods. Furthermore, there is limited research into how proliposomes will be converted into liposomes for the end-user, and how such a product can be prepared reproducibly in terms of vesicle size and drug loading. These hurdles must be overcome and with more research, SCF methods, especially where the SCF acts as a solvent, have the potential to offer a strong alternative to the conventional methods to prepare proliposomes.

  16. Self-consistent-field KKR-CPA calculations in the atomic-sphere approximations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Singh, P.P. Gonis, A.; de Fontaine, D.

    1991-12-03

    We present a formulation of the Korringa-Kohn-Rostoker coherent potential approximation (KKR-CPA) for the treatment of substitutionally disordered alloys within the KKR atomic-sphere approximations (ASA). This KKR-ASA-CPA represents the first step toward the implementation of a full cell potential CPA, and combines the accuracy of the KKR-CPA method with the flexibility of treating complex crystal structures. The accuracy of this approach has been tested by comparing the self-consistent-field (SCF) KKR-ASA-CPA calculations of Cu-Pd alloys with experimental results and previous SCF-KKR-CPA calculations.

  17. Self-consistent-field perturbation theory for the Schröautdinger equation

    NASA Astrophysics Data System (ADS)

    Goodson, David Z.

    1997-06-01

    A method is developed for using large-order perturbation theory to solve the systems of coupled differential equations that result from the variational solution of the Schröautdinger equation with wave functions of product form. This is a noniterative, computationally efficient way to solve self-consistent-field (SCF) equations. Possible applications include electronic structure calculations using products of functions of collective coordinates that include electron correlation, vibrational SCF calculations for coupled anharmonic oscillators with selective coupling of normal modes, and ab initio calculations of molecular vibration spectra without the Born-Oppenheimer approximation.

  18. Communication: A difference density picture for the self-consistent field ansatz.

    PubMed

    Parrish, Robert M; Liu, Fang; Martínez, Todd J

    2016-04-07

    We formulate self-consistent field (SCF) theory in terms of an interaction picture where the working variable is the difference density matrix between the true system and a corresponding superposition of atomic densities. As the difference density matrix directly represents the electronic deformations inherent in chemical bonding, this "difference self-consistent field (dSCF)" picture provides a number of significant conceptual and computational advantages. We show that this allows for a stable and efficient dSCF iterative procedure with wholly single-precision Coulomb and exchange matrix builds. We also show that the dSCF iterative procedure can be performed with aggressive screening of the pair space. These approximations are tested and found to be accurate for systems with up to 1860 atoms and >10 000 basis functions, providing for immediate overall speedups of up to 70% in the heavily optimized TeraChem SCF implementation.

  19. Communication: A difference density picture for the self-consistent field ansatz

    NASA Astrophysics Data System (ADS)

    Parrish, Robert M.; Liu, Fang; Martínez, Todd J.

    2016-04-01

    We formulate self-consistent field (SCF) theory in terms of an interaction picture where the working variable is the difference density matrix between the true system and a corresponding superposition of atomic densities. As the difference density matrix directly represents the electronic deformations inherent in chemical bonding, this "difference self-consistent field (dSCF)" picture provides a number of significant conceptual and computational advantages. We show that this allows for a stable and efficient dSCF iterative procedure with wholly single-precision Coulomb and exchange matrix builds. We also show that the dSCF iterative procedure can be performed with aggressive screening of the pair space. These approximations are tested and found to be accurate for systems with up to 1860 atoms and >10 000 basis functions, providing for immediate overall speedups of up to 70% in the heavily optimized TeraChem SCF implementation.

  20. Study of high-performance canonical molecular orbitals calculation for proteins

    NASA Astrophysics Data System (ADS)

    Hirano, Toshiyuki; Sato, Fumitoshi

    2017-11-01

    The canonical molecular orbital (CMO) calculation can help to understand chemical properties and reactions in proteins. However, it is difficult to perform the CMO calculation of proteins because of its self-consistent field (SCF) convergence problem and expensive computational cost. To certainly obtain the CMO of proteins, we work in research and development of high-performance CMO applications and perform experimental studies. We have proposed the third-generation density-functional calculation method of calculating the SCF, which is more advanced than the FILE and direct method. Our method is based on Cholesky decomposition for two-electron integrals calculation and the modified grid-free method for the pure-XC term evaluation. By using the third-generation density-functional calculation method, the Coulomb, the Fock-exchange, and the pure-XC terms can be given by simple linear algebraic procedure in the SCF loop. Therefore, we can expect to get a good parallel performance in solving the SCF problem by using a well-optimized linear algebra library such as BLAS on the distributed memory parallel computers. The third-generation density-functional calculation method is implemented to our program, ProteinDF. To achieve computing electronic structure of the large molecule, not only overcoming expensive computation cost and also good initial guess for safe SCF convergence are required. In order to prepare a precise initial guess for the macromolecular system, we have developed the quasi-canonical localized orbital (QCLO) method. The QCLO has the characteristics of both localized and canonical orbital in a certain region of the molecule. We have succeeded in the CMO calculations of proteins by using the QCLO method. For simplified and semi-automated calculation of the QCLO method, we have also developed a Python-based program, QCLObot.

  1. Dielectric function and plasmons in graphene: A self-consistent-field calculation within a Markovian master equation formalism

    DOE PAGES

    Karimi, F.; Davoody, A. H.; Knezevic, I.

    2016-05-12

    We introduce a method for calculating the dielectric function of nanostructures with an arbitrary band dispersion and Bloch wave functions. The linear response of a dissipative electronic system to an external electromagnetic field is calculated by a self-consistent-field approach within a Markovian master equation formalism (SCF-MMEF) coupled with full-wave electromagnetic equations. The SCF-MMEF accurately accounts for several concurrent scattering mechanisms. The method captures interband electron-hole-pair generation, as well as the interband and intraband electron scattering with phonons and impurities. We employ the SCF-MMEF to calculate the dielectric function, complex conductivity, and loss function for supported graphene. From the loss-function maximum,more » we obtain plasmon dispersion and propagation length for different substrate types [nonpolar diamondlike carbon (DLC) and polar SiO 2 and hBN], impurity densities, carrier densities, and temperatures. Plasmons on the two polar substrates are suppressed below the highest surface phonon energy, while the spectrum is broad on the nonpolar DLC. Plasmon propagation lengths are comparable on polar and nonpolar substrates and are on the order of tens of nanometers, considerably shorter than previously reported. As a result, they improve with fewer impurities, at lower temperatures, and at higher carrier densities.« less

  2. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can bemore » rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.« less

  3. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

    DOE PAGES

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; ...

    2017-03-03

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can bemore » rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.« less

  4. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory.

    PubMed

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; Drisdell, Walter S; Shirley, Eric L; Prendergast, David

    2017-03-03

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can be rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.

  5. Perturbation expansion theory corrected from basis set superposition error. I. Locally projected excited orbitals and single excitations.

    PubMed

    Nagata, Takeshi; Iwata, Suehiro

    2004-02-22

    The locally projected self-consistent field molecular orbital method for molecular interaction (LP SCF MI) is reformulated for multifragment systems. For the perturbation expansion, two types of the local excited orbitals are defined; one is fully local in the basis set on a fragment, and the other has to be partially delocalized to the basis sets on the other fragments. The perturbation expansion calculations only within single excitations (LP SE MP2) are tested for water dimer, hydrogen fluoride dimer, and colinear symmetric ArM+ Ar (M = Na and K). The calculated binding energies of LP SE MP2 are all close to the corresponding counterpoise corrected SCF binding energy. By adding the single excitations, the deficiency in LP SCF MI is thus removed. The results suggest that the exclusion of the charge-transfer effects in LP SCF MI might indeed be the cause of the underestimation for the binding energy. (c) 2004 American Institute of Physics.

  6. Self-Consistent Optimization of Excited States within Density-Functional Tight-Binding.

    PubMed

    Kowalczyk, Tim; Le, Khoa; Irle, Stephan

    2016-01-12

    We present an implementation of energies and gradients for the ΔDFTB method, an analogue of Δ-self-consistent-field density functional theory (ΔSCF) within density-functional tight-binding, for the lowest singlet excited state of closed-shell molecules. Benchmarks of ΔDFTB excitation energies, optimized geometries, Stokes shifts, and vibrational frequencies reveal that ΔDFTB provides a qualitatively correct description of changes in molecular geometries and vibrational frequencies due to excited-state relaxation. The accuracy of ΔDFTB Stokes shifts is comparable to that of ΔSCF-DFT, and ΔDFTB performs similarly to ΔSCF with the PBE functional for vertical excitation energies of larger chromophores where the need for efficient excited-state methods is most urgent. We provide some justification for the use of an excited-state reference density in the DFTB expansion of the electronic energy and demonstrate that ΔDFTB preserves many of the properties of its parent ΔSCF approach. This implementation fills an important gap in the extended framework of DFTB, where access to excited states has been limited to the time-dependent linear-response approach, and affords access to rapid exploration of a valuable class of excited-state potential energy surfaces.

  7. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Parrish, Robert M.; Liu, Fang; Martínez, Todd J., E-mail: toddjmartinez@gmail.com

    We formulate self-consistent field (SCF) theory in terms of an interaction picture where the working variable is the difference density matrix between the true system and a corresponding superposition of atomic densities. As the difference density matrix directly represents the electronic deformations inherent in chemical bonding, this “difference self-consistent field (dSCF)” picture provides a number of significant conceptual and computational advantages. We show that this allows for a stable and efficient dSCF iterative procedure with wholly single-precision Coulomb and exchange matrix builds. We also show that the dSCF iterative procedure can be performed with aggressive screening of the pair space.more » These approximations are tested and found to be accurate for systems with up to 1860 atoms and >10 000 basis functions, providing for immediate overall speedups of up to 70% in the heavily optimized TERACHEM SCF implementation.« less

  8. A multireference perturbation method using non-orthogonal Hartree-Fock determinants for ground and excited states

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yost, Shane R.; Kowalczyk, Tim; Van Voorhis, Troy, E-mail: tvan@mit.edu

    2013-11-07

    In this article we propose the ΔSCF(2) framework, a multireference strategy based on second-order perturbation theory, for ground and excited electronic states. Unlike the complete active space family of methods, ΔSCF(2) employs a set of self-consistent Hartree-Fock determinants, also known as ΔSCF states. Each ΔSCF electronic state is modified by a first-order correction from Møller-Plesset perturbation theory and used to construct a Hamiltonian in a configuration interactions like framework. We present formulas for the resulting matrix elements between nonorthogonal states that scale as N{sub occ}{sup 2}N{sub virt}{sup 3}. Unlike most active space methods, ΔSCF(2) treats the ground and excited statemore » determinants even-handedly. We apply ΔSCF(2) to the H{sub 2}, hydrogen fluoride, and H{sub 4} systems and show that the method provides accurate descriptions of ground- and excited-state potential energy surfaces with no single active space containing more than 10 ΔSCF states.« less

  9. A general parallel sparse-blocked matrix multiply for linear scaling SCF theory

    NASA Astrophysics Data System (ADS)

    Challacombe, Matt

    2000-06-01

    A general approach to the parallel sparse-blocked matrix-matrix multiply is developed in the context of linear scaling self-consistent-field (SCF) theory. The data-parallel message passing method uses non-blocking communication to overlap computation and communication. The space filling curve heuristic is used to achieve data locality for sparse matrix elements that decay with “separation”. Load balance is achieved by solving the bin packing problem for blocks with variable size.With this new method as the kernel, parallel performance of the simplified density matrix minimization (SDMM) for solution of the SCF equations is investigated for RHF/6-31G ∗∗ water clusters and RHF/3-21G estane globules. Sustained rates above 5.7 GFLOPS for the SDMM have been achieved for (H 2 O) 200 with 95 Origin 2000 processors. Scalability is found to be limited by load imbalance, which increases with decreasing granularity, due primarily to the inhomogeneous distribution of variable block sizes.

  10. Three-dimensional carbon fibers and method and apparatus for their production

    DOEpatents

    Muradov, Nazim Z [Melbourne, FL

    2012-02-21

    This invention relates to novel three-dimensional (3D) carbon fibers which are original (or primary) carbon fibers (OCF) with secondary carbon filaments (SCF) grown thereon, and, if desired, tertiary carbon filaments (TCF) are grown from the surface of SCF forming a filamentous carbon network with high surface area. The methods and apparatus are provided for growing SCF on the OCF by thermal decomposition of carbonaceous gases (CG) over the hot surface of the OCF without use of metal-based catalysts. The thickness and length of SCF can be controlled by varying operational conditions of the process, e.g., the nature of CG, temperature, residence time, etc. The optional activation step enables one to produce 3D activated carbon fibers with high surface area. The method and apparatus are provided for growing TCF on the SCF by thermal decomposition of carbonaceous gases over the hot surface of the SCF using metal catalyst particles.

  11. Polarized atomic orbitals for self-consistent field electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Lee, Michael S.; Head-Gordon, Martin

    1997-12-01

    We present a new self-consistent field approach which, given a large "secondary" basis set of atomic orbitals, variationally optimizes molecular orbitals in terms of a small "primary" basis set of distorted atomic orbitals, which are simultaneously optimized. If the primary basis is taken as a minimal basis, the resulting functions are termed polarized atomic orbitals (PAO's) because they are valence (or core) atomic orbitals which have distorted or polarized in an optimal way for their molecular environment. The PAO's derive their flexibility from the fact that they are formed from atom-centered linear-combinations of the larger set of secondary atomic orbitals. The variational conditions satisfied by PAO's are defined, and an iterative method for performing a PAO-SCF calculation is introduced. We compare the PAO-SCF approach against full SCF calculations for the energies, dipoles, and molecular geometries of various molecules. The PAO's are potentially useful for studying large systems that are currently intractable with larger than minimal basis sets, as well as offering potential interpretative benefits relative to calculations in extended basis sets.

  12. A Phase-Space Approach to Collisionless Stellar Systems Using a Particle Method

    NASA Astrophysics Data System (ADS)

    Hozumi, Shunsuke

    1997-10-01

    A particle method for reproducing the phase space of collisionless stellar systems is described. The key idea originates in Liouville's theorem, which states that the distribution function (DF) at time t can be derived from tracing necessary orbits back to t = 0. To make this procedure feasible, a self-consistent field (SCF) method for solving Poisson's equation is adopted to compute the orbits of arbitrary stars. As an example, for the violent relaxation of a uniform density sphere, the phase-space evolution generated by the current method is compared to that obtained with a phase-space method for integrating the collisionless Boltzmann equation, on the assumption of spherical symmetry. Excellent agreement is found between the two methods if an optimal basis set for the SCF technique is chosen. Since this reproduction method requires only the functional form of initial DFs and does not require any assumptions to be made about the symmetry of the system, success in reproducing the phase-space evolution implies that there would be no need of directly solving the collisionless Boltzmann equation in order to access phase space even for systems without any special symmetries. The effects of basis sets used in SCF simulations on the reproduced phase space are also discussed.

  13. A Field-Shaking System to Reduce the Screening Current-Induced Field in the 800-MHz HTS Insert of the MIT 1.3-GHz LTS/HTS NMR Magnet: A Small-Model Study.

    PubMed

    Lee, Jiho; Park, Dongkeun; Michael, Philip C; Noguchi, So; Bascuñán, Juan; Iwasa, Yukikazu

    2018-04-01

    In this paper, we present experimental results, of a small-model study, from which we plan to develop and apply a full-scale field-shaking system to reduce the screening current-induced field (SCF) in the 800-MHz HTS Insert (H800) of the MIT 1.3-GHz LTS/HTS NMR magnet (1.3G) currently under construction-the H800 is composed of 3 nested coils, each a stack of no-insulation (NI) REBCO double-pancakes. In 1.3G, H800 is the chief source of a large error field generated by its own SCF. To study the effectiveness of the field-shaking technique, we used two NI REBCO double-pancakes, one from Coil 2 (HCoil2) and one from Coil 3 (HCoil3) of the 3 H800 coils, and placed them in the bore of a 5-T/300-mm room-temperature bore low-temperature superconducting (LTS) background magnet. The background magnet is used not only to induce the SCF in the double-pancakes but also to reduce it by the field-shaking technique. For each run, we induced the SCF in the double-pancakes at an axial location where the external radial field Br > 0, then for the field-shaking, moved them to another location where the external axial field Bz ≫ B R . Due to the geometry of H800 and L500, top double-pancakes of 3 H800 coils will experience the considerable radial magnetic field perpendicular to the REBCO tape surface. To examine the effect of the field-shaking on the SCF, we tested each NI REBCO DP in the absence or presence of a radial field. In this paper, we report 77-K experimental results and analysis of the effect and a few significant remarks of the field-shaking.

  14. Maier-Saupe model of polymer nematics: Comparing free energies calculated with Self Consistent Field theory and Monte Carlo simulations.

    PubMed

    Greco, Cristina; Jiang, Ying; Chen, Jeff Z Y; Kremer, Kurt; Daoulas, Kostas Ch

    2016-11-14

    Self Consistent Field (SCF) theory serves as an efficient tool for studying mesoscale structure and thermodynamics of polymeric liquid crystals (LC). We investigate how some of the intrinsic approximations of SCF affect the description of the thermodynamics of polymeric LC, using a coarse-grained model. Polymer nematics are represented as discrete worm-like chains (WLC) where non-bonded interactions are defined combining an isotropic repulsive and an anisotropic attractive Maier-Saupe (MS) potential. The range of the potentials, σ, controls the strength of correlations due to non-bonded interactions. Increasing σ (which can be seen as an increase of coarse-graining) while preserving the integrated strength of the potentials reduces correlations. The model is studied with particle-based Monte Carlo (MC) simulations and SCF theory which uses partial enumeration to describe discrete WLC. In MC simulations the Helmholtz free energy is calculated as a function of strength of MS interactions to obtain reference thermodynamic data. To calculate the free energy of the nematic branch with respect to the disordered melt, we employ a special thermodynamic integration (TI) scheme invoking an external field to bypass the first-order isotropic-nematic transition. Methodological aspects which have not been discussed in earlier implementations of the TI to LC are considered. Special attention is given to the rotational Goldstone mode. The free-energy landscape in MC and SCF is directly compared. For moderate σ the differences highlight the importance of local non-bonded orientation correlations between segments, which SCF neglects. Simple renormalization of parameters in SCF cannot compensate the missing correlations. Increasing σ reduces correlations and SCF reproduces well the free energy in MC simulations.

  15. Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: Application to solvatochromic shift calculations

    NASA Astrophysics Data System (ADS)

    Minezawa, Noriyuki; Kato, Shigeki

    2007-02-01

    The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

  16. Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: application to solvatochromic shift calculations.

    PubMed

    Minezawa, Noriyuki; Kato, Shigeki

    2007-02-07

    The authors present an implementation of the three-dimensional reference interaction site model self-consistent-field (3D-RISM-SCF) method. First, they introduce a robust and efficient algorithm for solving the 3D-RISM equation. The algorithm is a hybrid of the Newton-Raphson and Picard methods. The Jacobian matrix is analytically expressed in a computationally useful form. Second, they discuss the solute-solvent electrostatic interaction. For the solute to solvent route, the electrostatic potential (ESP) map on a 3D grid is constructed directly from the electron density. The charge fitting procedure is not required to determine the ESP. For the solvent to solute route, the ESP acting on the solute molecule is derived from the solvent charge distribution obtained by solving the 3D-RISM equation. Matrix elements of the solute-solvent interaction are evaluated by the direct numerical integration. A remarkable reduction in the computational time is observed in both routes. Finally, the authors implement the first derivatives of the free energy with respect to the solute nuclear coordinates. They apply the present method to "solute" water and formaldehyde in aqueous solvent using the simple point charge model, and the results are compared with those from other methods: the six-dimensional molecular Ornstein-Zernike SCF, the one-dimensional site-site RISM-SCF, and the polarizable continuum model. The authors also calculate the solvatochromic shifts of acetone, benzonitrile, and nitrobenzene using the present method and compare them with the experimental and other theoretical results.

  17. Dynamic Self-Consistent Field Theories for Polymer Blends and Block Copolymers

    NASA Astrophysics Data System (ADS)

    Kawakatsu, Toshihiro

    Understanding the behavior of the phase separated domain structures and rheological properties of multi-component polymeric systems require detailed information on the dynamics of domains and that of conformations of constituent polymer chains. Self-consistent field (SCF) theory is a useful tool to treat such a problem because the conformation entropy of polymer chains in inhomogeneous systems can be evaluated quantitatively using this theory. However, when we turn our attention to the dynamic properties in a non-equilibrium state, the basic assumption of the SCF theory, i.e. the assumption of equilibrium chain conformation, breaks down. In order to avoid such a difficulty, dynamic SCF theories were developed. In this chapter, we give a brief review of the recent developments of dynamic SCF theories, and discuss where the cutting-edge of this theory is.

  18. Spatial and Temporal Variations of a Screening Current Induced Magnetic Field in a Double-Pancake HTS Insert of an LTS/HTS NMR Magnet

    PubMed Central

    Ahn, Min Cheol; Yagai, Tsuyoshi; Hahn, Seungyong; Ando, Ryuya; Bascuñán, Juan; Iwasa, Yukikazu

    2010-01-01

    This paper presents experimental and simulation results of a screening current induced magnetic field (SCF) in a high temperature superconductor (HTS) insert that constitutes a low-/high-temperature superconductor (LTS/HTS) NMR magnet. In this experiment, the HTS insert, a stack of 50 double-pancake coils, each wound with Bi2223 tape, was operated at 77 K. A screening current was induced in the HTS insert by three magnetic field sources: 1) a self field from the HTS insert; 2) an external field from a 5-T background magnet; and 3) combinations of 1) and 2). For each field excitation, which induced an SCF, its axial field distribution and temporal variations were measured and compared with simulation results based on the critical state model. Agreement on field profile between experiment and simulation is satisfactory but more work is needed to make the simulation useful for designing shim coils that will cancel the SCF. PMID:20401187

  19. A complete active space valence bond method with nonorthogonal orbitals

    NASA Astrophysics Data System (ADS)

    Hirao, Kimihiko; Nakano, Haruyuki; Nakayama, Kenichi

    1997-12-01

    A complete active space self-consistent field (SCF) wave function is transformed into a valence bond type representation built from nonorthogonal orbitals, each strongly localized on a single atom. Nonorthogonal complete active space SCF orbitals are constructed by Ruedenberg's projected localization procedure so that they have maximal overlaps with the corresponding minimum basis set of atomic orbitals of the free-atoms. The valence bond structures which are composed of such nonorthogonal quasiatomic orbitals constitute the wave function closest to the concept of the oldest and most simple valence bond method. The method is applied to benzene, butadiene, hydrogen, and methane molecules and compared to the previously proposed complete active space valence bond approach with orthogonal orbitals. The results demonstrate the validity of the method as a powerful tool for describing the electronic structure of various molecules.

  20. The ordering of symmetric diblock copolymers: A comparison of self-consistent-field and density functional approaches

    NASA Astrophysics Data System (ADS)

    Nath, Shyamal K.; McCoy, John D.; Curro, John G.; Saunders, Randall S.

    1997-02-01

    Polymer reference interaction site model (PRISM) based density functional (DF) theory is used to evaluate the structure and thermodynamics of structurally symmetric, freely jointed, diblock chains with 0.50 volume fraction. These results are compared to the results of self-consistent-field (SCF) theory. Agreement between the predictions of the SCF and DF theories is found for the lamella spacing well above the order-disorder transition (ODT) and for the qualitative behavior of the interfacial thickness as a function of both chain length and Flory-Huggins χ parameter. Disagreement is found for the magnitude of the interfacial thickness where DF theory indicates that the thickness is 1.7±0.2 times larger than that predicted by SCF theory. It appears that behavior on the monomer length scale is sensitive to system specific details which are neglected by SCF theory.

  1. In vitro hydrolytic digestion, glycemic response in dogs, and true metabolizable energy content of soluble corn fibers.

    PubMed

    de Godoy, M R C; Knapp, B K; Parsons, C M; Swanson, K S; Fahey, George C

    2014-06-01

    The objective of this research was to measure in vitro hydrolytic digestion, glycemic and insulinemic responses in dogs, and true ME (TMEn) content of select soluble corn fibers (SCF) in roosters. The first generation (G1) SCF included hydrochloric acid-treated corn syrup (G1-CS-HCl), an SCF with an increased total dietary fiber (TDF) content (G1-SCF-HCl), an SCF that was spray-dried (G1-SCF-SD), and a hydrogenated SCF (G1-SCF-hydrog). The second generation (G2) SCF included those prepared using phosphoric acid catalyzation in both a liquid [G2-SCF-phos (Lq)] and powder [G2-SCF-phos (Pw)] form, and SCF that were prepared using hydrochloric acid catalyzation in both a liquid [G2-SCF-HCl (Lq)] and powder [G2-SCF-HCl (Pw)] form. Also, in the G2 set of samples were SCF prepared using the same method, but in 3 separate batches, all of which contained 70% TDF and 15% sugars. Two were in liquid form [G2-SCF-phos+HCl (Lq1)] and [G2-SCF-phos+HCl (Lq2)], and one in powder form ([G2-SCF-phos+HCl (Pw)]. A lower sugar form (80% TDF and 5% sugar) of SCF was also evaluated (G2-SCF-low sugar). Glucose was the major free sugar and bound monosaccharide in all SCF except for G1-SCF-hydrog that had greater concentrations of sorbitol. All SCF had intermediate to low amounts of monosaccharides released as a result of in vitro hydrolytic digestion, with glucose being the primary sugar component released. The G1-SCF were more digestible in vitro (approximately 50%) compared to G2-SCF (approximately 32%). All SCF had attenuated glycemic responses in adult dogs compared to a maltodextrin control (P < 0.05). The G2-SCF, on average, had lower glycemic responses and TMEn values in roosters than G1-SCF. All SCF had low free sugar concentrations with varying degrees of resistance to digestion, reduced caloric content, and attenuated glycemic and insulinemic responses in adult dogs. These ingredients are potential candidates for inclusion in reduced calorie and low glycemic canine diets.

  2. Structure and vibrational spectra of pyridine betaine hydrochloride

    NASA Astrophysics Data System (ADS)

    Szafran, Mirosław; Koput, Jacek; Baran, Jan; Głowiak, Tadeusz

    1997-12-01

    The crystal structure of pyridine betaine hydrochloride (PBET·HCl) was determined by X-ray diffraction to be monoclinic, space group {P2 1}/{c} with a = 8.533(2) Å, b = 9.548(2) Å, c = 10.781(2) Å, β = 107.228(3)° and Z = 4. Betaine is protonated and the carboxyl group forms a hydrogen bond with the chloride ion: O·Cl - distance is 2.928(3) Å. The interaction of pyridine betaine (PBET) with HCl was examined by ab initio self-consistent field (SCF), second-order Møller-Plesset (MP2) and density functional theory (DFT) methods using the 6-31G(d,p) basis set. Two minima are located in the potential surface at the SCF level (PBETH +·Cl - and PBET·HCl, with the latter being 1.2 kcal mol -1 lower in energy) and only one minimum (PBET·HCl) at the MP2 and DFT levels. The molecular parameters of PBETH +·Cl -, computed by the SCF method, reproduce the corresponding experimental data. The computed vibrational frequencies of PBETH +·Cl - resemble correctly the experimental vibrational spectrum in the solid state. The root-mean-square (r.m.s.) deviations between the experimental and calculated SCF frequencies are 65 cm -1 for all bands and 15 cm -1 without the νClH band. All measured IR bands were interpreted in terms of the calculated vibrational models.

  3. Implementation of the diagonalization-free algorithm in the self-consistent field procedure within the four-component relativistic scheme.

    PubMed

    Hrdá, Marcela; Kulich, Tomáš; Repiský, Michal; Noga, Jozef; Malkina, Olga L; Malkin, Vladimir G

    2014-09-05

    A recently developed Thouless-expansion-based diagonalization-free approach for improving the efficiency of self-consistent field (SCF) methods (Noga and Šimunek, J. Chem. Theory Comput. 2010, 6, 2706) has been adapted to the four-component relativistic scheme and implemented within the program package ReSpect. In addition to the implementation, the method has been thoroughly analyzed, particularly with respect to cases for which it is difficult or computationally expensive to find a good initial guess. Based on this analysis, several modifications of the original algorithm, refining its stability and efficiency, are proposed. To demonstrate the robustness and efficiency of the improved algorithm, we present the results of four-component diagonalization-free SCF calculations on several heavy-metal complexes, the largest of which contains more than 80 atoms (about 6000 4-spinor basis functions). The diagonalization-free procedure is about twice as fast as the corresponding diagonalization. Copyright © 2014 Wiley Periodicals, Inc.

  4. Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

    PubMed

    Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

    2018-06-11

    Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

  5. Acceleration of Semiempirical QM/MM Methods through Message Passage Interface (MPI), Hybrid MPI/Open Multiprocessing, and Self-Consistent Field Accelerator Implementations.

    PubMed

    Ojeda-May, Pedro; Nam, Kwangho

    2017-08-08

    The strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in CHARMM are described. The serial version of the code was first profiled to identify routines that required parallelization. Afterward, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM message passage interface (MPI) machinery. In the second approach, two different self-consistent field (SCF) energy convergence accelerators were implemented using density and Fock matrices as targets for their extrapolations in the SCF procedure. In the third approach, the entire QM/MM and MM energy routines were accelerated by implementing the hybrid MPI/open multiprocessing (OpenMP) model in which both the task- and loop-level parallelization strategies were adopted to balance loads between different OpenMP threads. The present implementation was tested on two solvated enzyme systems (including <100 QM atoms) and an S N 2 symmetric reaction in water. The MPI version exceeded existing SE QM methods in CHARMM, which include the SCC-DFTB and SQUANTUM methods, by at least 4-fold. The use of SCF convergence accelerators further accelerated the code by ∼12-35% depending on the size of the QM region and the number of CPU cores used. Although the MPI version displayed good scalability, the performance was diminished for large numbers of MPI processes due to the overhead associated with MPI communications between nodes. This issue was partially overcome by the hybrid MPI/OpenMP approach which displayed a better scalability for a larger number of CPU cores (up to 64 CPUs in the tested systems).

  6. Dosimetry and field matching for radiotherapy to the breast and superclavicular fossa

    NASA Astrophysics Data System (ADS)

    Winfield, Elizabeth

    Radiotherapy for early breast cancer aims to achieve local disease control and decrease loco-regional recurrence rates. Treatment may be directed to breast or chest wall alone or, include regional lymph nodes. When using tangential fields to treat the breast a separate anterior field directed to the axilla and supraclavicular fossa (SCF) is needed to treat nodal areas. The complex geometry of this region necessitates matching of adjacent radiation fields in three dimensions. The potential exists for zones of overdosage or underdosage along the match line. Cosmetic results may be compromised if treatment fields are not accurately aligned. Techniques for field matching vary between centres in the UK. A study of dosimetry across the match line region using different techniques, as reported in the multi-centre START Trial Quality Assurance (QA) programme, was undertaken. A custom-made anthropomorphic phantom was designed to assess dose distribution in three dimensions using film dosimetry. Methods with varying degrees of complexity were employed to match tangential and SCF beams. Various techniques combined half beam blocking and machine rotations to achieve geometric alignment. Matching of asymmetric beams allowed a single isocentre technique to be used. Where field matching was not undertaken a gap between tangential and SCF fields was employed. Results demonstrated differences between techniques in addition to variations within the same technique between different centres. Geometric alignment techniques produced more homogenous dose distributions in the match region than gap techniques or those techniques not correcting for field divergence. For this multi-centre assessment of match plane techniques film dosimetry used in conjunction with a breast shaped phantom provided relative dose information. This study has highlighted the difficulties of matching treatment fields to achieve homogenous dose distribution through the region of the match plane and the degree of inhomogeneity as a consequence of a gap between treatment fields.

  7. Composition engineering of single crystalline films based on the multicomponent garnet compounds

    NASA Astrophysics Data System (ADS)

    Zorenko, Yuriy; Gorbenko, Vitalii; Zorenko, Tetiana; Paprocki, Kazimierz; Bilski, Paweł; Twardak, Anna; Voznyak, Taras; Sidletskiy, Oleg; Gerasimov, Yaroslav; Gryniov, Boris; Fedorov, Alexandr

    2016-11-01

    The paper demonstrates our last achievement in development of the novel scintillating screens based on single crystalline films (SCF) of Ce doped multicomponent garnets using the Liquid Phase Epitaxy (LPE) method. We report in this work the optimized content and excellent scintillation properties of SCF of Lu3-xGdxAl5-yGayO12, Lu3-xTbxAl5-yGayO12 and TbxGdxAl5-yGayO12 garnet compounds grown by the LPE method from PbOsbnd B2O3 based melt-solution onto Gd3Al2.5Ga2.5O12 and YAG substrates. We also show that the Tb1.5Gd1.5Al2.5Ga2.5O12:Ce SCF possess the highest light yield (LY) in comparison with all ever grown garnet SCF scintillators. Namely, the LY of these SCF exceeds by 3.8 and 1.85 times the LY values of the best samples of YAG:Ce and LuAG:Ce SCF scintillators, respectively. The SCF samples of the mentioned compounds show low thermoluminescence in the above room temperature range and relatively fast scintillation decay time t1/e in the 180-200 ns range.

  8. Characterization and stability studies of a novel liposomal cyclosporin A prepared using the supercritical fluid method: comparison with the modified conventional Bangham method

    PubMed Central

    Karn, Pankaj Ranjan; Cho, Wonkyung; Park, Hee-Jun; Park, Jeong-Sook; Hwang, Sung-Joo

    2013-01-01

    A novel method to prepare cyclosporin A encapsulated liposomes was introduced using supercritical fluid of carbon dioxide (SCF-CO2) as an antisolvent. To investigate the strength of the newly developed SCF-CO2 method compared with the modified conventional Bangham method, particle size, zeta potential, and polydispersity index (PDI) of both liposomal formulations were characterized and compared. In addition, entrapment efficiency (EE) and drug loading (DL) characteristics were analyzed by reversed-phase high-performance liquid chromatography. Significantly larger particle size and PDI were revealed from the conventional method, while EE (%) and DL (%) did not exhibit any significant differences. The SCF-CO2 liposomes were found to be relatively smaller, multilamellar, and spherical with a smoother surface as determined by transmission electron microscopy. SCF-CO2 liposomes showed no significant differences in their particle size and PDI after more than 3 months, whereas conventional liposomes exhibited significant changes in their particle size. The initial yield (%), EE (%), and DL (%) of SCF-CO2 liposomes and conventional liposomes were 90.98 ± 2.94, 92.20 ± 1.36, 20.99 ± 0.84 and 90.72 ± 2.83, 90.24 ± 1.37, 20.47 ± 0.94, respectively, which changed after 14 weeks to 86.65 ± 0.30, 87.63 ± 0.72, 18.98 ± 0.22 and 75.04 ± 8.80, 84.59 ± 5.13, 15.94 ± 2.80, respectively. Therefore, the newly developed SCF-CO2 method could be a better alternative compared with the conventional method and may provide a promising approach for large-scale production of liposomes. PMID:23378759

  9. Comparison of the Effects of Carbon Ion and Photon Irradiation on the Angiogenic Response in Human Lung Adenocarcinoma Cells

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kamlah, Florentine, E-mail: Kamlah@staff.uni-marburg.de; Haenze, Joerg; Arenz, Andrea

    2011-08-01

    Purpose: Radiotherapy resistance is a commonly encountered problem in cancer treatment. In this regard, stabilization of endothelial cells and release of angiogenic factors by cancer cells contribute to this problem. In this study, we used human lung adenocarcinoma (A549) cells to compare the effects of carbon ion and X-ray irradiation on the cells' angiogenic response. Methods and Materials: A549 cells were irradiated with biologically equivalent doses for cell survival of either carbon ions (linear energy transfer, 170 keV/{mu}m; energy of 9.8 MeV/u on target) or X-rays and injected with basement membrane matrix into BALB/c nu/nu mice to generate a plug,more » allowing quantification of angiogenesis by blood vessel enumeration. The expression of angiogenic factors (VEGF, PlGF, SDF-1, and SCF) was assessed at the mRNA and secreted protein levels by using real-time reverse transcription-PCR and enzyme-linked immunosorbent assay. Signal transduction mediated by stem cell factor (SCF) was assessed by phosphorylation of its receptor c-Kit. For inhibition of SCF/c-Kit signaling, a specific SCF/c-Kit inhibitor (ISCK03) was used. Results: Irradiation of A549 cells with X-rays (6 Gy) but not carbon ions (2 Gy) resulted in a significant increase in blood vessel density (control, 20.71 {+-} 1.55; X-ray, 36.44 {+-} 3.44; carbon ion, 16.33 {+-} 1.03; number per microscopic field). Concordantly, irradiation with X-rays but not with carbon ions increased the expression of SCF and subsequently caused phosphorylation of c-Kit in endothelial cells. ISCK03 treatment of A549 cells irradiated with X-rays (6 Gy) resulted in a significant decrease in blood vessel density (X-ray, 36.44 {+-} 3.44; X-ray and ISCK03, 4.33 {+-} 0.71; number of microscopic field). These data indicate that irradiation of A549 cells with X-rays but not with carbon ions promotes angiogenesis. Conclusions: The present study provides evidence that SCF is an X-ray-induced mediator of angiogenesis in A549 cells, a phenomenon that could not be observed with carbon ion irradiation. Thus, in this model system evaluating angiogenesis, carbon ion irradiation may have a therapeutic advantage. This observation should be confirmed in orthotopic lung tumor models.« less

  10. Discovering geothermal supercritical fluids: a new frontier for seismic exploration.

    PubMed

    Piana Agostinetti, Nicola; Licciardi, Andrea; Piccinini, Davide; Mazzarini, Francesco; Musumeci, Giovanni; Saccorotti, Gilberto; Chiarabba, Claudio

    2017-11-06

    Exploiting supercritical geothermal resources represents a frontier for the next generation of geothermal electrical power plant, as the heat capacity of supercritical fluids (SCF),which directly impacts on energy production, is much higher than that of fluids at subcritical conditions. Reconnaissance and location of intensively permeable and productive horizons at depth is the present limit for the development of SCF geothermal plants. We use, for the first time, teleseismic converted waves (i.e. receiver function) for discovering those horizons in the crust. Thanks to the capability of receiver function to map buried anisotropic materials, the SCF-bearing horizon is seen as the 4km-depth abrupt termination of a shallow, thick, ultra-high (>30%) anisotropic rock volume, in the center of the Larderello geothermal field. The SCF-bearing horizon develops within the granites of the geothermal field, bounding at depth the vapor-filled heavily-fractured rock matrix that hosts the shallow steam-dominated geothermal reservoirs. The sharp termination at depth of the anisotropic behavior of granites, coinciding with a 2 km-thick stripe of seismicity and diffuse fracturing, points out the sudden change in compressibility of the fluid filling the fractures and is a key-evidence of deep fluids that locally traversed the supercritical conditions. The presence of SCF and fracture permeability in nominally ductile granitic rocks open new scenarios for the understanding of magmatic systems and for geothermal exploitation.

  11. Subcritical Fluid Extraction of Chinese Quince Seed: Optimization and Product Characterization.

    PubMed

    Wang, Li; Wu, Min; Liu, Hua-Min; Ma, Yu-Xiang; Wang, Xue-De; Qin, Guang-Yong

    2017-03-25

    Chinese quince seed (CQS) is an underutilized oil source and a potential source of unsaturated fatty acids and α-tocopherol-rich oil. Subcritical fluid (SCF) extraction is executed at lower pressures and temperatures than the pressures and temperatures used in supercritical fluid extraction. However, no studies on the SCF extraction of CQS oil are reported. Therefore, the objective of this study was to evaluate the use of SCF for the extraction of CQS oil and to compare the use of SCF with the classical Soxhlet (CS) and supercritical CO₂ (SC-CO₂) extraction methods. Response surface methodology (RSM) was used to investigate the extraction conditions: temperature (45-65 °C), time (30-50 min), and solvent/solid ratio (5-15 mL/g). The optimization results showed that the highest yield (27.78%) was obtained at 56.18 °C, 40.20 min, and 12.57 mL/g. The oil extracted by SCF had a higher unsaturated fatty acid content (86.37%-86.75%), higher α-tocopherol content (576.0-847.6 mg/kg), lower acid value (3.97 mg/g), and lower peroxide value (0.02 meq O₂/kg) than extractions using CS and SC-CO 2 methods. The SCF-defatted meal of oilseed exhibited the highest nitrogen solubility index (49.64%) and protein dispersibility index (50.80%), demonstrating that SCF extraction was a promising and efficient technique as an alternative to CS and SC-CO 2 methods, as very mild operating conditions and an eco-friendly solvent can be used in the process with maximum preservation of the quality of the meal.

  12. Pressure calculation in hybrid particle-field simulations

    NASA Astrophysics Data System (ADS)

    Milano, Giuseppe; Kawakatsu, Toshihiro

    2010-12-01

    In the framework of a recently developed scheme for a hybrid particle-field simulation techniques where self-consistent field (SCF) theory and particle models (molecular dynamics) are combined [J. Chem. Phys. 130, 214106 (2009)], we developed a general formulation for the calculation of instantaneous pressure and stress tensor. The expressions have been derived from statistical mechanical definition of the pressure starting from the expression for the free energy functional in the SCF theory. An implementation of the derived formulation suitable for hybrid particle-field molecular dynamics-self-consistent field simulations is described. A series of test simulations on model systems are reported comparing the calculated pressure with those obtained from standard molecular dynamics simulations based on pair potentials.

  13. On the bonding mechanism of CO to Pt(111) and its effect on the vibrational frequency of chemisorbed CO

    NASA Astrophysics Data System (ADS)

    Illas, F.; Zurita, S.; Márquez, A. M.; Rubio, J.

    1997-04-01

    The chemisorption of CO on the atop site of Pt(111) has been simulated by a Pt4 cluster model. Ab initio self consistent field (SCF) and complete active space self consistent field (CASSCF) cluster model wave functions have been obtained for the electronic ground state. Likewise, ab initio SCF wavefunctions have been obtained for two other electronic states. The optimum geometry and vibrational frequencies of chemisorbed CO are reported for the three states. The interaction energy and vibrational shift of chemisorbed CO, with respect to free gas phase CO, have been analyzed for the three electronic states. This analysis is carried out by means of the constrained space orbital variation (CSOV) method. In all cases the bond is found to be dominated by σ donation and π back-donation, known as Blyholder's mechanism. This mechanism is further supported by SCF calculations on a larger, Pt13, cluster model. For both clusters, the CSOV analysis of the vibrational frequency definitely shows that, contrary to previous recent studies, a major contribution to the experimentally observed vibrational shift comes from the π back-donation mechanism. However, we found that, contrary to common belief, σ donation also acts to lower the CO frequency and not to increase it. Physical reasons for such unexpected behaviour are given.

  14. Robust determination of the chemical potential in the pole expansion and selected inversion method for solving Kohn-Sham density functional theory

    NASA Astrophysics Data System (ADS)

    Jia, Weile; Lin, Lin

    2017-10-01

    Fermi operator expansion (FOE) methods are powerful alternatives to diagonalization type methods for solving Kohn-Sham density functional theory (KSDFT). One example is the pole expansion and selected inversion (PEXSI) method, which approximates the Fermi operator by rational matrix functions and reduces the computational complexity to at most quadratic scaling for solving KSDFT. Unlike diagonalization type methods, the chemical potential often cannot be directly read off from the result of a single step of evaluation of the Fermi operator. Hence multiple evaluations are needed to be sequentially performed to compute the chemical potential to ensure the correct number of electrons within a given tolerance. This hinders the performance of FOE methods in practice. In this paper, we develop an efficient and robust strategy to determine the chemical potential in the context of the PEXSI method. The main idea of the new method is not to find the exact chemical potential at each self-consistent-field (SCF) iteration but to dynamically and rigorously update the upper and lower bounds for the true chemical potential, so that the chemical potential reaches its convergence along the SCF iteration. Instead of evaluating the Fermi operator for multiple times sequentially, our method uses a two-level strategy that evaluates the Fermi operators in parallel. In the regime of full parallelization, the wall clock time of each SCF iteration is always close to the time for one single evaluation of the Fermi operator, even when the initial guess is far away from the converged solution. We demonstrate the effectiveness of the new method using examples with metallic and insulating characters, as well as results from ab initio molecular dynamics.

  15. Robust determination of the chemical potential in the pole expansion and selected inversion method for solving Kohn-Sham density functional theory.

    PubMed

    Jia, Weile; Lin, Lin

    2017-10-14

    Fermi operator expansion (FOE) methods are powerful alternatives to diagonalization type methods for solving Kohn-Sham density functional theory (KSDFT). One example is the pole expansion and selected inversion (PEXSI) method, which approximates the Fermi operator by rational matrix functions and reduces the computational complexity to at most quadratic scaling for solving KSDFT. Unlike diagonalization type methods, the chemical potential often cannot be directly read off from the result of a single step of evaluation of the Fermi operator. Hence multiple evaluations are needed to be sequentially performed to compute the chemical potential to ensure the correct number of electrons within a given tolerance. This hinders the performance of FOE methods in practice. In this paper, we develop an efficient and robust strategy to determine the chemical potential in the context of the PEXSI method. The main idea of the new method is not to find the exact chemical potential at each self-consistent-field (SCF) iteration but to dynamically and rigorously update the upper and lower bounds for the true chemical potential, so that the chemical potential reaches its convergence along the SCF iteration. Instead of evaluating the Fermi operator for multiple times sequentially, our method uses a two-level strategy that evaluates the Fermi operators in parallel. In the regime of full parallelization, the wall clock time of each SCF iteration is always close to the time for one single evaluation of the Fermi operator, even when the initial guess is far away from the converged solution. We demonstrate the effectiveness of the new method using examples with metallic and insulating characters, as well as results from ab initio molecular dynamics.

  16. The role of urotensin II and atherosclerotic risk factors in patients with slow coronary flow

    PubMed Central

    Şatıroğlu, Ömer; Emre Durakoğlugil, Murtaza; Çetin, Mustafa; Çiçek, Yüksel; Erdoğan, Turan; Duman, Hakan

    2016-01-01

    Background Slow coronary flow (SCF) is an angiographic finding characterized with delayed opacification of epicardial coronary arteries without obstructive coronary disease. Urotensin II (UII) is an important vascular peptide, which has an important role in hypertension, coronary artery disease, and vascular remodeling in addition to potent vasoconstrictor effect. Objectives We investigated UII levels, hypertension, and other atherosclerotic risk factors in patients with SCF, a variety of coronary artery disease. Methods We enrolled 14 patients with SCF and 29 subjects with normal coronary arteries without SCF. We compared the UII levels and the atherosclerotic risk factors between patients with SCF and control subjects with normal coronary flow. Results UII concentrations were significantly higher in patients with SCF compared to controls (711.0 ± 19.4 vs. 701.5 ± 27.2 ng/mL, p = 0.006). We detected a positive correlation between SCF and age (r = 0.476, p = 0.001), BMI (r = 0.404, p = .002), UII concentrations (r = 0.422, p = 0.006), and hypertension (r = 0.594, p = 0.001). Conclusion We identified increased UII levels in patients with SCF. We think that UII concentrations may be informative on SCF pathogenesis due to relationship with inflammation, atherosclerosis, and vascular remodeling. PMID:28180005

  17. Lack of association between the Glu298Asp polymorphism of endothelial nitric oxide synthase and slow coronary flow in the Turkish population

    PubMed Central

    Caglayan, Ahmet Okay; Kalay, Nihat; Saatci, Cetin; Yalcın, Arif; Akalın, Hilal; Dundar, Munis

    2009-01-01

    BACKGROUND: Coronary endothelial dysfunction plays an important pathogenetic role in patients with slow coronary flow (SCF). No data exist regarding the possible contribution of the Glu298Asp polymorphism genotype of the endothelial nitric oxide synthase (eNOS) gene to human SCF in the literature. OBJECTIVE: To investigate the association between SCF and the Glu298Asp polymorphism of the eNOS gene. METHODS: The study population consisted of 85 consecutive patients. The patient group included 66 patients with angiographically proven normal coronary arteries with SCF, and 19 subjects with normal coronary arteries with no SCF. The thrombolysis in myocardial infarction frame count was used for the diagnosis of SCF. The Glu298Asp polymorphism was determined by polymerase chain reaction and restriction fragment length polymorphism. RESULTS: The baseline characteristics were similar between the two groups, except for high-density lipoprotein cholesterol, which was higher in the SCF group than in the controls. The genotype distribution of Glu298Asp was as follows: GG 26%, GT 56% and TT 12%, where G is guanine and T is thymine. There was no difference in the frequency of the various genotypes or the alleles in patients with SCF versus normal controls. CONCLUSIONS: The Glu298Asp polymorphism genotype of the eNOS gene is not a risk factor for SCF in the present study population. PMID:19279989

  18. The self-consistent calculation of pseudo-molecule energy levels, construction of energy level correlation diagrams and an automated computation system for SCF-X(Alpha)-SW calculations

    NASA Technical Reports Server (NTRS)

    Schlosser, H.

    1981-01-01

    The self consistent calculation of the electronic energy levels of noble gas pseudomolecules formed when a metal surface is bombarded by noble gas ions is discussed along with the construction of energy level correlation diagrams as a function of interatomic spacing. The self consistent field x alpha scattered wave (SCF-Xalpha-SW) method is utilized. Preliminary results on the Ne-Mg system are given. An interactive x alpha programming system, implemented on the LeRC IBM 370 computer, is described in detail. This automated system makes use of special PROCDEFS (procedure definitions) to minimize the data to be entered manually at a remote terminal. Listings of the special PROCDEFS and of typical input data are given.

  19. Nonlinear optical response in narrow graphene nanoribbons

    NASA Astrophysics Data System (ADS)

    Karimi, Farhad; Knezevic, Irena

    We present an iterative method to calculate the nonlinear optical response of armchair graphene nanoribbons (aGNRs) and zigzag graphene nanoribbons (zGNRs) while including the effects of dissipation. In contrast to methods that calculate the nonlinear response in the ballistic (dissipation-free) regime, here we obtain the nonlinear response of an electronic system to an external electromagnetic field while interacting with a dissipative environment (to second order). We use a self-consistent-field approach within a Markovian master-equation formalism (SCF-MMEF) coupled with full-wave electromagnetic equations, and we solve the master equation iteratively to obtain the higher-order response functions. We employ the SCF-MMEF to calculate the nonlinear conductance and susceptibility, as well as to calculate the dependence of the plasmon dispersion and plasmon propagation length on the intensity of the electromagnetic field in GNRs. The electron scattering mechanisms included in this work are scattering with intrinsic phonons, ionized impurities, surface optical phonons, and line-edge roughness. Unlike in wide GNRs, where ionized-impurity scattering dominates dissipation, in ultra-narrow nanoribbons on polar substrates optical-phonon scattering and ionized-impurity scattering are equally prominent. Support by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering under Award DE-SC0008712.

  20. Luminescent and scintillation properties of Lu3Al5O12:Sc single crystal and single crystalline films

    NASA Astrophysics Data System (ADS)

    Zorenko, Y.; Gorbenko, V.; Voznyak, T.; Savchyn, V.; Nizhankovskiy, S.; Dan'ko, A.; Puzikov, V.; Laguta, V.; Mares, J. A.; Nikl, M.; Nejezchleb, K.; Batentschuk, M.; Winnacker, A.

    2012-10-01

    The work is dedicated to growth by the liquid phase epitaxy method and study of the luminescence and scintillation properties of Sc3+ doped single crystalline films (SCF) of Lu3Al5O12 (LuAG) garnet. The scintillation properties of SCF are compared with single crystal (SC) analogues grown by the Horizontal Direct Crystallization and Czochralski methods. We consider the dependence of intensity of the Sc3+ emission in LuAG host on the activator concentration and influence of flux contamination on the light yield (LY) of the Sc3+ luminescence in LuAG:Sc SCF with respect to their SC counterparts and the reference YAP:Ce scintillator. From the NMR investigations of LuAG:Sc SCF we confirm the substitution by Sc3+ ions both the octahedral and dodecahedral positions of LuAG host and formation of the ScAl and ScLu related emission centers, respectively. We also show that the luminescence spectrum in the UV range and decay kinetics of LuAG:Sc SCF can be effectively tuned by changing the scandium content.

  1. Ab initio study of Fe(+)-benzyne

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.

    1993-01-01

    The interaction of Fe(+) with benzyne is studied using the self-consistent-field (SCF), complete active space SCF, and modified-coupled-pair functional levels of theory. The most stable structure is planar, where the Fe(+) has inserted into the in-plane pi bond, although the C-C bond distance suggests that some in-plane pi bonding remains. This system is compared with Sc(+) bonding to benzyne and other ligands.

  2. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach

    NASA Astrophysics Data System (ADS)

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-01

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  3. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach.

    PubMed

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-07

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  4. Luminescent properties of Al2O3:Ce single crystalline films under synchrotron radiation excitation

    NASA Astrophysics Data System (ADS)

    Zorenko, Yu.; Zorenko, T.; Gorbenko, V.; Savchyn, V.; Voznyak, T.; Fabisiak, K.; Zhusupkalieva, G.; Fedorov, A.

    2016-09-01

    The paper is dedicated to study the luminescent and scintillation properties of the Al2O3:Ce single crystalline films (SCF) grown by LPE method onto saphire substrates from PbO based flux. The structural quality of SCF samples was investigated by XRD method. For characterization of luminescent properties of Al2O3:Ce SCFs the cathodoluminescence spectra, scintillation light yield (LY) and decay kinetics under excitation by α-particles of Pu239 source were used. We have found that the scintillation LY of Al2O3:Ce SCF samples is relatively large and can reach up to 50% of the value realized in the reference YAG:Ce SCF. Using the synchrotron radiation excitation in the 3.7-25 eV range at 10 K we have also determined the basic parameters of the Ce3+ luminescence in Al2O3 host.

  5. Geometric integration in Born-Oppenheimer molecular dynamics.

    PubMed

    Odell, Anders; Delin, Anna; Johansson, Börje; Cawkwell, Marc J; Niklasson, Anders M N

    2011-12-14

    Geometric integration schemes for extended Lagrangian self-consistent Born-Oppenheimer molecular dynamics, including a weak dissipation to remove numerical noise, are developed and analyzed. The extended Lagrangian framework enables the geometric integration of both the nuclear and electronic degrees of freedom. This provides highly efficient simulations that are stable and energy conserving even under incomplete and approximate self-consistent field (SCF) convergence. We investigate three different geometric integration schemes: (1) regular time reversible Verlet, (2) second order optimal symplectic, and (3) third order optimal symplectic. We look at energy conservation, accuracy, and stability as a function of dissipation, integration time step, and SCF convergence. We find that the inclusion of dissipation in the symplectic integration methods gives an efficient damping of numerical noise or perturbations that otherwise may accumulate from finite arithmetics in a perfect reversible dynamics. © 2011 American Institute of Physics

  6. Photovoltaic dependence of photorefractive grating on the externally applied dc electric field

    NASA Astrophysics Data System (ADS)

    Maurya, M. K.; Yadav, R. A.

    2013-04-01

    Photovoltaic dependence of photorefractive grating (i.e., space-charge field and phase-shift of the index grating) on the externally applied dc electric field in photovoltaic-photorefractive materials has been investigated. The influence of photovoltaic field (EPhN), diffusion field and carrier concentration ratio r (donor/acceptor impurity concentration ratio) on the space-charge field (SCF) and phase-shift of the index grating in the presence and absence of the externally applied dc electric field have also been studied in details. Our results show that, for a given value of EPhN and r, the magnitude of the SCF and phase-shift of the index grating can be enhanced significantly by employing the lower dc electric field (EON<10) across the photovoltaic-photorefractive crystal and higher value of diffusion field (EDN>40). Such an enhancement in the magnitude of the SCF and phase-shift of the index grating are responsible for the strongest beam coupling in photovoltaic-photorefractive materials. This sufficiently strong beam coupling increases the two-beam coupling gain that may be exceed the absorption and reflection losses of the photovoltaic-photorefractive sample, and optical amplification can occur. The higher value of optical amplification in photovoltaic-photorefractive sample is required for the every applications of photorefractive effect so that technology based on the photorefractive effect such as holographic storage devices, optical information processing, acousto-optic tunable filters, gyro-sensors, optical modulators, optical switches, photorefractive-photovoltaic solitons, biomedical applications, and frequency converters could be improved.

  7. Practice Patterns of Radiation Field Design for Sentinel Lymph Node-Positive Early-Stage Breast Cancer.

    PubMed

    Azghadi, Soheila; Daly, Megan; Mayadev, Jyoti

    2016-10-01

    Recent randomized trials have led to decreased use of completion axillary lymph node dissection (ALND) in early-stage breast cancer patients with a positive sentinel lymph node (SLN), causing controversy surrounding radiotherapy coverage of the axilla. We investigated the practice variation among radiation oncologists for regional nodal coverage for clinicopathologic scenarios and evaluated axillary field design decision-making processes. A customized, web-based questionnaire was e-mailed to 983 community (n = 617) and academic (n = 366) radiation oncologists with a breast cancer subspecialty practicing in the United States. The survey consisted of 18 multiple-choice questions evaluating general clinical preferences surrounding radiation therapy (RT) field design for patients with early-stage breast cancer and a positive SLN. Seven case scenarios were developed to investigate the field design in the setting of specific clinical and pathologic risk factors. Nodal coverage was classified as standard tangents (STs), high tangents (HTs), STs and a supraclavicular field (SCF), or STs and full axillary coverage (AX). A total of 145 evaluable responses were collected, with a response rate of 15.0%. Of the respondents, 12 (8.3%) reported using completion ALND for patients with 1 to 3 positive SLNs without extracapsular extension (ECE) and 66 (45.5%) performed ALND with 1 to 3 positive SLNs with ECE. For micrometastatic SLNs, with no lymphovascular system invasion, 115 (87.1%) used STs or HTs. The use of neoadjuvant chemotherapy (NAC) influenced RT field design for patients with a positive SLN without ECE, with 64 (48.5%) using STs and SCF or STs and AX treatment without NAC and 94 (70.7%) using SCF and AX after NAC. With macrometastatic SLN involvement, most respondents preferred SCF (45.27%) and AX (45.66%). In contrast, for micrometastatic involvement, HTs (43.61%) were frequently chosen. Forty (27.8%) reported using online predictive nomograms to predict further axillary involvement, with no difference between the academic and community radiation oncologists (P = .11). In SLN biopsy-positive early-stage breast cancer with omission of completion ALND, axillary RT is increasing used to cover the undissected axilla. Most respondents use SCF or AX for patients with low to intermediate pathologic features. Online prediction nomograms are used by a few practitioners to assist in clinical decision-making in this setting. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Three Dimensional Parametric Analyses of Stress Concentration Factor and Its Mitigation in Isotropic and Orthotropic Plate with Central Circular Hole Under Axial In-Plane Loading

    NASA Astrophysics Data System (ADS)

    Nagpal, Shubhrata; Jain, Nitin Kumar; Sanyal, Shubhashis

    2016-01-01

    The problem of finding the stress concentration factor of a loaded rectangular plate has offered considerably analytical difficulty. The present work focused on understanding of behavior of isotropic and orthotropic plate subjected to static in-plane loading using finite element method. The complete plate model configuration has been analyzed using finite element method based software ANSYS. In the present work two parameters: thickness to width of plate (T/A) and diameter of hole to width of plate (D/A) have been varied for analysis of stress concentration factor (SCF) and its mitigation. Plates of five different materials have been considered for complete analysis to find out the sensitivity of stress concentration factor. The D/A ratio varied from 0.1 to 0.7 for analysis of SCF and varied from 0.1 to 0.5 for analyzing the mitigation of SCF. 0.01, 0.05 and 0.1 are considered as T/A ratio for all the cases. The results are presented in graphical form and discussed. The mitigation in SCF reported is very encouraging. The SCF is more sensitive to D/A ratio as compared to T/A.

  9. A novel strategy to design sustained-release poorly water-soluble drug mesoporous silica microparticles based on supercritical fluid technique.

    PubMed

    Li-Hong, Wang; Xin, Che; Hui, Xu; Li-Li, Zhou; Jing, Han; Mei-Juan, Zou; Jie, Liu; Yi, Liu; Jin-Wen, Liu; Wei, Zhang; Gang, Cheng

    2013-09-15

    The organic solvent solution immersion method was often used to achieve the loading of the drugs into mesoporous silica, but the drugs that have loaded into the pores of the mesoporous silica would inevitable migrate from the inside to the external surface or near the outside surface during the process of drying. Hence, it often leads to the pores of mesoporous materials not be fully utilized, and results in a low drug loading efficiency and a fast releasing rate. The purpose of this study was to develop a novel drug loading strategy to avoid soluble component migration during the process of drying, then, to prepare poorly water-soluble drug mesoporous silica microparticles with higher drug loading efficiency and longer sustained-release time. Ibuprofen was used as model drug. The microparticles were prepared by a novel method based on mesoporous silica and supercritical fluid (SCF) technique. The drug-loaded mesoporous silica microparticles prepared by SCF technique were analyzed by thermogravimetric analysis (TGA), N2 adsorption/desorption, scanning electron microscopy (SEM), powder X-ray diffraction (XRD) and differential scanning calorimetry (DSC). In vitro releasing study was used to evaluate the sustained-release effect of the drug-loaded microparticles. By virtue of the high diffusibility and the high dissolving capacity of the supercritical carbon dioxide (SCF-CO2), the poorly water-soluble drugs, ibuprofen, entered the pores of the mesoporous silica. The amount and the depth of ibuprofen entered the pores of the mesoporous silica by SCF technique were both larger than those by the solution immersion method. It was found that ibuprofen loaded into the mesoporous silica by SCF technique was amorphous and the largest amount of the ibuprofen loaded into the mesoporous silica by SCF technique could reach 386 mg/g (w/w, ibuprofen/SiO2), it was more than that by the solution immersion method. In vitro releasing study showed that the sustained-release effect of ibuprofen in the samples prepared by SCF technique was 50% in 15 min and 90% in 60 min. It was longer than that prepared by the solution immersion method. Present study showed that sustained-release poorly water-soluble drug mesoporous silica microparticle based on SCF technique has twofold advantages. One is the larger drug loading amount in internal pores of the mesoporous silica, the other is the longer drug releasing time. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Modern supercritical fluid technology for food applications.

    PubMed

    King, Jerry W

    2014-01-01

    This review provides an update on the use of supercritical fluid (SCF) technology as applied to food-based materials. It advocates the use of the solubility parameter theory (SPT) for rationalizing the results obtained when employing sub- and supercritical media to food and nutrient-bearing materials and for optimizing processing conditions. Total extraction and fractionation of foodstuffs employing SCFs are compared and are illustrated by using multiple fluids and unit processes to obtain the desired food product. Some of the additional prophylactic benefits of using carbon dioxide as the processing fluid are explained and illustrated with multiple examples of commercial products produced using SCF media. I emphasize the role of SCF technology in the context of environmentally benign and sustainable processing, as well as its integration into an overall biorefinery concept. Conclusions are drawn in terms of current trends in the field and future research that is needed to secure new applications of the SCF platform as applied in food science and technology.

  11. Scintillating screens based on the LPE grown Tb3Al5O12:Ce single crystalline films

    NASA Astrophysics Data System (ADS)

    Zorenko, Yuriy; Douissard, Paul-Antoine; Martin, Thierry; Riva, Federica; Gorbenko, Vitaliy; Zorenko, Tetiana; Paprocki, Kazimierz; Iskalieva, Aizhan; Witkiewicz, Sandra; Fedorov, Alexander; Bilski, Paweł; Twardak, Anna

    2017-03-01

    We report in this work the creation of new heavy and efficient Tb3Al5O12:Ce (TbAG:Ce) single crystalline film (SCF) scintillators, grown by LPE method from PbO-B2O3 based flux onto Y3Al5O12 (YAG) and Gd3Ga2.5Al2.5O12 (GAGG) substrates, for different optoelectronic applications. The luminescent and scintillation properties of the TbAG:Ce SCF screens, grown onto different types of substrates, are studied and compared with the properties of the Lu3Al5O12:Ce (LuAG:Ce) and YAG:Ce SCF counterparts. TbAG:Ce SCFs show very high scintillation light yield (LY) under α-particles excitation, which overcomes by 30% the LY of high-quality LuAG:Ce SCF samples. In comparison with YAG:Ce and LuAG:Ce SCFs, TbAG:Ce SCF screens show also significantly lower afterglow (up to 10-4 level at X-ray burst duration of 0.1 s), which is comparable with the afterglow level of the best samples of LSO:Ce, Tb SCFs typically being used now for microimaging. Together with a high light output of X-ray excited luminescence, such extremely low afterglow of TbAG:Ce SCF is a very good reason for future development of scintillating screens based on the mentioned garnet. We also introduce the possibility to create new types of ;film-substrate; hybrid scintillators using the LPE method for simultaneous registration of different components of ionizing radiation and microimaging based on the TbAG:Ce SCF and GAGG:Ce substrates.

  12. Assessing the usability and potential value of seasonal climate forecasts in land management decisions in the southwest UK: challenges and reflections

    NASA Astrophysics Data System (ADS)

    Soares, Marta Bruno

    2017-06-01

    The potential usability and benefits of seasonal climate forecasts (SCF) to help inform decision-making processes is widely accepted. However, the practical use of SCF in Europe is still fairly recent and, as such, current knowledge of the added benefits of SCF in supporting and improving decision-making is limited. This study is based on research conducted to co-develop a semi-operational climate service prototype - the Land Management Tool (LMTool) - with farmers in South West regions of the UK. The value of the SCF provided to the farmers was examined to help us understand the usability and (potential) value of these forecasts in farmers' decisions during the winter months of 2015/2016. The findings from the study point to the need to explore and develop (new) research methods capable of addressing the complexity of the decision-making processes, such as those in the farming sector. The farmers who used the SCF perceived it as useful and usable as it helped them change and adapt their decision-making and thus, avoid unnecessary costs. However, to fully grasp the potential value of using SCF, farmers emphasised the need for the provision of SCF for longer periods of time to allow them to build trust and confidence in the information provided. This paper contributes to ongoing discussions about how to assess the use and value of SCF in decision-making processes in a meaningful and effective way.

  13. Low temperature improvement method on characteristics of Ba(Zr0.1Ti0.9)O3 thin films deposited on indium tin oxide/glass substrates

    NASA Astrophysics Data System (ADS)

    Chen, Kai-Huang; Chang, Ting-Chang; Chang, Guan-Chang; Hsu, Yung-En; Chen, Ying-Chung; Xu, Hong-Quan

    2010-04-01

    To improve the electrical properties of as-deposited BZ1T9 ferroelectric thin films, the supercritical carbon dioxide fluid (SCF) process were used by a low temperature treatment. In this study, the BZ1T9 ferroelectric thin films were post-treated by SCF process which mixed with propyl alcohol and pure H2O. After SCF process treatment, the remnant polarization increased in hysteresis curves, and the passivation of oxygen vacancy and defect in leakage current density curves were found. Additionally, the improvement qualities of as-deposited BZ1T9 thin films after SCF process treatment were carried out XPS, C- V, and J- E measurements.

  14. Skp1: Implications in cancer and SCF-oriented anti-cancer drug discovery.

    PubMed

    Hussain, Muzammal; Lu, Yongzhi; Liu, Yong-Qiang; Su, Kai; Zhang, Jiancun; Liu, Jinsong; Zhou, Guang-Biao

    2016-09-01

    In the last decade, the ubiquitin proteasome system (UPS), in general, and E3 ubiquitin ligases, in particular, have emerged as valid drug targets for the development of novel anti-cancer therapeutics. Cullin RING Ligases (CRLs), which can be classified into eight groups (CRL1-8) and comprise approximately 200 members, represent the largest family of E3 ubiquitin ligases which facilitate the ubiquitination-derived proteasomal degradation of a myriad of functionally and structurally diverse substrates. S phase kinase-associated protein 1 (Skp1)-Cullin1-F-Box protein (SCF) complexes are the best characterized among CRLs, which play crucial roles in numerous cellular processes and physiological dysfunctions, such as in cancer biology. Currently, there is growing interest in developing SCF-targeting anti-cancer therapies for clinical application. Indeed, the research in this field has seen some progress in the form of cullin neddylation- and Skp2-inhibitors. However, it still remains an underdeveloped area and needs to design new strategies for developing improved form of therapy. In this review, we venture a novel strategy that rational pharmacological targeting of Skp1, a central regulator of SCF complexes, may provide a novel avenue for SCF-oriented anti-cancer therapy, expected: (i) to simultaneously address the critical roles that multiple SCF oncogenic complexes play in cancer biology, (ii) to selectively target cancer cells with minimal normal cell toxicity, and (iii) to offer multiple chemical series, via therapeutic interventions at the Skp1 binding interfaces in SCF complex, thereby maximizing chances of success for drug discovery. In addition, we also discuss the challenges that might be posed regarding rational pharmacological interventions against Skp1. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Catalytic asymmetric trifluoromethylthiolation via enantioselective [2,3]-sigmatropic rearrangement of sulfonium ylides

    NASA Astrophysics Data System (ADS)

    Zhang, Zhikun; Sheng, Zhe; Yu, Weizhi; Wu, Guojiao; Zhang, Rui; Chu, Wen-Dao; Zhang, Yan; Wang, Jianbo

    2017-10-01

    The trifluoromethylthio (SCF3) functional group has been of increasing importance in drug design and development as a consequence of its unique electronic properties and high stability coupled with its high lipophilicity. As a result, methods to introduce this highly electronegative functional group have attracted considerable attention in recent years. Although significant progress has been made in the introduction of SCF3 functionality into a variety of molecules, there remain significant challenges regarding the enantioselective synthesis of SCF3-containing compounds. Here, an asymmetric trifluoromethylthiolation that proceeds through the enantioselective [2,3]-sigmatropic rearrangement of a sulfonium ylide generated from a metal carbene and sulfide (Doyle-Kirmse reaction) has been developed using chiral Rh(II) and Cu(I) catalysts. This transformation features mild reaction conditions and excellent enantioselectivities (up to 98% yield and 98% e.e.), thus providing a unique, highly efficient and enantioselective method for the construction of C(sp3)-SCF3 bonds bearing chiral centres.

  16. Two-Level Chebyshev Filter Based Complementary Subspace Method: Pushing the Envelope of Large-Scale Electronic Structure Calculations.

    PubMed

    Banerjee, Amartya S; Lin, Lin; Suryanarayana, Phanish; Yang, Chao; Pask, John E

    2018-06-12

    We describe a novel iterative strategy for Kohn-Sham density functional theory calculations aimed at large systems (>1,000 electrons), applicable to metals and insulators alike. In lieu of explicit diagonalization of the Kohn-Sham Hamiltonian on every self-consistent field (SCF) iteration, we employ a two-level Chebyshev polynomial filter based complementary subspace strategy to (1) compute a set of vectors that span the occupied subspace of the Hamiltonian; (2) reduce subspace diagonalization to just partially occupied states; and (3) obtain those states in an efficient, scalable manner via an inner Chebyshev filter iteration. By reducing the necessary computation to just partially occupied states and obtaining these through an inner Chebyshev iteration, our approach reduces the cost of large metallic calculations significantly, while eliminating subspace diagonalization for insulating systems altogether. We describe the implementation of the method within the framework of the discontinuous Galerkin (DG) electronic structure method and show that this results in a computational scheme that can effectively tackle bulk and nano systems containing tens of thousands of electrons, with chemical accuracy, within a few minutes or less of wall clock time per SCF iteration on large-scale computing platforms. We anticipate that our method will be instrumental in pushing the envelope of large-scale ab initio molecular dynamics. As a demonstration of this, we simulate a bulk silicon system containing 8,000 atoms at finite temperature, and obtain an average SCF step wall time of 51 s on 34,560 processors; thus allowing us to carry out 1.0 ps of ab initio molecular dynamics in approximately 28 h (of wall time).

  17. The Relationship Between Serum Endocan Levels With the Presence of Slow Coronary Flow: A Cross-Sectional Study.

    PubMed

    Kundi, Harun; Gok, Murat; Kiziltunc, Emrullah; Topcuoglu, Canan; Cetin, Mustafa; Cicekcioglu, Hulya; Ugurlu, Burcu; Ulusoy, Feridun Vasfi

    2017-07-01

    The aim of this study was to investigate the relationship between endocan levels with the presence of slow coronary flow (SCF). In this cross-sectional study, a total of 88 patients, who admitted to our hospital, were included in this study. Of these, 53 patients with SCF and 35 patients with normal coronary flow were included in the final analysis. Coronary flow rates of all patients were determined by the Timi Frame Count (TFC) method. In correlation analysis, endocan levels revealed a significantly positive correlation with high sensitive C-reactive protein and corrected TFC. In multivariate logistic regression analysis, the endocan levels were found as independently associated with the presence of SCF. Finally, using a cutoff level of 2.3, endocan level predicted the presence of SCF with a sensitivity of 77.2% and specificity of 75.2%. In conclusion, our study showed that higher endocan levels were significantly and independently related to the presence of SCF.

  18. Second-order perturbation theory with a density matrix renormalization group self-consistent field reference function: theory and application to the study of chromium dimer.

    PubMed

    Kurashige, Yuki; Yanai, Takeshi

    2011-09-07

    We present a second-order perturbation theory based on a density matrix renormalization group self-consistent field (DMRG-SCF) reference function. The method reproduces the solution of the complete active space with second-order perturbation theory (CASPT2) when the DMRG reference function is represented by a sufficiently large number of renormalized many-body basis, thereby being named DMRG-CASPT2 method. The DMRG-SCF is able to describe non-dynamical correlation with large active space that is insurmountable to the conventional CASSCF method, while the second-order perturbation theory provides an efficient description of dynamical correlation effects. The capability of our implementation is demonstrated for an application to the potential energy curve of the chromium dimer, which is one of the most demanding multireference systems that require best electronic structure treatment for non-dynamical and dynamical correlation as well as large basis sets. The DMRG-CASPT2/cc-pwCV5Z calculations were performed with a large (3d double-shell) active space consisting of 28 orbitals. Our approach using large-size DMRG reference addressed the problems of why the dissociation energy is largely overestimated by CASPT2 with the small active space consisting of 12 orbitals (3d4s), and also is oversensitive to the choice of the zeroth-order Hamiltonian. © 2011 American Institute of Physics

  19. Theoretical research program to study chemical reactions in AOTV bow shock tubes

    NASA Technical Reports Server (NTRS)

    Taylor, P.

    1986-01-01

    Progress in the development of computational methods for the characterization of chemical reactions in aerobraking orbit transfer vehicle (AOTV) propulsive flows is reported. Two main areas of code development were undertaken: (1) the implementation of CASSCF (complete active space self-consistent field) and SCF (self-consistent field) analytical first derivatives on the CRAY X-MP; and (2) the installation of the complete set of electronic structure codes on the CRAY 2. In the area of application calculations the main effort was devoted to performing full configuration-interaction calculations and using these results to benchmark other methods. Preprints describing some of the systems studied are included.

  20. Teaching the Indirect Method of the Statement of Cash Flows in Introductory Financial Accounting: A Comprehensive, Problem-Based Approach

    ERIC Educational Resources Information Center

    Brickner, Daniel R.; McCombs, Gary B.

    2004-01-01

    In this article, the authors provide an instructional resource for presenting the indirect method of the statement of cash flows (SCF) in an introductory financial accounting course. The authors focus primarily on presenting a comprehensive example that illustrates the "why" of SCF preparation and show how journal entries and T-accounts can be…

  1. Hierarchy of stroma-derived factors in supporting growth of stroma-dependent hemopoietic cells: membrane-bound SCF is sufficient to confer stroma competence to epithelial cells.

    PubMed

    Friel, Jutta; Itoh, Katsuhiko; Bergholz, Ulla; Jücker, Manfred; Stocking, Carol; Harrison, Paul; Ostertag, Wolfram

    2002-03-01

    Hemopoiesis takes place in a microenvironment where hemopoietic cells are closely associated with stroma by various interactions. Stroma coregulates the proliferation and differentiation of hemopoietic cells. Stroma-hemopoietic-cell contact can be supported by locally produced membrane associated growth factors. The stroma derived growth factor, stem cell factor (SCF) is important in hemopoiesis. We examined the different biological interactions of membrane bound and soluble SCF with human hemopoietic cells expressing the SCF receptor, c-kit. To analyze the function of the SCF isoforms in inducing the proliferation of hemopoietic TF1 or Cord blood (CB) CD34+ cells we used stroma cell lines that differ in their presentation of no SCF, membrane SCF, or soluble SCF. We established a new coculture system using an epithelial cell line that excludes potential interfering effects with other known stroma encoded hemopoietic growth factors. We show that soluble SCF, in absence of membrane-bound SCF, inhibits long term clonal growth of primary or established CD34+ hemopoietic cells, whereas membrane-inserted SCF "dominantly" induces long term proliferation of these cells. We demonstrate a hierarchy of these SCF isoforms in the interaction of stroma with hemopoietic TF1 cells. Membrane-bound SCF is "dominant" over soluble SCF, whereas soluble SCF acts epistatically in interacting with hemopoietic cells compared with other stroma derived factors present in SCF deficient stroma. A hierarchy of stroma cell lines can be arranged according to their presentation of membrane SCF or soluble SCF. In our model system, membrane-bound SCF expression is sufficient to confer stroma properties to an epithelial cell line but soluble SCF does not.

  2. On the comparisons between dissipative particle dynamics simulations and self-consistent field calculations of diblock copolymer microphase separation

    NASA Astrophysics Data System (ADS)

    Sandhu, Paramvir; Zong, Jing; Yang, Delian; Wang, Qiang

    2013-05-01

    To highlight the importance of quantitative and parameter-fitting-free comparisons among different models/methods, we revisited the comparisons made by Groot and Madden [J. Chem. Phys. 108, 8713 (1998), 10.1063/1.476300] and Chen et al. [J. Chem. Phys. 122, 104907 (2005), 10.1063/1.1860351] between their dissipative particle dynamics (DPD) simulations of the DPD model and the self-consistent field (SCF) calculations of the "standard" model done by Matsen and Bates [Macromolecules 29, 1091 (1996), 10.1021/ma951138i] for diblock copolymer (DBC) A-B melts. The small values of the invariant degree of polymerization used in the DPD simulations do not justify the use of the fluctuation theory of Fredrickson and Helfand [J. Chem. Phys. 87, 697 (1987), 10.1063/1.453566] by Groot and Madden, and their fitting between the DPD interaction parameters and the Flory-Huggins χ parameter in the "standard" model also has no rigorous basis. Even with their use of the fluctuation theory and the parameter-fitting, we do not find the "quantitative match" for the order-disorder transition of symmetric DBC claimed by Groot and Madden. For lamellar and cylindrical structures, we find that the system fluctuations/correlations decrease the bulk period and greatly suppress the large depletion of the total segmental density at the A-B interfaces as well as its oscillations in A- and B-domains predicted by our SCF calculations of the DPD model. At all values of the A-block volume fractions in the copolymer f (which are integer multiples of 0.1), our SCF calculations give the same sequence of phase transitions with varying χN as the "standard" model, where N denotes the number of segments on each DBC chain. All phase boundaries, however, are shifted to higher χN due to the finite interaction range in the DPD model, except at f = 0.1 (and 0.9), where χN at the transition between the disordered phase and the spheres arranged on a body-centered cubic lattice is lower due to N = 10 in the DPD model. Finally, in 11 of the total 20 cases (f-χN combinations) studied in the DPD simulations, a morphology different from the SCF prediction was obtained due to the differences between these two methods.

  3. An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture

    DOE PAGES

    Mironov, Vladimir; Moskovsky, Alexander; D’Mello, Michael; ...

    2017-10-04

    The Hartree-Fock (HF) method in the quantum chemistry package GAMESS represents one of the most irregular algorithms in computation today. Major steps in the calculation are the irregular computation of electron repulsion integrals (ERIs) and the building of the Fock matrix. These are the central components of the main Self Consistent Field (SCF) loop, the key hotspot in Electronic Structure (ES) codes. By threading the MPI ranks in the official release of the GAMESS code, we not only speed up the main SCF loop (4x to 6x for large systems), but also achieve a significant (>2x) reduction in the overallmore » memory footprint. These improvements are a direct consequence of memory access optimizations within the MPI ranks. We benchmark our implementation against the official release of the GAMESS code on the Intel R Xeon PhiTM supercomputer. Here, scaling numbers are reported on up to 7,680 cores on Intel Xeon Phi coprocessors.« less

  4. The Calculation of Accurate Harmonic Frequencies of Large Molecules: The Polycyclic Aromatic Hydrocarbons, a Case Study

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Arnold, James O. (Technical Monitor)

    1996-01-01

    The vibrational frequencies and infrared intensities of naphthalene neutral and cation are studied at the self-consistent-field (SCF), second-order Moller-Plesset (MP2), and density functional theory (DFT) levels using a variety of one-particle basis sets. Very accurate frequencies can be obtained at the DFT level in conjunction with large basis sets if they are scaled with two factors, one for the C-H stretches and a second for all other modes. We also find remarkably good agreement at the B3LYP/4-31G level using only one scale factor. Unlike the neutral PAHs where all methods do reasonably well for the intensities, only the DFT results are accurate for the PAH cations. The failure of the SCF and MP2 methods is caused by symmetry breaking and an inability to describe charge delocalization. We present several interesting cases of symmetry breaking in this study. An assessment is made as to whether an ensemble of PAH neutrals or cations could account for the unidentified infrared bands observed in many astronomical sources.

  5. Optimization of auxiliary basis sets for the LEDO expansion and a projection technique for LEDO-DFT.

    PubMed

    Götz, Andreas W; Kollmar, Christian; Hess, Bernd A

    2005-09-01

    We present a systematic procedure for the optimization of the expansion basis for the limited expansion of diatomic overlap density functional theory (LEDO-DFT) and report on optimized auxiliary orbitals for the Ahlrichs split valence plus polarization basis set (SVP) for the elements H, Li--F, and Na--Cl. A new method to deal with near-linear dependences in the LEDO expansion basis is introduced, which greatly reduces the computational effort of LEDO-DFT calculations. Numerical results for a test set of small molecules demonstrate the accuracy of electronic energies, structural parameters, dipole moments, and harmonic frequencies. For larger molecular systems the numerical errors introduced by the LEDO approximation can lead to an uncontrollable behavior of the self-consistent field (SCF) process. A projection technique suggested by Löwdin is presented in the framework of LEDO-DFT, which guarantees for SCF convergence. Numerical results on some critical test molecules suggest the general applicability of the auxiliary orbitals presented in combination with this projection technique. Timing results indicate that LEDO-DFT is competitive with conventional density fitting methods. (c) 2005 Wiley Periodicals, Inc.

  6. Surface tension and phase coexistence properties of the lattice fluid from a virtual site removal Monte Carlo strategy

    NASA Astrophysics Data System (ADS)

    Provata, Astero; Prassas, Vassilis D.; Theodorou, Doros N.

    1997-10-01

    A thin liquid film of lattice fluid in equilibrium with its vapor is studied in 2 and 3 dimensions with canonical Monte Carlo simulation (MC) and Self-Consistent Field Theory (SCF) in the temperature range 0.45Tc to Tc, where Tc the liquid-gas critical temperature. Extending the approach of Oates et al. [Philos. Mag. B 61, 337 (1990)] to anisotropic systems, we develop a method for the MC computation of the transverse and normal pressure profiles, hence of the surface tension, based on virtual removals of individual sites or blocks of sites from the system. Results from implementation of this new method, obtained at very modest computational cost, are in reasonable agreement with exact values and other MC estimates of the surface tension of the 2-d and 3-d model systems, respectively. SCF estimates of the interfacial density profiles, the surface tension, the vapor pressure curve and the binodal curve compare well with MC results away from Tc, but show the expected deviations at high temperatures.

  7. The calculation of accurate harmonic frequencies of large molecules: the polycyclic aromatic hydrocarbons, a case study

    NASA Astrophysics Data System (ADS)

    Bauschlicher, Charles W.; Langhoff, Stephen R.

    1997-07-01

    The vibrational frequencies and infrared intensities of naphthalene neutral and cation are studied at the self-consistent-field (SCF), second-order Møller-Plesset (MP2), and density functional theory (DFT) levels using a variety of one-particle basis sets. Very accurate frequencies can be obtained at the DFT level in conjunction with large basis sets if they are scaled with two factors, one for the C-H stretches and a second for all other modes. We also find remarkably good agreement at the B3LYP/4-31G level using only one scale factor. Unlike the neutral polycyclic aromatic hydrocarbons (PAHs) where all methods do reasonably well for the intensities, only the DFT results are accurate for the PAH cations. The failure of the SCF and MP2 methods is caused by symmetry breaking and an inability to describe charge delocalization. We present several interesting cases of symmetry breaking in this study. An assessment is made as to whether an ensemble of PAH neutrals or cations could account for the unidentified infrared bands observed in many astronomical sources.

  8. Symmetry and equivalence restrictions in electronic structure calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Taylor, Peter R.

    1988-01-01

    A simple method for obtaining MCSCF orbitals and CI natural orbitals adapted to degenerate point groups, with full symmetry and equivalnece restrictions, is described. Among several advantages accruing from this method are the ability to perform atomic SCF calculations on states for which the SCF energy expression cannot be written in terms of Coulomb and exchange integrals over real orbitals, and the generation of symmetry-adapted atomic natural orbitals for use in a recently proposed method for basis set contraction.

  9. Association between Abdominal Fat (DXA) and Its Subcomponents (CT Scan) before and after Weight Loss in Obese Postmenopausal Women: A MONET Study.

    PubMed

    Doyon, Caroline Y; Brochu, Martin; Messier, Virginie; Lavoie, Marie-Ève; Faraj, May; Doucet, Eric; Rabasa-Lhoret, Rémi; Dionne, Isabelle J

    2011-01-01

    Introduction. Subcutaneous fat (ScF) and visceral fat (VF) measurements using CT scan are expensive and may imply significant radiation doses. Cross-sectional studies using CT scan showed that ScF and VF are significantly correlated with abdominal fat measured by DXA (AF-DXA). The association has not been studied after a weight loss. Objective. To determine (1) the associations between AF-DXA and ScF and VF before and after weight loss and (2) the associations between their changes. Methods. 137 overweight/obese postmenopausal women were divided in two groups (1-caloric restriction or 2-caloric restriction + resistance training). AF was assessed using DXA and CT scan. Results. Correlations between AF-DXA and ScF (before: r = 0.87, after; r = 0.87; P < .01) and, AF-DXA and VF (before: r = 0.61, after; r = 0.69; P < .01) are not different before and after the weight loss. Correlations between delta AF-DXA and delta ScF (r = 0.72; P < .01) or delta VF (r = 0.51; P < .01) were found. Conclusion. The use of AF-DXA as a surrogate for VF after weight loss is questionable, but may be interesting for ScF.

  10. Association between Abdominal Fat (DXA) and Its Subcomponents (CT Scan) before and after Weight Loss in Obese Postmenopausal Women: A MONET Study

    PubMed Central

    Doyon, Caroline Y.; Brochu, Martin; Messier, Virginie; Lavoie, Marie-Ève; Faraj, May; Doucet, Éric; Rabasa-Lhoret, Rémi; Dionne, Isabelle J.

    2011-01-01

    Introduction. Subcutaneous fat (ScF) and visceral fat (VF) measurements using CT scan are expensive and may imply significant radiation doses. Cross-sectional studies using CT scan showed that ScF and VF are significantly correlated with abdominal fat measured by DXA (AF-DXA). The association has not been studied after a weight loss. Objective. To determine (1) the associations between AF-DXA and ScF and VF before and after weight loss and (2) the associations between their changes. Methods. 137 overweight/obese postmenopausal women were divided in two groups (1-caloric restriction or 2-caloric restriction + resistance training). AF was assessed using DXA and CT scan. Results. Correlations between AF-DXA and ScF (before: r = 0.87, after; r = 0.87; P < .01) and, AF-DXA and VF (before: r = 0.61, after; r = 0.69; P < .01) are not different before and after the weight loss. Correlations between delta AF-DXA and delta ScF (r = 0.72; P < .01) or delta VF (r = 0.51; P < .01) were found. Conclusion. The use of AF-DXA as a surrogate for VF after weight loss is questionable, but may be interesting for ScF. PMID:21603261

  11. Skipping of Exons by Premature Termination of Transcription and Alternative Splicing within Intron-5 of the Sheep SCF Gene: A Novel Splice Variant

    PubMed Central

    Saravanaperumal, Siva Arumugam; Pediconi, Dario; Renieri, Carlo; La Terza, Antonietta

    2012-01-01

    Stem cell factor (SCF) is a growth factor, essential for haemopoiesis, mast cell development and melanogenesis. In the hematopoietic microenvironment (HM), SCF is produced either as a membrane-bound (−) or soluble (+) forms. Skin expression of SCF stimulates melanocyte migration, proliferation, differentiation, and survival. We report for the first time, a novel mRNA splice variant of SCF from the skin of white merino sheep via cloning and sequencing. Reverse transcriptase (RT)-PCR and molecular prediction revealed two different cDNA products of SCF. Full-length cDNA libraries were enriched by the method of rapid amplification of cDNA ends (RACE-PCR). Nucleotide sequencing and molecular prediction revealed that the primary 1519 base pair (bp) cDNA encodes a precursor protein of 274 amino acids (aa), commonly known as ‘soluble’ isoform. In contrast, the shorter (835 and/or 725 bp) cDNA was found to be a ‘novel’ mRNA splice variant. It contains an open reading frame (ORF) corresponding to a truncated protein of 181 aa (vs 245 aa) with an unique C-terminus lacking the primary proteolytic segment (28 aa) right after the D175G site which is necessary to produce ‘soluble’ form of SCF. This alternative splice (AS) variant was explained by the complete nucleotide sequencing of splice junction covering exon 5-intron (5)-exon 6 (948 bp) with a premature termination codon (PTC) whereby exons 6 to 9/10 are skipped (Cassette Exon, CE 6–9/10). We also demonstrated that the Northern blot analysis at transcript level is mediated via an intron-5 splicing event. Our data refine the structure of SCF gene; clarify the presence (+) and/or absence (−) of primary proteolytic-cleavage site specific SCF splice variants. This work provides a basis for understanding the functional role and regulation of SCF in hair follicle melanogenesis in sheep beyond what was known in mice, humans and other mammals. PMID:22719917

  12. Scintillating Screens Based on the Single Crystalline Films of Multicomponent Garnets: New Achievements and Possibilities

    NASA Astrophysics Data System (ADS)

    Zorenko, Yuriy; Gorbenko, Vitalii; Zorenko, Tetiana; Paprocki, Kazimierz; Nikl, Martin; Mares, Jiri A.; Bilski, Pawel; Twardak, Anna; Sidletskiy, Oleg; Gerasymov, Iaroslav; Grinyov, Boris; Fedorov, Alexandr

    2016-04-01

    The paper is dedicated to development of the novel scintillating screens based on single crystalline films (SCF) of Ce doped Lu3 - xTbxAl5 - yGayO12 multicomponent garnets at x = 2 - 3 and y = 0 - 2.5 onto Y3Al5O12 (YAG) and Gd3Al2.5Ga2.5O12 (GAGG) substrates using the liquid phase epitaxy (LPE) method. We report the optimized content and high scintillation figure of merit of SCF of these garnets grown by the LPE method with using PbO based flux. Namely, the Tb3Al2.5Ga2.5O12:Ce SCFs possess the highest values of light yield (LY) compared to all earlier investigated SCF samples, with their LY exceeding by 2.35 and 1.15 times the LY values for YAG:Ce and LuAG:Ce SCF scintillators, respectively. The SCFs of the mentioned compounds show very lower thermoluminescence in the above room temperature range and relatively fast scintillation decay.

  13. Applicability of Kerker preconditioning scheme to the self-consistent density functional theory calculations of inhomogeneous systems

    NASA Astrophysics Data System (ADS)

    Zhou, Yuzhi; Wang, Han; Liu, Yu; Gao, Xingyu; Song, Haifeng

    2018-03-01

    The Kerker preconditioner, based on the dielectric function of homogeneous electron gas, is designed to accelerate the self-consistent field (SCF) iteration in the density functional theory calculations. However, a question still remains regarding its applicability to the inhomogeneous systems. We develop a modified Kerker preconditioning scheme which captures the long-range screening behavior of inhomogeneous systems and thus improves the SCF convergence. The effectiveness and efficiency is shown by the tests on long-z slabs of metals, insulators, and metal-insulator contacts. For situations without a priori knowledge of the system, we design the a posteriori indicator to monitor if the preconditioner has suppressed charge sloshing during the iterations. Based on the a posteriori indicator, we demonstrate two schemes of the self-adaptive configuration for the SCF iteration.

  14. Blending of soluble corn fiber with pullulan, sorbitol, or fructose attenuates glycemic and insulinemic responses in the dog and affects hydrolytic digestion in vitro.

    PubMed

    de Godoy, M R C; Knapp, B K; Bauer, L L; Swanson, K S; Fahey, G C

    2013-08-01

    The objective of these experiments was to measure in vitro hydrolytic digestion and glycemic and insulinemic responses of select carbohydrate blends, all containing the novel carbohydrate soluble corn fiber (SCF). Two SCF that varied in their method of production were used to formulate the carbohydrate blends. One set of blends contained a SCF that was spray dried (SCFsd) and then blended with different amounts of either pullulan, sorbitol, or fructose. The other set of blends contained a SCF produced using longer evaporation time (SCF) and then blended with different ratios of pullulan, sorbitol, and fructose. Free sugar concentrations found in the individual SCFsd and SCF substrates were low but varied. Spray-dried soluble corn fiber had a reduced free sugar concentration compared with SCF (2.8 vs. 14.2%). Glucose was the main free sugar found in both SCFsd and SCF but at different concentrations (2.7 vs. 12.7%, respectively). The majority of the SCFsd blends were completely hydrolyzed to their monosaccharide components. Glucose accounted for most of the hydrolyzed monosaccharides for SCFsd and all the SCFsd blends. Hydrolyzed monosaccharide concentrations for the SCF:pullulan:sorbitol:fructose blends followed similar trends to the SCFsd blends where greater percentages of fructose and sorbitol resulted in decreased (P < 0.05) hydrolyzed monosaccharide concentrations. The SCFsd blends had intermediate to high amounts of monosaccharides released as a result of in vitro hydrolytic digestion. The SCFsd:pullulan blends were more digestible in vitro (approximately 91%; P < 0.05) than SCFsd:fructose or SCFsd:sorbitol. Total released monosaccharides were high in SCFsd blends containing either 50% fructose or sorbitol, but the combination resulted in reduced concentrations of glucose released (P < 0.05). The SCF:pullulan:sorbitol:fructose blends also had intermediate to high released monosaccharides as a result of in vitro hydrolytic digestion. All SCF blends resulted in decreased glycemic and insulinemic responses compared with the maltodextrin control (P < 0.05) using a canine model. The addition of pullulan reduced the glycemic response compared with maltodextrin at all concentrations, but only 50:50 SCFsd:pullulan resulted in a reduction of the glycemic response compared with SCFsd alone (P < 0.05). The addition of fructose and sorbitol in the blends had the greatest impact on glycemic and insulinemic responses, even at concentrations as low as 5% of the blends. Overall, SCF and their blends may prove beneficial as components of low glycemic foodstuffs.

  15. A reformulation of the coupled perturbed self-consistent field equations entirely within a local atomic orbital density matrix-based scheme

    NASA Astrophysics Data System (ADS)

    Ochsenfeld, Christian; Head-Gordon, Martin

    1997-05-01

    To exploit the exponential decay found in numerical studies for the density matrix and its derivative with respect to nuclear displacements, we reformulate the coupled perturbed self-consistent field (CPSCF) equations and a quadratically convergent SCF (QCSCF) method for Hartree-Fock and density functional theory within a local density matrix-based scheme. Our D-CPSCF (density matrix-based CPSCF) and D-QCSCF schemes open the way for exploiting sparsity and to achieve asymptotically linear scaling of computational complexity with molecular size ( M), in case of D-CPSCF for all O( M) derivative densities. Furthermore, these methods are even for small molecules strongly competitive to conventional algorithms.

  16. Statistics of wormlike chains. II. Phase transition of polymer liquid crystals and its mixture with low molecular weight liquid crystals

    NASA Astrophysics Data System (ADS)

    Zhang, W. X.; Zhao, S. R.; Sun, C. P.

    1997-02-01

    A general self-consistent field (SCF) for the mixture of polymer and low molecular weight (LMW) molecules has been derived by variation principle. Considering a Maier-Saupe type of interaction, the analytical expressions of the SCF for polymer liquid crystals (PLCs) and the mixture of PLCs and LMW liquid crystals are obtained, from which the phase behaviors of PLCs as well as the mixture are studied. The theoretical results are in agreement with experimental results by adjusting a parameter.

  17. Quantum supercharger library: hyper-parallelism of the Hartree-Fock method.

    PubMed

    Fernandes, Kyle D; Renison, C Alicia; Naidoo, Kevin J

    2015-07-05

    We present here a set of algorithms that completely rewrites the Hartree-Fock (HF) computations common to many legacy electronic structure packages (such as GAMESS-US, GAMESS-UK, and NWChem) into a massively parallel compute scheme that takes advantage of hardware accelerators such as Graphical Processing Units (GPUs). The HF compute algorithm is core to a library of routines that we name the Quantum Supercharger Library (QSL). We briefly evaluate the QSL's performance and report that it accelerates a HF 6-31G Self-Consistent Field (SCF) computation by up to 20 times for medium sized molecules (such as a buckyball) when compared with mature Central Processing Unit algorithms available in the legacy codes in regular use by researchers. It achieves this acceleration by massive parallelization of the one- and two-electron integrals and optimization of the SCF and Direct Inversion in the Iterative Subspace routines through the use of GPU linear algebra libraries. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  18. Quantum Transport Theory of Optical and Plasmonic Response of Nanomaterials

    NASA Astrophysics Data System (ADS)

    Karimi, Farhad

    The light-matter interaction is the cornerstone of photonics and optoelectronics. Advances in the fabrication techniques that has enabled the miniaturization of the semiconductor devices, along with emergence of nanomaterials such as graphene, have brought the fields of photonics and optoelectronics down to the nanoscale. Controlling the light-matter interaction at the nanoscale will impact on the development and improvement of many technologies, ranging from solar-energy harvesting to biosensing. However, the quantum confinement at the nanoscale makes nanostructured devices behave significantly differently than their larger counterparts, which turns the nanoscale control into a grand challenge. In order to pave the path toward it, we need to have a clear and accurate picture of how electrons interact with light at the nanoscale. This dissertation presents a rigorous quantum-transport method for studying the optical and plasmonic properties of nanomaterials. This method is based on a self-consistent-field approach within a Markovian master equation formalism (SCF-MMEF) coupled with the full-wave electromagnetic equations. The SCF-MMEF captures the interband electron-hole generation, as well as the interband and intraband transitions due to multiple competing scattering mechanisms, where the transition rates can have pronounced and widely differing dependencies on both carrier energy and momentum. The SCF-MMEF is applicable to any type of material with an arbitrary band dispersion and Bloch wave functions. We employ the SCF-MMEF to calculate the dielectric function, complex conductivity, and loss function for supported graphene. From the loss-function maximum, we obtain the plasmon dispersion and propagation length for different substrate types [nonpolar diamondlike carbon (DLC) and polar SiO2 and hBN], impurity densities, carrier densities, and temperatures. We find that plasmon propagation lengths are comparable on polar and nonpolar substrates and are on the order of tens of nanometers, considerably shorter than previously reported. In pursuit of finding less dissipative plasmonic materials, we calculate the dielectric function and plasmonic response of armchair (aGNRs)and zigzag (zGNRs) graphene nanoribbons via the SCF-MMEF. Supported GNRs provide almost the same interesting plasmonic features as graphene, with the added benefit of a less dissipative environment for electrons, owing to the low electronic density of states and thus lower electron scattering rates. Midinfrared plasmons in supported (3N+2)-aGNRs can propagate as far as several microns at room temperature, with 4-5-nm-wide ribbons having the longest propagation length. In other types of aGNRs and in zGNRs, the plasmon propagation length seldom exceeds 100 nm. Plasmon propagation lengths are much greater on nonpolar (e.g., diamondlike carbon) than on polar substrates (e.g., SiO2 or hBN), where electrons scatter strongly with surface optical phonons. Another advantage of the SCF-MMEF is that it can be used perturbatively to calculate the nonlinear optical response. We perturbatively employ the SCF-MMEF to calculate the GNRs optical nonlinearity. We show that graphene nanoribbons have a remarkably strong nonlinear optical response in the long-wavelength regime and over a broad frequency range, from terahertz to the nearinfrared. In the retarded regime, electron scattering has a critical effect on the optical nonlinearity of graphene nanoribbons, which cannot be captured via the commonly used relaxation-time approximation. At terahertz frequencies, where intrasubband optical transitions dominate, the strong nonlinearity (in particular, third-order Kerr nonlinearity) stems from the jagged shape of the electron energy distribution, caused by the interband electron scattering mechanisms along with the intraband inelastic scattering mechanisms. At the midinfrared to nearinfrared frequencies, where interband optical transitions dominate, the Kerr nonlinearity is significantly overestimated within the relaxation-time approximation. These findings unveil the critical effect of electron scattering on the optical nonlinearity of nanostructured graphene, and also underscore the capability of this class of materials for nonlinear nanophotonic applications.

  19. Supercritical fluid-mediated liposomes containing cyclosporin A for the treatment of dry eye syndrome in a rabbit model: comparative study with the conventional cyclosporin A emulsion

    PubMed Central

    Karn, Pankaj Ranjan; Kim, Hyun Do; Kang, Han; Sun, Bo Kyung; Jin, Su-Eon; Hwang, Sung-Joo

    2014-01-01

    Background The objective of this study was to compare the efficacy of cyclosporin (CsA)-encapsulated liposomes with the commercially available CsA emulsion (Restasis®) for the treatment of dry eye syndrome in rabbits. Methods Liposomes containing CsA were prepared by the supercritical fluid (SCF) method consisted of phosphatidylcholine from soybean (SCF-S100) and egg lecithins (SCF-EPCS). An in vitro permeation study was carried out using artificial cellulose membrane in Franz diffusion cells. Dry eye syndrome was induced in male albino rabbits and further subdivided into untreated, Restasis®-treated, EPCS, and S100-treated groups. Tear formation in the dry-eye-induced rabbits was evaluated using the Schirmer tear test. All formulations were also evaluated by ocular irritation tests using the Draize eye and winking methods with the determination of CsA concentration in rabbit tears. Results After the treatment, the Schirmer tear test value significantly improved in EPCS-treated (P=0.005) and S100-treated (P=0.018) groups compared to the Restasis®-treated group. The AUC0–24 h for rabbit’s tear film after the administration of SCF-S100 was 32.75±9.21 μg·h/mg which was significantly higher than that of 24.59±8.69 μg·h/mg reported with Restasis®. Liposomal CsA formulations used in this study showed lower irritation in rabbit eyes compared with Restasis®. Conclusion These results demonstrate that the novel SCF-mediated liposomal CsA promises a significant improvement in overcoming the challenges associated with the treatment of dry eyes. PMID:25143728

  20. Turtle Bayou - 1936 to 1983: case history of a major gas field in south Louisiana

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cronquist, C.

    1983-01-01

    Turtle Bayou field, located in the middle Miocene trend in S. Louisiana, is nearing the end of a productive life which spans over 30 yr. Discovered by Shell Oil Co. in 1949 after unsuccessful attempts by 2 other majors, the field is a typical, low relief, moderately faulted Gulf Coast structure, probably associated with deep salt movement. The productive interval includes 22 separate gas-bearing sands in a regressive sequence of sands and shales from approx. 6500 to 12,000 ft. Now estimated to have contained ca 1.2 trillion scf of gas in place, cumulative production through 1982 was 702 billion scf.more » Cumulative condensate-gas ratio has been 20 bbl/million. Recovery mechanisms in individual reservoirs include strong bottom water drive, partial edgewater drive, and pressure depletion. Recovery efficiencies in major reservoirs range from 40 to 75% of original gas in place.« less

  1. A systematic and feasible method for computing nuclear contributions to electrical properties of polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Luis, Josep M.; Duran, Miquel; Andrés, José L.

    1997-08-01

    An analytic method to evaluate nuclear contributions to electrical properties of polyatomic molecules is presented. Such contributions control changes induced by an electric field on equilibrium geometry (nuclear relaxation contribution) and vibrational motion (vibrational contribution) of a molecular system. Expressions to compute the nuclear contributions have been derived from a power series expansion of the potential energy. These contributions to the electrical properties are given in terms of energy derivatives with respect to normal coordinates, electric field intensity or both. Only one calculation of such derivatives at the field-free equilibrium geometry is required. To show the useful efficiency of the analytical evaluation of electrical properties (the so-called AEEP method), results for calculations on water and pyridine at the SCF/TZ2P and the MP2/TZ2P levels of theory are reported. The results obtained are compared with previous theoretical calculations and with experimental values.

  2. Expression of the stem cell factor in fibroblasts, endothelial cells, and macrophages in periapical tissues in human chronic periapical diseases.

    PubMed

    Shen, S Q; Wang, R; Huang, S G

    2017-03-08

    Stem cell factor (SCF), an important stem cell cytokine, has multiple functions. Fibroblasts (FBs), mature mast cells, endothelial cells (ECs), and eosinophil granulocytes can produce SCF in the inflammatory process. Therefore, we aimed to observe SCF expression in FBs, ECs, and macrophages (MPs) in periapical tissues in human chronic periapical disease and investigate the effects of cells expressing SCF in pathogenesis of the disease. Healthy (N = 20), periapical cyst (N = 15), and periapical granuloma (N = 15) tissues were fixed in 10% formalin for 48 h, embedded in paraffin, and stained with hematoxylin and eosin to observe histological changes. SCF expression was observed in FBs, ECs, and MPs in periapical tissues by double immunofluorescence. CD334, CD31, and CD14 are specific markers of FBs, ECs, and MPs, respectively. Results showed that densities of CD334-SCF double-positive FBs, CD31-SCF double-positive ECs, and CD14-SCF double-positive MPs were significantly increased in periapical tissue groups (P < 0.01). There were no significant differences in CD334-SCF double-positive FB and CD31-SCF double-positive EC levels between the two periapical tissue groups (P > 0.05). CD14-SCF double-positive MP density was considerably higher in periapical granulomas than in cysts (P < 0.01). FB, EC, and MP levels were significantly high and densities of CD334-SCF double-positive FBs, CD31-SCF double-positive ECs, and CD14-SCF double-positive MPs improved considerably in chronic periapical tissues, suggesting that the cells might be related to occurrence, development, and pathogenesis of chronic periapical disease.

  3. The Hartree-Fock calculation of the magnetic properties of molecular solutes

    NASA Astrophysics Data System (ADS)

    Cammi, R.

    1998-08-01

    In this paper we set the formal bases for the calculation of the magnetic susceptibility and of the nuclear magnetic shielding tensors for molecular solutes described within the framework of the polarizable continuum model (PCM). The theory has been developed at self-consistent field (SCF) level and adapted to be used within the framework of some of the computational procedures of larger use, i.e., the gauge invariant atomic orbital method (GIAO) and the continuous set gauge transformation method (CSGT). The numerical results relative to the magnetizabilities and chemical shielding of acetonitrile and nitrometane in various solvents computed with the PCM-CSGT method are also presented.

  4. Single molecule conductivity: the role of junction-orbital degeneracy in the artificially high currents predicted by ab initio approaches.

    PubMed

    Solomon, Gemma C; Reimers, Jeffrey R; Hush, Noel S

    2004-10-08

    A priori evaluations, using Hartree-Fock self-consistent-field (SCF) theory or density-functional theory (DFT), of the current passing between two electrodes through a single bridging molecule result in predicted conductivities that may be up to one to two orders of magnitude larger than observed ones. We demonstrate that this is, in part, often due to the improper application of the computational methods. Conductivity is shown to arise from tunneling between junction states of the electrodes through the molecule; these states are inherently either quasi two-fold or four-fold degenerate and always comprise the (highest occupied molecular orbital) HOMO band at the Fermi energy of the system. Frequently, in previous cluster based molecular conduction calculations, closed-shell SCF or Kohn-Sham DFT methods have been applied to systems that we demonstrate to be intrinsically open shell in nature. Such calculations are shown to induce artificial HOMO-LUMO (LUMO-lowest unoccupied molecular orbital) band splittings that Landauer-based formalisms for steady-state conduction interpret as arising from extremely rapid through-molecule tunneling at the Fermi energy, hence, overestimating the low-voltage conductivity. It is demonstrated that these shortcomings can be eliminated, dramatically reducing calculated current magnitudes, through the alternate use of electronic-structure calculations based on the spin-restricted open-shell formalism and related multiconfigurational SCF of DFT approaches. Further, we demonstrate that most anomalies arising in DFT implementations arise through the use of hybrid density functionals such as B3LYP. While the enhanced band-gap properties of these functionals have made them the defacto standard in molecular conductivity calculations, we demonstrate that it also makes them particularly susceptible to open-shell anomalies.

  5. The Effects of Hematopoietic Growth Factors on Neurite Outgrowth

    PubMed Central

    Su, Ye; Cui, Lili; Piao, Chunshu; Li, Bin; Zhao, Li-Ru

    2013-01-01

    Stem cell factor (SCF) and granulocyte colony-stimulating factor (G-CSF) are initially discovered as the essential hematopoietic growth factors regulating bone marrow stem cell proliferation and differentiation, and SCF in combination with G-CSF (SCF+G-CSF) has synergistic effects on bone marrow stem cell mobilization. In this study we have determined the effect of SCF and G-CSF on neurite outgrowth in rat cortical neurons. Using molecular and cellular biology and live cell imaging approaches, we have revealed that receptors for SCF and G-CSF are expressed on the growth core of cortical neurons, and that SCF+G-CSF synergistically enhances neurite extension through PI3K/AKT and NFκB signaling pathways. Moreover, SCF+G-CSF induces much greater NFκB activation, NFκB transcriptional binding and brain-derived neurotrophic factor (BDNF) production than SCF or G-CSF alone. In addition, we have also observed that BDNF, the target gene of NFκB, is required for SCF+G-CSF-induced neurite outgrowth. These data suggest that SCF+G-CSF has synergistic effects to promote neurite growth. This study provides new insights into the contribution of hematopoietic growth factors in neuronal plasticity. PMID:24116056

  6. Climate-Agriculture-Modeling and Decision Tool for Disease (CAMDT-Disease) for seasonal climate forecast-based crop disease risk management in agriculture

    NASA Astrophysics Data System (ADS)

    Kim, K. H.; Lee, S.; Han, E.; Ines, A. V. M.

    2017-12-01

    Climate-Agriculture-Modeling and Decision Tool (CAMDT) is a decision support system (DSS) tool that aims to facilitate translations of probabilistic seasonal climate forecasts (SCF) to crop responses such as yield and water stress. Since CAMDT is a software framework connecting different models and algorithms with SCF information, it can be easily customized for different types of agriculture models. In this study, we replaced the DSSAT-CSM-Rice model originally incorporated in CAMDT with a generic epidemiological model, EPIRICE, to generate a seasonal pest outlook. The resulting CAMDT-Disease generates potential risks for selected fungal, viral, and bacterial diseases of rice over the next months by translating SCFs into agriculturally-relevant risk information. The integrated modeling procedure of CAMDT-Disease first disaggregates a given SCF using temporal downscaling methods (predictWTD or FResampler1), runs EPIRICE with the downscaled weather inputs, and finally visualizes the EPIRICE outputs as disease risk compared to that of the previous year and the 30-year-climatological average. In addition, the easy-to-use graphical user interface adopted from CAMDT allows users to simulate "what-if" scenarios of disease risks over different planting dates with given SCFs. Our future work includes the simulation of the effect of crop disease on yields through the disease simulation models with the DSSAT-CSM-Rice model, as disease remains one of the most critical yield-reducing factors in the field.

  7. Stem cell factor (SCF) protects osteoblasts from oxidative stress through activating c-Kit-Akt signaling

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, Lei; Wu, Zhong; Yin, Gang

    2014-12-12

    Highlights: • SCF receptor c-Kit is functionally expressed in primary and transformed osteoblasts. • SCF protects primary and transformed osteoblasts from H{sub 2}O{sub 2}. • SCF activation of c-Kit in osteoblasts, required for its cyto-protective effects. • c-Kit mediates SCF-induced Akt activation in cultured osteoblasts. • Akt activation is required for SCF-regulated cyto-protective effects in osteoblasts. - Abstract: Osteoblasts regulate bone formation and remodeling, and are main target cells of oxidative stress in the progression of osteonecrosis. The stem cell factor (SCF)-c-Kit pathway plays important roles in the proliferation, differentiation and survival in a range of cell types, but littlemore » is known about its functions in osteoblasts. In this study, we found that c-Kit is functionally expressed in both osteoblastic-like MC3T3-E1 cells and primary murine osteoblasts. Its ligand SCF exerted significant cyto-protective effects against hydrogen peroxide (H{sub 2}O{sub 2}). SCF activated its receptor c-Kit in osteoblasts, which was required for its cyto-protective effects against H{sub 2}O{sub 2}. Pharmacological inhibition (by Imatinib and Dasatinib) or shRNA-mediated knockdown of c-Kit thus inhibited SCF-mediated osteoblast protection. Further investigations showed that protection by SCF against H{sub 2}O{sub 2} was mediated via activation of c-Kit-dependent Akt pathway. Inhibition of Akt activation, through pharmacological or genetic means, suppressed SCF-mediated anti-H{sub 2}O{sub 2} activity in osteoblasts. In summary, we have identified a new SCF-c-Kit-Akt physiologic pathway that protects osteoblasts from H{sub 2}O{sub 2}-induced damages, and might minimize the risk of osteonecrosis caused by oxidative stress.« less

  8. Dynamic polarizabilities and Van der Waals coefficients for alkali atoms Li, Na and alkali dimer molecules Li2, Na2 and NaLi

    NASA Astrophysics Data System (ADS)

    Mérawa, M.; Dargelos, A.

    1998-07-01

    The present paper gives an account of investigations of the polarizability of the alkali atoms Li, Na, diatomics homonuclear and heteronuclear Li2, Na2 and NaLi at SCF (Self Consistent Field) level of approximation and at correlated level, using a time Time-Dependent Gauge Invariant method (TDGI). Our static polarizability values agree with the best experimental and theoretical determinations. The Van der Waals C6 coefficients for the atom-atom, atom-dimer and dimer-dimer interactions have been evaluated. Les polarisabilités des atomes alcalins Li, Na, et des molécules diatomiques homonucléaires et hétéronucléaire Li2, Na2 et NaLi, ont été calculées au niveau SCF (Self Consistent Field) et au niveau corrélé à partir d'une méthode invariante de jauge dépendante du temps(TDGI). Nos valeurs des polarisabilités statiques sont en accord avec les meilleurs déterminations expérimentales et théoriques. Les coefficients C6 de Van de Waals pour les interactions atome-atome, atome-dimère et dimère-dimère ont également été évalués.

  9. Development of novel UV emitting single crystalline film scintillators

    NASA Astrophysics Data System (ADS)

    Zorenko, Yu; Gorbenko, V.; Savchyn, V.; Voznyak, T.; Nikl, M.; Mares, J. A.; Martin, T.; Douissard, P.-A.

    2011-04-01

    The work is dedicated to development of new types of UV -emitting scintillators based on single crystalline films (SCF) of aluminimum perovskites and garnets grown by the liquid phase epitaxy (LPE) method. The development of the following three types of UV SCF scintillators is considered in this work: i) Ce-doped SCF of Y-Lu-Al-perovskites with Ce3+ emission in the 360-370 nm range with a decay time of 16-17 ns; ii) Pr-doped SCF of Y-Lu-Al garnets with Pr3+ emission in the 300-400 nm range with a decay time of 13-17 ns; iii) La3+ and Sc3+ doped SCF of Y-Lu-Al-garnets, emitting in the 290-400 nm range due to formation of the LaY,Lu, ScY,Lu and ScAl centers with decay time of 250-575 ns. The results of testing the several novel UV-emitting SCFs scintillators for visualization of X-ray images at ESFR are presented. It is shown that the UV emission of the LuAG:Sc, LuAG:La and LuAG:Pr SCFs is efficient enough for conversion of X-ray to the UV light and that these scintillators can be used for improvement of the resolution of imaging detectors in synchrotron radiation applications.

  10. Design of Recombinant Stem Cell Factor macrophage Colony Stimulating Factor Fusion Proteins and their Biological Activity In Vitro

    NASA Astrophysics Data System (ADS)

    Chen, Tao; Yang, Jie; Wang, Yuelang; Zhan, Chenyang; Zang, Yuhui; Qin, Junchuan

    2005-05-01

    Stem cell factor (SCF) and macrophage colony stimulating factor (M-CSF) can act in synergistic way to promote the growth of mononuclear phagocytes. SCF-M-CSF fusion proteins were designed on the computer using the Homology and Biopolymer modules of the software packages InsightII. Several existing crystal structures were used as templates to generate models of the complexes of receptor with fusion protein. The structure rationality of the fusion protein incorporated a series of flexible linker peptide was analyzed on InsightII system. Then, a suitable peptide GGGGSGGGGSGG was chosen for the fusion protein. Two recombinant SCF-M-CSF fusion proteins were generated by construction of a plasmid in which the coding regions of human SCF (1-165aa) and M-CSF (1-149aa) cDNA were connected by this linker peptide coding sequence followed by subsequent expression in insect cell. The results of Western blot and activity analysis showed that these two recombinant fusion proteins existed as a dimer with a molecular weight of 84 KD under non-reducing conditions and a monomer of 42 KD at reducing condition. The results of cell proliferation assays showed that each fusion protein induced a dose-dependent proliferative response. At equimolar concentration, SCF/M-CSF was about 20 times more potent than the standard monomeric SCF in stimulating TF-1 cell line growth, while M-CSF/SCF was 10 times of monomeric SCF. No activity difference of M-CSF/SCF or SCF/M-CSF to M-CSF (at same molar) was found in stimulating the HL-60 cell linear growth. The synergistic effect of SCF and M-CSF moieties in the fusion proteins was demonstrated by the result of clonogenic assay performed with human bone mononuclear, in which both SCF/M-CSF and M-CSF/SCF induced much higher number of CFU-M than equimolar amount of SCF or M-CSF or that of two cytokines mixture.

  11. Indexes of Land Use Change to Predict Aggregate Stability in a Mollisol and a Vertisol of Argentina

    NASA Astrophysics Data System (ADS)

    Novelli, L. E.; Caviglia, O. P.; Wilson, M. G.; Sasal, M. C.

    2012-04-01

    In several areas of South America, the extensive cropping systems in traditional agricultural lands have increase the area cropped with soybean, mainly as a single annual crop. Also nowadays agriculture has a progressive expansion toward more environmentally fragile areas that were traditionally occupied by livestock or native forests. This change of land use may be characterized through different indexes as the length of the growth period or the frequency of a particular crop in the cropping sequence. On the other hand the consequences of land-use changes on soil physical condition may be monitored through the aggregate stability, which is directly related to soil functionality. However, there are different methods for aggregate stability analysis, which may vary in their potential for prediction. The aim of our work was to assess different quantitative indexes of change in the land use on aggregate stability through two methods in two soils differing in the main agents of aggregation. The study was conducted in a Mollisol and a Vertisol from Argentina. Eleven fields (agricultural and crop-pasture rotation) under no-tillage and one natural grassland were selected in each soil type. The fraction of annual time with vegetal cover (as a measure of the intensification in the land use - ISI) and the frequency of a given crop (soybean - SCF; wheat - WCF; and wheat plus maize - CCF) in the cropping sequence over a 6-year period were calculated. Samples were collected at 0-5 and 5-15 cm depths from each soil. The mean weight diameter (MWD) of the soil aggregates where determined by two methods: Le Bissonnais with three pretreatment (fast wetting, slow wetting and stirring after prewetting) and by wet sieving using an instrument similar to the Yoder apparatus. The MWD by wet-sieving was affected by ISI and SCF, but the impact only was recorded in 0-5cm depth of the Mollisol. The MWD by fast and slow wetting and the means of three pretreatments (MWDm) were directly related to ISI, SCF and WCF in both depth of the Mollisol. Although in the Vertisol, the aggregate stability in natural grassland was higher than under agricultural use, indexes did not show the change in the land use for any pretreatment or depth, except by ISI and SCF in the slow wetting pretreatment at 5-15 cm depth. The method of Le Bissonnais was more sensitive to predict changes in the land use driven by the frequency of a given crop in the cropping sequence that the wet-sieving, mainly in the Mollisol.

  12. Scaling behavior of ground-state energy cluster expansion for linear polyenes

    NASA Astrophysics Data System (ADS)

    Griffin, L. L.; Wu, Jian; Klein, D. J.; Schmalz, T. G.; Bytautas, L.

    Ground-state energies for linear-chain polyenes are additively expanded in a sequence of terms for chemically relevant conjugated substructures of increasing size. The asymptotic behavior of the large-substructure limit (i.e., high-polymer limit) is investigated as a means of characterizing the rapidity of convergence and consequent utility of this energy cluster expansion. Consideration is directed to computations via: simple Hückel theory, a refined Hückel scheme with geometry optimization, restricted Hartree-Fock self-consistent field (RHF-SCF) solutions of fixed bond-length Parisier-Parr-Pople (PPP)/Hubbard models, and ab initio SCF approaches with and without geometry optimization. The cluster expansion in what might be described as the more "refined" approaches appears to lead to qualitatively more rapid convergence: exponentially fast as opposed to an inverse power at the simple Hückel or SCF-Hubbard levels. The substructural energy cluster expansion then seems to merit special attention. Its possible utility in making accurate extrapolations from finite systems to extended polymers is noted.

  13. Four-component relativistic calculations in solution with the polarizable continuum model of solvation: theory, implementation, and application to the group 16 dihydrides H2X (X = O, S, Se, Te, Po).

    PubMed

    Remigio, Roberto Di; Bast, Radovan; Frediani, Luca; Saue, Trond

    2015-05-28

    We present a formulation of four-component relativistic self-consistent field (SCF) theory for a molecular solute described within the framework of the polarizable continuum model (PCM) for solvation. The linear response function for a four-component PCM-SCF state is also derived, as well as the explicit form of the additional contributions to the first-order response equations. The implementation of such a four-component PCM-SCF model, as carried out in a development version of the DIRAC program package, is documented. In particular, we present the newly developed application programming interface PCMSolver used in the actual implementation with DIRAC. To demonstrate the applicability of the approach, we present and analyze calculations of solvation effects on the geometries, electric dipole moments, and static electric dipole polarizabilities for the group 16 dihydrides H2X (X = O, S, Se, Te, Po).

  14. Growth and luminescent properties of Lu 2SiO 5:Ce and (Lu 1- xGd x) 2SiO 5:Ce single crystalline films

    NASA Astrophysics Data System (ADS)

    Zorenko, Yu.; Gorbenko, V.; Savchyn, V.; Voznyak, T.; Grinyov, B.; Sidletskiy, O.; Kurtsev, D.; Fedorov, A.; Baumer, V.; Nikl, M.; Mares, J. A.; Beitlerova, A.; Prusa, P.; Kucera, M.

    2011-12-01

    Single crystalline films (SCF) of Lu 2SiO 5:Ce (LSO:Ce), (Lu 1- xGd x) 2SiO 5:Ce (LGSO:Ce) and LGSO:Ce,Tb orthosilicates with thickness of 2.5-21 μm were crystallized by liquid phase epitaxy method onto undoped LSO substrates from melt-solution based on PbO-B 2O 3 flux. The concentration of Gd was varied in the range of x=0.2-0.7 formula units (f.u.). In the case of LGSO:Ce SCF growth we do not use any additional doping for reducing the misfit between the SCF and substrate lattices. The luminescence and scintillation properties of LSO:Ce, LGSO:Ce and LGSO:Ce,Tb SCFs were mutually compared and confronted with the performance of reference LSO:Ce and LYSO:Ce crystals. With increasing Gd content the luminescence spectrum of LGSO:Ce SCF is gradually red-shifted with respect to that of LSO:Ce SCF. The LY of (Lu 1- xGd x)SO:Ce SCF becomes lower in comparison with that for LSO:Ce SC at increasing Gd content in the range of x=0.2-0.7 f.u. The peculiarities of luminescence properties of LSO:Ce and LGSO:Ce SCFs in comparison with crystal analogs are explained by the different distribution of Ce 3+ over Lu1 and Lu2 positions of LSO host and by the influence of Pb 2+ contamination coming from the flux used for the film growth.

  15. Cadmium exposure in newborn rats ovary induces developmental disorders of primordial follicles and the differential expression of SCF/c-kit gene.

    PubMed

    Zhang, Wenchang; Wu, Tingting; Zhang, Chenyun; Luo, Lingfeng; Xie, Meimei; Huang, Huiling

    2017-10-05

    Since the 1990s, the rising problem that gonad reproductive toxicity on adult female after exposing to cadmium (Cd), an environmental endocrine disruptor, has attracted high attention at home and abroad,and was systematically studied. Our research focuses on a further problem is that early cadmium exposure (during birth to before puberty) impact on development and function of ovarian cells and its possible mechanism. Our research focuses on the changes of ovarian cells growth and development after the newborn rat ovaries with cadmium exposure in vitro, and different expression of ovarian cells development-related factors, SCF/c-kit and changes of their DNA methylation status. We obtained ovaries from 4-day-old SD rats and cultured them in DMEM/F12 mixed with α-MEM media in vitro. Different doses of cadmium were designed as control, 0.5, 5, 10 and 50μM, and then the constituent ratio of ovarian follicle and follicular oocytes diameter were observed with microscope after 4-h exposure. We found that the increased constituent ratio of original follicle and decreased diameter of all levels of follicular oocytes(compared with control, with statistically significant differences, P<0.01).After the measurement of expression of SCF/c-kit by qRT-PCR and Western Blotting, the mRNA and protein expression of SCF/c-kit in ovarian were both decreased. We further found that the increased constituent ratio of growth follicle and increased diameter of oocytes under the treatment of adding SCF in cell culture media. Finally, MALDI-TOF-MS method showed DNA-low methylation status of SCF/c-kit promoter region after Cd exposure. Overall, we concluded that the exposure of cadimium (5-50μM) on newborn rats ovaries could inhibit follicle development.SCF/c-kit system might mediate follicle development damage caused by cadmium, which is associated with DNA hypomethylation of SCF/c-kit promoter region may be worthy of further study. Copyright © 2017. Published by Elsevier B.V.

  16. Acquisition and evaluation of verb subcategorization resources for biomedicine.

    PubMed

    Rimell, Laura; Lippincott, Thomas; Verspoor, Karin; Johnson, Helen L; Korhonen, Anna

    2013-04-01

    Biomedical natural language processing (NLP) applications that have access to detailed resources about the linguistic characteristics of biomedical language demonstrate improved performance on tasks such as relation extraction and syntactic or semantic parsing. Such applications are important for transforming the growing unstructured information buried in the biomedical literature into structured, actionable information. In this paper, we address the creation of linguistic resources that capture how individual biomedical verbs behave. We specifically consider verb subcategorization, or the tendency of verbs to "select" co-occurrence with particular phrase types, which influences the interpretation of verbs and identification of verbal arguments in context. There are currently a limited number of biomedical resources containing information about subcategorization frames (SCFs), and these are the result of either labor-intensive manual collation, or automatic methods that use tools adapted to a single biomedical subdomain. Either method may result in resources that lack coverage. Moreover, the quality of existing verb SCF resources for biomedicine is unknown, due to a lack of available gold standards for evaluation. This paper presents three new resources related to verb subcategorization frames in biomedicine, and four experiments making use of the new resources. We present the first biomedical SCF gold standards, capturing two different but widely-used definitions of subcategorization, and a new SCF lexicon, BioCat, covering a large number of biomedical sub-domains. We evaluate the SCF acquisition methodologies for BioCat with respect to the gold standards, and compare the results with the accuracy of the only previously existing automatically-acquired SCF lexicon for biomedicine, the BioLexicon. Our results show that the BioLexicon has greater precision while BioCat has better coverage of SCFs. Finally, we explore the definition of subcategorization using these resources and its implications for biomedical NLP. All resources are made publicly available. The SCF resources we have evaluated still show considerably lower accuracy than that reported with general English lexicons, demonstrating the need for domain- and subdomain-specific SCF acquisition tools for biomedicine. Our new gold standards reveal major differences when annotators use the different definitions. Moreover, evaluation of BioCat yields major differences in accuracy depending on the gold standard, demonstrating that the definition of subcategorization adopted will have a direct impact on perceived system accuracy for specific tasks. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Induction of NKCF-like activity in mixed lymphocyte-tumor cell culture: direct involvement of mycoplasma infection of tumor cells.

    PubMed

    Wayner, E A; Brooks, C G

    1984-04-01

    Co-culture of CBA/J spleen cells and certain lines of YAC-1 stimulators resulted in the appearance of NKCF-like activity in 24- to 48-hr supernatants. Numerous other in vitro cell lines were effective stimulators of this splenic cytotoxic factor (SCF). The cells participating in SCF production were absent from normal thymocytes and were present in BALB/c nu/nu spleen, were nonadherent, asialo GM1+, and bore low levels of Thy-1.2. SCF could mediate lysis of certain NK-sensitive tumor targets in an 18-hr 51Cr-release assay. However, the induction of SCF was not correlated with the ability of a particular cell line to be lysed by NK cells, but showed an absolute correlation with the presence of mycoplasma contamination in cultured tumor cell lines. Mycoplasma negative cell lines, including an uninfected but NK-sensitive subline of YAC-1, were unable to induce SCF. Decontamination of mycoplasma-infected lines with antibiotics or by passage through syngeneic mice abrogated the ability of infected tumor cells to stimulate SCF. The ability to induce SCF could be restored by reinfection with mycoplasma. Tumor cell-free supernatants from contaminated cultures were mitogenic for CBA spleen cells and could themselves induce SCF activity in spleen cell supernatants. SCF production and the agent responsible could be removed by passing such supernatants through 0.1-micron filters. The organism apparently responsible for SCF induction from CBA spleen cells was typed and found to be Mycoplasma orale, a nonfermentative, arginine-dependent, common tissue culture contaminant. About 50 to 60% of SCF activity could be removed by 0.1-micron filters, suggesting that SCF is composed of two components: mycoplasma organisms themselves and a soluble cytotoxic factor produced in response to mycoplasma.

  18. Glucose transformation to 5-hydroxymethylfurfural in acidic ionic liquid: A quantum mechanical study.

    PubMed

    Arifin; Puripat, Maneeporn; Yokogawa, Daisuke; Parasuk, Vudhichai; Irle, Stephan

    2016-01-30

    Isomerization and transformation of glucose and fructose to 5-hydroxymethylfurfural (HMF) in both ionic liquids (ILs) and water has been studied by the reference interaction site model self-consistent field spatial electron density distribution (RISM-SCF-SEDD) method coupled with ab initio electronic structure theory, namely coupled cluster single, double, and perturbative triple excitation (CCSD(T)). Glucose isomerization to fructose has been investigated via cyclic and open chain mechanisms. In water, the calculations support the cyclic mechanism of glucose isomerization; with the predicted activation free energy is 23.8 kcal mol(-1) at experimental condition. Conversely, open ring mechanism is more favorable in ILs with the energy barrier is 32.4 kcal mol(-1) . Moreover, the transformation of fructose into HMF via cyclic mechanism is reasonable; the calculated activation barriers are 16.0 and 21.5 kcal mol(-1) in aqueous and ILs solutions, respectively. The solvent effects of ILs could be explained by the decomposition of free energies and radial distribution functions of solute-solvent that are produced by RISM-SCF-SEDD. © 2015 Wiley Periodicals, Inc.

  19. Vibrational self-consistent field theory using optimized curvilinear coordinates.

    PubMed

    Bulik, Ireneusz W; Frisch, Michael J; Vaccaro, Patrick H

    2017-07-28

    A vibrational SCF model is presented in which the functions forming the single-mode functions in the product wavefunction are expressed in terms of internal coordinates and the coordinates used for each mode are optimized variationally. This model involves no approximations to the kinetic energy operator and does not require a Taylor-series expansion of the potential. The non-linear optimization of coordinates is found to give much better product wavefunctions than the limited variations considered in most previous applications of SCF methods to vibrational problems. The approach is tested using published potential energy surfaces for water, ammonia, and formaldehyde. Variational flexibility allowed in the current ansätze results in excellent zero-point energies expressed through single-product states and accurate fundamental transition frequencies realized by short configuration-interaction expansions. Fully variational optimization of single-product states for excited vibrational levels also is discussed. The highlighted methodology constitutes an excellent starting point for more sophisticated treatments, as the bulk characteristics of many-mode coupling are accounted for efficiently in terms of compact wavefunctions (as evident from the accurate prediction of transition frequencies).

  20. All-electron density functional calculation on insulin with quasi-canonical localized orbitals.

    PubMed

    Inaba, Toru; Tahara, Saisei; Nisikawa, Nobutaka; Kashiwagi, Hiroshi; Sato, Fumitoshi

    2005-07-30

    An all-electron density functional (DF) calculation on insulin was performed by the Gaussian-based DF program, ProteinDF. Quasi-canonical localized orbitals (QCLOs) were used to improve the initial guess for the self-consistent field (SCF) calculation. All calculations were carried out by parallel computing on eight processors of an Itanium2 cluster (SGI Altix3700) with a theoretical peak performance of 41.6 GFlops. It took 35 h for the whole calculation. Insulin is a protein hormone consisting of two peptide chains linked by three disulfide bonds. The numbers of residues, atoms, electrons, orbitals, and auxiliary functions are 51, 790, 3078, 4439, and 8060, respectively. An all-electron DF calculation on insulin was successfully carried out, starting from connected QCLOs. Regardless of a large molecule with complicated topology, the differences in the total energy and the Mulliken atomic charge between initial and converged wavefunctions were very small. The calculation proceeded smoothly without any trial and error, suggesting that this is a promising method to obtain SCF convergence on large molecules such as proteins.

  1. Excited State Studies of Polyacenes Using the All-Order Constricted Variational Density Functional Theory with Orbital Relaxation.

    PubMed

    Senn, Florian; Krykunov, Mykhaylo

    2015-10-22

    For the polyacenes series from naphthalene to hexacene, we present the vertical singlet excitation energies 1 (1)La and 1 (1)Lb, as well as the first triplet excitation energies obtained by the all-order constricted variational density functional theory with orbital relaxation (R-CV(∞)-DFT). R-CV(∞)-DFT is a further development of variational density functional theory (CV(∞)-DFT), which has already been successfully applied for the calculation of the vertical singlet excitation energies (1)La and (1)Lb for polyacenes,15 and we show that one obtains consistent excitation energies using the local density approximation as a functional for singlet as well as for triplet excitations when going beyond the linear response theory. Furthermore, we apply self-consistent field density functional theory (ΔSCF-DFT) and compare the obtained excitation energies for the first triplet excitations T1, where, due to the character of the transition, ΔSCF-DFT and R-CV(∞)-DFT become numerically equivalent, and for the singlet excitations 1 (1)La and 1 (1)Lb, where the two methods differ.

  2. The Structure of Li7 and K7

    NASA Technical Reports Server (NTRS)

    Bauschlicher. Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The self-consistent-field (SCF) approach and density functional theory, using the B3LYP hybrid functional, yield three low-lying structures for Li7(-). The relative separations differ for the SCF and B3LYP approaches, however the B3LYP results are in good agreement with the coupled cluster results. For K7(-), only an octahedron with one face capped is found to be a minimum; this the second most stable structure for Li7(-). A comparison of the computed separations between the low-lying states of K7 and the photoelectron detachment spectra does not allow an unambiguous assignment of the structure of K7(-).

  3. Benchmark quality total atomization energies of small polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Martin, Jan M. L.; Taylor, Peter R.

    1997-05-01

    Successive coupled-cluster [CCSD(T)] calculations in basis sets of spdf, spdfg, and spdfgh quality, combined with separate Schwartz-type extrapolations A+B/(l+1/2)α of the self-consistent field (SCF) and correlation energies, permit the calculations of molecular total atomization energies (TAEs) with a mean absolute error of as low as 0.12 kcal/mol. For the largest molecule treated, C2H4, we find ∑D0=532.0 kcal/mol, in perfect agreement with experiment. The aug-cc-pV5Z basis set recovers on average about 99% of the valence correlation contribution to the TAE, and essentially the entire SCF contribution.

  4. Supercritical fluid-mediated liposomes containing cyclosporin A for the treatment of dry eye syndrome in a rabbit model: comparative study with the conventional cyclosporin A emulsion.

    PubMed

    Karn, Pankaj Ranjan; Kim, Hyun Do; Kang, Han; Sun, Bo Kyung; Jin, Su-Eon; Hwang, Sung-Joo

    2014-01-01

    The objective of this study was to compare the efficacy of cyclosporin (CsA)-encapsulated liposomes with the commercially available CsA emulsion (Restasis) for the treatment of dry eye syndrome in rabbits. Liposomes containing CsA were prepared by the supercritical fluid (SCF) method consisted of phosphatidylcholine from soybean (SCF-S100) and egg lecithins (SCF-EPCS). An in vitro permeation study was carried out using artificial cellulose membrane in Franz diffusion cells. Dry eye syndrome was induced in male albino rabbits and further subdivided into untreated, Restasis-treated, EPCS, and S100-treated groups. Tear formation in the dry-eye-induced rabbits was evaluated using the Schirmer tear test. All formulations were also evaluated by ocular irritation tests using the Draize eye and winking methods with the determination of CsA concentration in rabbit tears. After the treatment, the Schirmer tear test value significantly improved in EPCS-treated (P=0.005) and S100-treated (P=0.018) groups compared to the Restasis-treated group. The AUC₀₋₂₄ h for rabbit's tear film after the administration of SCF-S100 was 32.75±9.21 μg·h/mg which was significantly higher than that of 24.59±8.69 μg·h/mg reported with Restasis. Liposomal CsA formulations used in this study showed lower irritation in rabbit eyes compared with Restasis. These results demonstrate that the novel SCF-mediated liposomal CsA promises a significant improvement in overcoming the challenges associated with the treatment of dry eyes.

  5. Chymase Cleavage of Stem Cell Factor Yields a Bioactive, Soluble Product

    NASA Astrophysics Data System (ADS)

    Longley, B. Jack; Tyrrell, Lynda; Ma, Yongsheng; Williams, David A.; Halaban, Ruth; Langley, Keith; Lu, Hsieng S.; Schechter, Norman M.

    1997-08-01

    Stem cell factor (SCF) is produced by stromal cells as a membrane-bound molecule, which may be proteolytically cleaved at a site close to the membrane to produce a soluble bioactive form. The proteases producing this cleavage are unknown. In this study, we demonstrate that human mast cell chymase, a chymotrypsin-like protease, cleaves SCF at a novel site. Cleavage is at the peptide bond between Phe-158 and Met-159, which are encoded by exon 6 of the SCF gene. This cleavage results in a soluble bioactive product that is 7 amino acids shorter at the C terminus than previously identified soluble SCF. This research shows the identification of a physiologically relevant enzyme that specifically cleaves SCF. Because mast cells express the KIT protein, the receptor for SCF, and respond to SCF by proliferation and degranulation, this observation identifies a possible feedback loop in which chymase released from mast cell secretory granules may solubilize SCF bound to the membrane of surrounding stromal cells. The liberated soluble SCF may in turn stimulate mast cell proliferation and differentiated functions; this loop could contribute to abnormal accumulations of mast cells in the skin and hyperpigmentation at sites of chronic cutaneous inflammation.

  6. Supercritical fluid extraction. Principles and practice

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McHugh, M.A.; Krukonis, V.J.

    This book is a presentation of the fundamentals and application of super-critical fluid solvents (SCF). The authors cover virtually every facet of SCF technology: the history of SCF extraction, its underlying thermodynamic principles, process principles, industrial applications, and analysis of SCF research and development efforts. The thermodynamic principles governing SCF extraction are covered in depth. The often complex three-dimensional pressure-temperature composition (PTx) phase diagrams for SCF-solute mixtures are constructed in a coherent step-by-step manner using the more familiar two-dimensional Px diagrams. The experimental techniques used to obtain high pressure phase behavior information are described in detail and the advantages andmore » disadvantages of each technique are explained. Finally, the equations used to model SCF-solute mixtures are developed, and modeling results are presented to highlight the correlational strengths of a cubic equation of state.« less

  7. The DV-Xα Calculations of Optical Spectra and Their Pressure-Induced Shifts for Ruby

    NASA Astrophysics Data System (ADS)

    Ma, Dongping; Ellis, D. E.; Liu, Yanyun; Chen, Jurong

    1997-10-01

    The R line and U band at normal pressure and their pressure-induced shifts of ruby have been calculated by making use of the SCF embedded-cluster discrete variational (DV-Xα) method. The calculated results of the spectral pressure-induced shifts of ruby by making use of the crystal-field theory have also been given. The results of the first-principle calculations are in very good agreement with the experimental data and the calculated results by using crystal-field theory. The results of local lattice relaxations around the Cr3+ ion are obtained by the DV-Xα calculations. The project supported by National Natural Science Foundation of China

  8. Ultrafast absorption of intense x rays by nitrogen molecules

    NASA Astrophysics Data System (ADS)

    Buth, Christian; Liu, Ji-Cai; Chen, Mau Hsiung; Cryan, James P.; Fang, Li; Glownia, James M.; Hoener, Matthias; Coffee, Ryan N.; Berrah, Nora

    2012-06-01

    We devise a theoretical description for the response of nitrogen molecules (N2) to ultrashort and intense x rays from the free electron laser Linac Coherent Light Source (LCLS). We set out from a rate-equation description for the x-ray absorption by a nitrogen atom. The equations are formulated using all one-x-ray-photon absorption cross sections and the Auger and radiative decay widths of multiply-ionized nitrogen atoms. Cross sections are obtained with a one-electron theory and decay widths are determined from ab initio computations using the Dirac-Hartree-Slater (DHS) method. We also calculate all binding and transition energies of nitrogen atoms in all charge states with the DHS method as the difference of two self-consistent field (SCF) calculations (ΔSCF method). To describe the interaction with N2, a detailed investigation of intense x-ray-induced ionization and molecular fragmentation are carried out. As a figure of merit, we calculate ion yields and the average charge state measured in recent experiments at the LCLS. We use a series of phenomenological models of increasing sophistication to unravel the mechanisms of the interaction of x rays with N2: a single atom, a symmetric-sharing model, and a fragmentation-matrix model are developed. The role of the formation and decay of single and double core holes, the metastable states of N_2^{2+}, and molecular fragmentation are explained.

  9. On the existence of the optimal order for wavefunction extrapolation in Born-Oppenheimer molecular dynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fang, Jun; Wang, Han, E-mail: wang-han@iapcm.ac.cn; CAEP Software Center for High Performance Numerical Simulation, Beijing

    2016-06-28

    Wavefunction extrapolation greatly reduces the number of self-consistent field (SCF) iterations and thus the overall computational cost of Born-Oppenheimer molecular dynamics (BOMD) that is based on the Kohn–Sham density functional theory. Going against the intuition that the higher order of extrapolation possesses a better accuracy, we demonstrate, from both theoretical and numerical perspectives, that the extrapolation accuracy firstly increases and then decreases with respect to the order, and an optimal extrapolation order in terms of minimal number of SCF iterations always exists. We also prove that the optimal order tends to be larger when using larger MD time steps ormore » more strict SCF convergence criteria. By example BOMD simulations of a solid copper system, we show that the optimal extrapolation order covers a broad range when varying the MD time step or the SCF convergence criterion. Therefore, we suggest the necessity for BOMD simulation packages to open the user interface and to provide more choices on the extrapolation order. Another factor that may influence the extrapolation accuracy is the alignment scheme that eliminates the discontinuity in the wavefunctions with respect to the atomic or cell variables. We prove the equivalence between the two existing schemes, thus the implementation of either of them does not lead to essential difference in the extrapolation accuracy.« less

  10. Structure and vibrational spectra of low-energy silicon clusters

    NASA Astrophysics Data System (ADS)

    Sieck, A.; Porezag, D.; Frauenheim, Th.; Pederson, M. R.; Jackson, K.

    1997-12-01

    We have identified low-energy structures of silicon clusters with 9 to 14 atoms using a nonorthogonal tight-binding method (TB) based on density-functional theory (DF). We have further investigated the resulting structures with an accurate all-electron first-principles technique. The results for cohesive energies, cluster geometries, and highest occupied to lowest unoccupied molecular orbital (HOMO-LUMO) gaps show an overall good agreement between DF-TB and self-consistent-field (SCF) DF theory. For Si9 and Si14, we have found equilibrium structures, whereas for Si11, Si12, and Si13, we present clusters with energies close to that of the corresponding ground-state structure recently proposed in the literature. The bonding scheme of clusters in this size range is different from the bulk tetrahedral symmetry. The most stable structures, characterized by low energies and large HOMO-LUMO gaps, have similar common subunits. To aid in their experimental identification, we have computed the full vibrational spectra of the structures, along with the Raman activities, IR intensities, and static polarizabilities, using SCF-DF theory within the local-density approximation (LDA). This method has already been successfully applied to the determination of Raman and IR spectra of silicon clusters with 3-8, 10, 13, 20, and 21 atoms.

  11. The stem cell factor (SCF)/c-KIT system in carcinogenesis of reproductive tissues: What does the hormonal regulation tell us?

    PubMed

    Figueira, Marília I; Cardoso, Henrique J; Correia, Sara; Maia, Cláudio J; Socorro, Sílvia

    2017-10-01

    The tyrosine kinase receptor c-KIT and its ligand, the stem cell factor (SCF) are expressed in several tissues of male and female reproductive tract, playing an important role in the regulation of basic biological processes. The activation of c-KIT by SCF controls, cell survival and death, cell differentiation and migration. Also, the SCF/c-KIT system has been implicated in carcinogenesis of reproductive tissues due to its altered expression pattern or overactivation in consequence of gain-of-functions mutations. Over the years, it has also been shown that hormones, the primary regulators of reproductive function and causative agents in the case of hormone-dependent cancers, are also able to control the SCF/c-KIT tissue levels. Therefore, it is liable to suppose that disturbed SCF/c-KIT expression driven by (de)regulated hormone actions can be a relevant step towards carcinogenesis. The present review describes the SCF and c-KIT expression in cancers of reproductive tissues, discussing the implications of the hormonal regulation of the SCF/c-KIT system in cancer development. Understanding the relationship between hormonal imbalance and the SCF/c-KIT expression and activity would be relevant in the context of novel therapeutic approaches in reproductive cancers. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Sustained release of stem cell factor in a double network hydrogel for ex vivo culture of cord blood-derived CD34+ cells.

    PubMed

    Zhang, Yuanhao; Pan, Xiuwei; Shi, Zhen; Cai, Haibo; Gao, Yun; Zhang, Weian

    2018-04-01

    Stem cell factor (SCF) is considered as a commonly indispensable cytokine for proliferation of haematopoietic stem cells (HSCs), which is used in large dosages during ex vivo culture. The work presented here aimed to reduce the consumption of SCF by sustained release but still support cells proliferation and maintain the multipotency of HSCs. Stem cell factor was physically encapsulated within a hyaluronic acid/gelatin double network (HGDN) hydrogel to achieve a slow release rate. CD34 + cells were cultured within the SCF-loaded HGDN hydrogel for 14 days. The cell number, phenotype and functional capacity were investigated after culture. The HGDN hydrogels had desirable properties and encapsulated SCF kept being released for more than 6 days. SCF remained the native bioactivity, and the proliferation of HSCs within the SCF-loaded HGDN hydrogel was not affected, although the consumption of SCF was only a quarter in comparison with the conventional culture. Moreover, CD34 + cells harvested from the SCF-loaded HGDN hydrogels generated more multipotent colony-forming units (CFU-GEMM). The data suggested that the SCF-loaded HGDN hydrogel could support ex vivo culture of HSCs, thus providing a cost-effective culture protocol for HSCs. © 2017 John Wiley & Sons Ltd.

  13. Influence of Chirality in Ordered Block Copolymer Phases

    NASA Astrophysics Data System (ADS)

    Prasad, Ishan; Grason, Gregory

    2015-03-01

    Block copolymers are known to assemble into rich spectrum of ordered phases, with many complex phases driven by asymmetry in copolymer architecture. Despite decades of study, the influence of intrinsic chirality on equilibrium mesophase assembly of block copolymers is not well understood and largely unexplored. Self-consistent field theory has played a major role in prediction of physical properties of polymeric systems. Only recently, a polar orientational self-consistent field (oSCF) approach was adopted to model chiral BCP having a thermodynamic preference for cholesteric ordering in chiral segments. We implement oSCF theory for chiral nematic copolymers, where segment orientations are characterized by quadrupolar chiral interactions, and focus our study on the thermodynamic stability of bi-continuous network morphologies, and the transfer of molecular chirality to mesoscale chirality of networks. Unique photonic properties observed in butterfly wings have been attributed to presence of chiral single-gyroid networks, this has made it an attractive target for chiral metamaterial design.

  14. Self-consistent hybrid functionals for solids: a fully-automated implementation

    NASA Astrophysics Data System (ADS)

    Erba, A.

    2017-08-01

    A fully-automated algorithm for the determination of the system-specific optimal fraction of exact exchange in self-consistent hybrid functionals of the density-functional-theory is illustrated, as implemented into the public Crystal program. The exchange fraction of this new class of functionals is self-consistently updated proportionally to the inverse of the dielectric response of the system within an iterative procedure (Skone et al 2014 Phys. Rev. B 89, 195112). Each iteration of the present scheme, in turn, implies convergence of a self-consistent-field (SCF) and a coupled-perturbed-Hartree-Fock/Kohn-Sham (CPHF/KS) procedure. The present implementation, beside improving the user-friendliness of self-consistent hybrids, exploits the unperturbed and electric-field perturbed density matrices from previous iterations as guesses for subsequent SCF and CPHF/KS iterations, which is documented to reduce the overall computational cost of the whole process by a factor of 2.

  15. Cotton-Mouton effect and shielding polarizabilities of ethylene: An MCSCF study

    NASA Astrophysics Data System (ADS)

    Coriani, Sonia; Rizzo, Antonio; Ruud, Kenneth; Helgaker, Trygve

    1997-03-01

    The static hypermagnetizabilities and nuclear shielding polarizabilities of the carbon and hydrogen atoms of ethylene have been computed using multiconfigurational linear-response theory and a finite-field method, in a mixed analytical-numerical approach. Extended sets of magnetic-field-dependent basis functions have been employed in large MCSCF calculations, involving active spaces giving rise to a few million configurations in the finite-field perturbed symmetry. The convergence of the observables with respect to the extension of the basis set as well as the effect of electron correlation have been investigated. Whereas for the shielding polarizabilities we can compare with other published SCF results, the ab initio estimates for the static hypermagnetizabilities and the observable to which they are related - the Cotton-Mouton constant, - are presented for the first time.

  16. Theoretical study of the dipole moments of selected alkaline-earth halides

    NASA Technical Reports Server (NTRS)

    Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.; Ahlrichs, R.

    1986-01-01

    Ab initio calculations at the self-consistent-field (SCF), singles-plus-doubles configuration-interaction (SDCI), and coupled-pair functional (CPF) level, are reported for the dipole moments and dipole derivatives of the X2Sigma(+) ground states of BeF, BeCl, MgF, MgCl, CaF, CaCl, and SrF. For comparison, analogous calculations are performed for the X1Sigma(+) state of KCl. The CPF results are found to be in remarkably better agreement with experiment than are the SCF and SDCI results. Apparently higher excitations are required to properly describe the radial extent along the bond axis of the remaining valence electron on the alkaline-earth metal.

  17. Deviations from idealised geometries part 4: approximately tetrahedral molecules of form MX 2Y 2 studied by SCF and MP2 localised orbital calculations

    NASA Astrophysics Data System (ADS)

    Palmer, Michael H.

    1997-03-01

    Using the delocalised wavefunctions from Part 3, for a series of molecules of type MX 2Y 2 where M is tetravalent, and X, Y are either H, Me or halogen, with a triple-zeta plus polarisation basis and either SCF of MP2 methods, the wavefunctions were converted to localised orbitals by the Foster-Boys method. This enabled the LMO to be subject to population analysis for changes in hybridisation in the individual total density of the MX and MY bonds, and some quantitative discussion of the role of hybridisation in Bent's Rule.

  18. Research into topology optimization and the FDM method for a space cracked membrane

    NASA Astrophysics Data System (ADS)

    Hu, Qingxi; Li, Wanyuan; Zhang, Haiguang; Liu, Dali; Peng, Fujun; Duan, Yongchao

    2017-07-01

    The problem that the space membranes are easily torn open is the main focus in this paper, and a bionic strengthening-ribs structure is proposed for a space membrane based on interdisciplinary strengths, such as topology optimization, composite materials, and rapid prototyping. The optimization method and modeling method of membranes with bionic strengthening-ribs was studied. The PEEK and SCF/PEEK composite material which are applied to the space environment are chosen, and FDM technology is used. Through topology optimization, bionic strengthening-ribs with good tensile and tear capacities were obtained. Cracked membranes, cracked membranes with PEEK strengthening-ribs and SCF/PEEK strengthening-ribs were tested and test data were obtained. An extension situation and tension fracture were compared for three cases. The experimental results showed that membranes with the bionic strengthening-ribs structure have better mechanical properties, and the strength of the membranes with PEEK and SCF/PEEK strengthening-ribs were raised, respectively, up to 266.9% and 185.9%. The strengthening-ribs structure greatly improves the capacity to halt membrane crack-growth, which has an important significance to avoid membrane tear, and to ensure the spacecraft orbital lifetime.

  19. Friction and wear of single-crystal and polycrystalline maganese-zinc ferrite in contact with various metals

    NASA Technical Reports Server (NTRS)

    Miyoshi, K.; Buckley, D. H.

    1977-01-01

    Sliding friction experiments were conducted with single-crystal (SCF) and hot-pressed polycrystalline (HPF) manganese-zinc ferrite in contact with various metals. Results indicate that the coefficients of friction for SCF and HPF are related to the relative chemical activity of those metals in high vacuum. The more active the metal, the higher the coefficient of friction. The coefficients of friction for both SCF and HPF were the same and much higher in vacuum than in argon at atmospheric pressure. All the metals tested transferred to the surface of both SCF and HPF in sliding. Both SCF and HPF exhibited cracking and fracture with sliding. Cracking in SCF is dependent on crystallographic characteristics. In HPF, cracking depends on the orientation of the individual crystallites.

  20. Growth and luminescent properties of Lu2SiO5 and Lu2SiO5:Ce single crystalline films

    NASA Astrophysics Data System (ADS)

    Zorenko, Yu; Nikl, M.; Gorbenko, V.; Mares, J. A.; Savchyn, V.; Voznyak, T.; Solsky, I.; Grynyov, B.; Sidletskiy, O.; Kurtsev, D.; Beitlerova, A.; Kucerkova, R.

    2010-11-01

    Single crystalline films (SCF) of Lu2SiO5 (LSO) and Lu2SiO5:Ce (LSO:Ce) silicates with thickness of 2.5-21 μm were crystallised by liquid phase epitaxy method onto undoped LSO substrates from melt-solution based on PbO-B2O3 flux. The luminescence and scintillation properties of LSO and LSO:Ce SCFs were compared with the properties of a reference LSO:Ce and LYSO:Ce crystals. The light yield (LY) of LSO and LSO:Ce SCF reaches up 30 % and 145 %, respectively, of that of a reference LSO:Ce crystal under excitation by α-particles of 241Am source (5.5 MeV). We found that the luminescence spectrum of LSO:Ce SCF is red-shifted with respect to the spectrum of a reference LSO:Ce crystal. Differences in luminescence properties of LSO:Ce SCF and single crystal are explained by the different distribution of Ce3+ over the Lu1 and Lu2 positions of LSO host and are also due to Pb2+ contamination in the former.

  1. Large-scale purification and characterization of recombinant human stem cell factor in Escherichia coli.

    PubMed

    Chen, Liang-Hua; Cai, Feng; Zhang, Dan-Ju; Zhang, Li; Zhu, Peng; Gao, Shun

    2017-07-01

    The pharmacological importance of recombinant human stem cell factor (rhSCF) has increased the demand to establish effective and large-scale production and purification processes. A good source of bioactive recombinant protein with capability of being scaled-up without losing activity has always been a challenge. The objectives of the study were the rapid and efficient pilot-scale expression and purification of rhSCF. The gene encoding stem cell factor (SCF) was cloned into pBV220 and transformed into Escherichia coli. The recombinant SCF was expressed and isolated using a procedure consisting of isolation of inclusion bodies (IBs), denaturation, and refolding followed by chromatographic steps toward purification. The yield of rhSCF reached 835.6 g/20 L, and the expression levels of rhSCF were about 33.9% of the total E. coli protein content. rhSCF was purified by isolation of IBs, denaturation, and refolding, followed by SP-Sepharose chromatography, Source 30 reversed-phase chromatography, and Q-Sepharose chromatography. This procedure was developed to isolate 5.5 g of rhSCF (99.5% purity) with specific activity at 0.96 × 10 6  IU/mg, endotoxin levels of pyrogen at 1.0 EU/mg, and bacterial DNA at 10 ng/mg. Pilot-scale fermentations and purifications were set up for the production of rhSCF that can be upscaled for industry. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  2. Analyzing Molecular Clouds with the Spectral Correlation Function

    NASA Astrophysics Data System (ADS)

    Rosolowsky, E. W.; Goodman, A. A.; Williams, J. P.; Wilner, D. J.

    1997-12-01

    The Spectral Correlation Function (SCF) is a new data analysis algorithm that measures how the properites of spectra vary from position to position in a spectral-line map. For each spectrum in a data cube, the SCF measures the ``difference" between that spectrum and a specified subset of its neighbors. This algorithm is intended for use on both simulated and observed position-position-velocity data cubes. In initial tests of the SCF, we have shown that a histogram of the SCF for a map is a good descriptor of the spatial-velocity distribution of material. In one test, we compare the SCF distributions for: 1) a real data cube; 2) a cube made from the real cube's spectra with randomized positions; and 3) the results of a preliminary MHD simulation by Gammie, Ostriker, and Stone. The results of the test show that the real cloud and the simulation are much closer to each other in their SCF distributions than is either to the randomized cube. We are now in the process of applying the SCF to a larger set of observed and simulated data cubes. Our ultimate aim is to use the SCF both on its own, as a descriptor of the spatial-kinetic properties of interstellar gas, and also as a tool for evaluating how well simulations resemble observations. Our expectation is that the SCF will be more discriminatory (less likely to produce a false match) than the data cube descriptors currently available.

  3. Time-dependent density functional theory (TD-DFT) coupled with reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yokogawa, D., E-mail: d.yokogawa@chem.nagoya-u.ac.jp; Institute of Transformative Bio-Molecules

    2016-09-07

    Theoretical approach to design bright bio-imaging molecules is one of the most progressing ones. However, because of the system size and computational accuracy, the number of theoretical studies is limited to our knowledge. To overcome the difficulties, we developed a new method based on reference interaction site model self-consistent field explicitly including spatial electron density distribution and time-dependent density functional theory. We applied it to the calculation of indole and 5-cyanoindole at ground and excited states in gas and solution phases. The changes in the optimized geometries were clearly explained with resonance structures and the Stokes shift was correctly reproduced.

  4. Assimilating MODIS-based albedo and snow cover fraction into the Common Land Model to improve snow depth simulation with direct insertion and deterministic ensemble Kalman filter methods

    NASA Astrophysics Data System (ADS)

    Xu, Jianhui; Shu, Hong

    2014-09-01

    This study assesses the analysis performance of assimilating the Moderate Resolution Imaging Spectroradiometer (MODIS)-based albedo and snow cover fraction (SCF) separately or jointly into the physically based Common Land Model (CoLM). A direct insertion method (DI) is proposed to assimilate the black and white-sky albedos into the CoLM. The MODIS-based albedo is calculated with the MODIS bidirectional reflectance distribution function (BRDF) model parameters product (MCD43B1) and the solar zenith angle as estimated in the CoLM for each time step. Meanwhile, the MODIS SCF (MOD10A1) is assimilated into the CoLM using the deterministic ensemble Kalman filter (DEnKF) method. A new DEnKF-albedo assimilation scheme for integrating the DI and DEnKF assimilation schemes is proposed. Our assimilation results are validated against in situ snow depth observations from November 2008 to March 2009 at five sites in the Altay region of China. The experimental results show that all three data assimilation schemes can improve snow depth simulations. But overall, the DEnKF-albedo assimilation shows the best analysis performance as it significantly reduces the bias and root-mean-square error (RMSE) during the snow accumulation and ablation periods at all sites except for the Fuyun site. The SCF assimilation via DEnKF produces better results than the albedo assimilation via DI, implying that the albedo assimilation that indirectly updates the snow depth state variable is less efficient than the direct SCF assimilation. For the Fuyun site, the DEnKF-albedo scheme tends to overestimate the snow depth accumulation with the maximum bias and RMSE values because of the large positive innovation (observation minus forecast).

  5. Approaching the basis set limit for DFT calculations using an environment-adapted minimal basis with perturbation theory: Formulation, proof of concept, and a pilot implementation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe

    2016-07-28

    Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set producesmore » <0.15 kcal/mol root-mean-square deviations for most of the tested TC datasets, and <0.1 kcal/mol for most of the NC datasets. The performance of density functionals near the basis set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.« less

  6. An Exact Separation of the Spin-Free and Spin-Dependent Terms of the Dirac-Coulomb-Breit Hamiltonian

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.

    1994-01-01

    The Dirac Hamiltonian is transformed by extracting the operator (sigma x p)/2mc from the small component of the wave function and applying it to the operators of the original Hamiltonian. The resultant operators contain products of Paull matrices that can be rearranged to give spin-free and spin-dependent operators. These operators are the ones encountered in the Breit-Pauli Hamiltonian, as well as some of higher order in alpha(sup 2). However, since the transformation of the original Dirac Hamiltonian is exact, the new Hamiltonian can be used in variational calculations, with or without the spin-dependent terms. The new small component functions have the same symmetry properties as the large component. Use of only the spin-free terms of the new Hamiltonian permits the same factorization over spin variables as in nonrelativistic theory, and therefore all the post-Self-Consistent Field (SCF) machinery of nonrelativistic calculations can be applied. However, the single-particle functions are two-component orbitals having a large and small component, and the SCF methods must be modified accordingly. Numerical examples are presented, and comparisons are made with the spin-free second-order Douglas-Kroll transformed Hamiltonian of Hess.

  7. Combined ab initio and density functional study on polaron to bipolaron transitions in oligophenyls and oligothiophenes

    NASA Astrophysics Data System (ADS)

    Irle, Stephan; Lischka, Hans

    1997-08-01

    Ab initio self-consistent-field (SCF), two-configuration SCF (TCSCF), and density functional theory (DFT) calculations on the charge-transfer complexes of doubly Li/Cl-doped oligothiophenes and oligo(p-phenyls) and on respective charged systems without counterions have been carried out in order to study polaron to bipolaron transitions. Oligomer chains up to octamers and the ring structures cyclo-dodecathiophene and cyclo-dodeca(p-phenyl) have been investigated. Special attention is paid to the open-shell biradical character of two isolated polaronic defects. It is found that the TCSCF and the spin-unrestricted DFT methods can be successfully applied. A bipolaron structure is obtained when the doping atoms are located on neighboring rings and when there is one undoped ring separating the two doped ones. If there are two or more undoped rings in between a two-polaron configuration (biradical) is found. The bipolaron system is calculated to be more stable than the two-polaron case when counterions are taken into account. The stabilities are reversed if the bare, doubly-charged systems are considered. A theoretical estimate for the barrier height of the polaron to bipolaron transition is given using model reaction coordinates.

  8. Workshop report on large-scale matrix diagonalization methods in chemistry theory institute

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bischof, C.H.; Shepard, R.L.; Huss-Lederman, S.

    The Large-Scale Matrix Diagonalization Methods in Chemistry theory institute brought together 41 computational chemists and numerical analysts. The goal was to understand the needs of the computational chemistry community in problems that utilize matrix diagonalization techniques. This was accomplished by reviewing the current state of the art and looking toward future directions in matrix diagonalization techniques. This institute occurred about 20 years after a related meeting of similar size. During those 20 years the Davidson method continued to dominate the problem of finding a few extremal eigenvalues for many computational chemistry problems. Work on non-diagonally dominant and non-Hermitian problems asmore » well as parallel computing has also brought new methods to bear. The changes and similarities in problems and methods over the past two decades offered an interesting viewpoint for the success in this area. One important area covered by the talks was overviews of the source and nature of the chemistry problems. The numerical analysts were uniformly grateful for the efforts to convey a better understanding of the problems and issues faced in computational chemistry. An important outcome was an understanding of the wide range of eigenproblems encountered in computational chemistry. The workshop covered problems involving self- consistent-field (SCF), configuration interaction (CI), intramolecular vibrational relaxation (IVR), and scattering problems. In atomic structure calculations using the Hartree-Fock method (SCF), the symmetric matrices can range from order hundreds to thousands. These matrices often include large clusters of eigenvalues which can be as much as 25% of the spectrum. However, if Cl methods are also used, the matrix size can be between 10{sup 4} and 10{sup 9} where only one or a few extremal eigenvalues and eigenvectors are needed. Working with very large matrices has lead to the development of« less

  9. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females.

    PubMed

    Whisner, Corrie M; Martin, Berdine R; Nakatsu, Cindy H; Story, Jon A; MacDonald-Clarke, Claire J; McCabe, Linda D; McCabe, George P; Weaver, Connie M

    2016-07-01

    Soluble corn fiber (SCF; 12 g fiber/d) is shown to increase calcium absorption efficiency, associated with shifts in the gut microbiota in adolescent males and females who participated in a controlled feeding study. We evaluated the dose response of 0, 10, and 20 g fiber/d delivered by PROMITOR SCF 85 (85% fiber) on calcium absorption, biochemical bone properties, and the fecal microbiome in free-living adolescents. Healthy adolescent females (n = 28; aged 11-14 y) randomly assigned into a 3-phase, double-blind, crossover study consumed SCF for 4 wk at each dose (0, 10, and 20 g fiber/d from SCF) alongside their habitual diet and were followed by 3-d clinical visits and 3-wk washout periods. Stable isotope ((44)Ca and (43)Ca) enrichment in pooled urine was measured by inductively coupled plasma mass spectrometry. Fecal microbial community composition was assessed by high-throughput sequencing (Illumina) of polymerase chain reaction-amplified 16S rRNA genes. Mixed model ANOVA and Friedman analysis were used to determine effects of SCF on calcium absorption and to compare mean microbial proportions, respectively. Calcium absorption increased significantly with 10 (13.3% ± 5.3%; P = 0.042) and 20 g fiber/d (12.9% ± 3.6%; P = 0.026) from SCF relative to control. Significant differences in fecal microbial community diversity were found after consuming SCF (operational taxonomic unit measures of 601.4 ± 83.5, 634.5 ± 83.8, and 649.6 ± 75.5 for 0, 10, and 20 g fiber/d, respectively; P < 0.05). Proportions of the genus Parabacteroides significantly increased with SCF dose (1.1% ± 0.8%, 2.1% ± 1.6%, and 3.0% ± 2.0% for 0, 10, and 20 g fiber/d from SCF, respectively; P < 0.05). Increases in calcium absorption positively correlated with increases in Clostridium (r = 0.44, P = 0.023) and unclassified Clostridiaceae (r = 0.40, P = 0.040). SCF, a nondigestible carbohydrate, increased calcium absorption in free-living adolescent females. Two groups of bacteria may be involved, one directly fermenting SCF and the second fermenting SCF metabolites further, thereby promoting increased calcium absorption. This trial was registered at clinicaltrials.gov as NCT01660503. © 2016 American Society for Nutrition.

  10. Combined effects of interleukin-7 and stem cell factor administration on lymphopoiesis after murine bone marrow transplantation.

    PubMed

    Chung, Brile; Min, Dullei; Joo, Lukas W; Krampf, Mark R; Huang, Jing; Yang, Yujun; Shashidhar, Sumana; Brown, Janice; Dudl, Eric P; Weinberg, Kenneth I

    2011-01-01

    The decreased ability of the thymus to generate T cells after bone marrow transplantation (BMT) is a clinically significant problem. Interleukin (IL)-7 and stem cell factor (SCF) induce proliferation, differentiation, and survival of thymocytes. Although previous studies have shown that administration of recombinant human IL-7 (rhIL-7) after murine and human BMT improves thymopoiesis and immune function, whether administration of SCF exerts similar effects is unclear. To evaluate independent or combinatorial effects of IL-7 and SCF in post-BMT thymopoiesis, bone marrow (BM)-derived mesenchymal stem cells transduced ex vivo with the rhIL-7 or murine SCF (mSCF) genes were cotransplanted with T cell-depleted BM cells into lethally irradiated mice. Although rhIL-7 and mSCF each improved immune reconstitution, the combination treatment had a significantly greater effect than either cytokine alone. Moreover, the combination treatment significantly increased donor-derived common lymphoid progenitors (CLPs) in BM, suggesting that transplanted CLPs expand more rapidly in response to IL-7 and SCF and may promote immune reconstitution. Our findings demonstrate that IL-7 and SCF might be therapeutically useful for enhancing de novo T cell development. Furthermore, combination therapy may allow the administration of lower doses of IL-7, thereby decreasing the likelihood of IL-7-mediated expansion of mature T cells. 2011. Published by Elsevier Inc.

  11. A numerical fragment basis approach to SCF calculations.

    NASA Astrophysics Data System (ADS)

    Hinde, Robert J.

    1997-11-01

    The counterpoise method is often used to correct for basis set superposition error in calculations of the electronic structure of bimolecular systems. One drawback of this approach is the need to specify a ``reference state'' for the system; for reactive systems, the choice of an unambiguous reference state may be difficult. An example is the reaction F^- + HCl arrow HF + Cl^-. Two obvious reference states for this reaction are F^- + HCl and HF + Cl^-; however, different counterpoise-corrected interaction energies are obtained using these two reference states. We outline a method for performing SCF calculations which employs numerical basis functions; this method attempts to eliminate basis set superposition errors in an a priori fashion. We test the proposed method on two one-dimensional, three-center systems and discuss the possibility of extending our approach to include electron correlation effects.

  12. Inhibition of human mast cell growth and differentiation by interferon gamma-1b.

    PubMed

    Kirshenbaum, A S; Worobec, A S; Davis, T A; Goff, J P; Semere, T; Metcalfe, D D

    1998-03-01

    In an effort to identify cytokines that inhibit human mast cell growth, we cultured HMC-1 cells and recombinant human stem cell factor (rhSCF)-dependent human bone marrow-derived mast cells (HBMCs) in the presence of interferon gamma (IFNgamma)-1b and interferon alpha (IFNalpha)-2b. HMC-1 cell numbers decreased in the presence of 1000 U/mL IFNgamma-1b but were unaffected by 1000 U/mL of IFNalpha-2b. HBMCs were then cultured for 0 to 7 days with 100 ng/mL rhSCF and 10 ng/mL recombinant human IL-3 (rhIL-3), followed by culture in rhSCF and administration of either 1000 U/mL IFNalpha-2b or 1000 U/mL IFNgamma-1b. HBMCs appearing in cultures with rhSCF alone or in combination with IFNalpha-2b were virtually identical in number through 8 weeks of culture. In cultures supplemented with IFNgamma-1b, HBMCs significantly decreased in number and incidence of granular metachromasia by 4 to 5 weeks (p<0.001). Similar results were obtained when human marrow was cultured from day 0 with rhSCF and IFNgamma-1b. Mature rhSCF-dependent HBMCs were also cultured at 5 weeks with rhSCF alone or in combination with IFNgamma-1b. Compared with cells cultured in rhSCF, mature 5-week HBMC cultures treated with rhSCF plus IFNgamma-1b revealed a decrease in mast cells, and those mast cells that remained had fewer toluidine blue- and tryptase-positive granules after 5 to 8 weeks. FACS analysis of rhSCF plus IFNgamma-1b-treated mature HBMCs revealed increased c-kit and Fc(epsilon)RI expression. Mast cell releasibility was not increased. IFNgamma-lb was thus able to suppress mast cell growth from CD34+ cells, suggesting that this agent should be considered as a candidate cytokine for the treatment of disorders of mast cell proliferation.

  13. Blended polymer materials extractable with supercritical carbon dioxide

    NASA Astrophysics Data System (ADS)

    Cai, Mei

    Supercritical carbon dioxide is drawing more and more attention because of its unique solvent properties along with being environmentally friendly. Historically most of the commercial interests of supercritical carbon dioxide extraction are in the food industry, pharmaceutical industry, environmental preservation and polymer processing. Recently attention has shifted from the extraction of relatively simple molecules to more complex systems with a much broader range of physical and chemical transformations. However the available data show that a lot of commercially valuable substances are not soluble in supercritical carbon dioxide due to their polar structures. This fact really limits the application of SCF extraction technology to much broader industrial applications. Therefore, the study of a polymer's solubility in a given supercritical fluid and its thermodynamic behavior becomes one of the most important research topics. The major objective of this dissertation is to develop a convenient and economic way to enhance the polymer's solubility in supercritical carbon dioxide. Further objective is to innovate a new process of making metal casting parts with blended polymer materials developed in this study. The key technique developed in this study to change a polymer's solubility in SCF CO2 is to thermally blend a commercially available and CO2 non-soluble polymer material with a low molecular weight CO2 soluble organic chemical that acts as a co-solute. The mixture yields a plastic material that can be completely solubilized in SCF CO2 over a range of temperatures and pressures. It also exhibits a variety of physical properties (strength, hardness, viscosity, etc.) depending on variations in the mixture ratio. The three organic chemicals investigated as CO2 soluble materials are diphenyl carbonate, naphthalene, and benzophenone. Two commercial polymers, polyethylene glycol and polystyrene, have been investigated as CO2 non-soluble materials. The chemical, physical, thermal, and phase behavior of the blended polymers studied in this dissertation includes solubility in SCF CO2, the melt viscosity, the melting temperature depression, and phase equilibrium under SCF conditions. Several hypotheses are investigated to determine which mechanism plays the major role in the extraction. Finally a novel metal casting process is discussed with the materials developed in this study. This new method utilizes an adhesive or binder film composition for the purpose of building up a casting pattern of resin-bonded aggregate particles. The pattern is then encased in a conventional rigid shell mold that is not susceptible to degradation by SCF CO2. The pattern is then disintegrated within an unaffected mold by exposure to SCF CO 2. This is an efficient and low cost method of making patterns and molds, especially for the casting of a relatively low number of parts such as in prototype evaluations.

  14. Generalization of the Hartree-Fock approach to collision processes

    NASA Astrophysics Data System (ADS)

    Hahn, Yukap

    1997-06-01

    The conventional Hartree and Hartree-Fock approaches for bound states are generalized to treat atomic collision processes. All the single-particle orbitals, for both bound and scattering states, are determined simultaneously by requiring full self-consistency. This generalization is achieved by introducing two Ansäauttze: (a) the weak asymptotic boundary condition, which maintains the correct scattering energy and target orbitals with correct number of nodes, and (b) square integrable amputated scattering functions to generate self-consistent field (SCF) potentials for the target orbitals. The exact initial target and final-state asymptotic wave functions are not required and thus need not be specified a priori, as they are determined simultaneously by the SCF iterations. To check the asymptotic behavior of the solution, the theory is applied to elastic electron-hydrogen scattering at low energies. The solution is found to be stable and the weak asymptotic condition is sufficient to produce the correct scattering amplitudes. The SCF potential for the target orbital shows the strong penetration by the projectile electron during the collision, but the exchange term tends to restore the original form. Potential applicabilities of this extension are discussed, including the treatment of ionization and shake-off processes.

  15. PP2A regulates SCF-induced cardiac stem cell migration through interaction with p38 MAPK.

    PubMed

    Wang, Ying; Xia, Yanli; Kuang, Dong; Duan, Yaqi; Wang, Guoping

    2017-12-15

    Previous studies have shown that stem cell factor (SCF) induces the migration of cardiac stem cells (CSCs) and helps to repair myocardial infarctions. Earlier studies on the migration mechanism only focused on the activation of kinases; here, we aimed to explore the functional role of protein phosphatase 2A (PP2A) in SCF-induced CSC migration. CSCs were treated with SCF, PP2A enzymatic activity was measured, the phosphorylation levels of PP2A, p38 MAPK and cofilin were evaluated using western blot. Transwell assay was used to determine the migratory ability of CSCs. In vitro, SCF induced the phosphorylation of p38 MAPK and cofilin, leading to the migration of CSCs. Cofilin acted as a downstream signal of p38 MAPK. PP2A was involved in this process. Further studies revealed that PP2A was inactivated via phosphorylation at Tyr307 by SCF and the inactivation/phosphorylation was mediated by activated p38 MAPK, as p38 MAPK inhibitor SB203580 or siRNA prevented SCF-induced inactivation and phosphorylation of PP2A. When CSCs were pretreated with PP2A inhibitor (okadaic acid, OA), SCF-induced CSC migration and the downstream signals were enhanced, and the enhancement was reversed when p38 MAPK was blocked. Additionally, co-immunoprecipitation showed a direct interaction of PP2A with p38 MAPK. Our results indicated that PP2A regulated the SCF-induced activation of p38 MAPK/cofilin signaling pathway and subsequent migration of CSCs by interaction with p38 MAPK. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Resveratrol Improved the Progression of Chronic Prostatitis via the Downregulation of c-kit/SCF by Activating Sirt1.

    PubMed

    He, Yi; Zeng, Huizhi; Yu, Yang; Zhang, Jiashu; Zeng, Xiaona; Gong, Fengtao; Duan, Xingping; Liu, Qi; Yang, Bo

    2017-07-19

    The regulation mechanism of inflammation inducing prostate carcinogenesis remains largely unknown. Therefore, we investigated the role of the c-kit/SCF pathway, which has been associated with the control of prostate carcinogenesis, in chronic prostatitis (CP) rats and evaluated the anti-prostatitis effect of resveratrol. We performed hemolysin and eosin staining to evaluate the histopathological changes in prostates. Multiple approaches evaluated the expression levels of c-kit, stem cell factor (SCF), Sirt1, and carcinogenesis-associated proteins. The CP group exhibited severe diffuse chronic inflammation. Meanwhile, the prostate cells appeared atypia; the activity of c-kit/SCF was upregulated, and carcinogenesis-associated proteins are dysregulated significantly in CP rats. Resveratrol treatment significantly improved these factors by Sirt1 activation. In summary, CP could further cause prostate carcinogenesis, which may be associated with activated c-kit/SCF signaling. Resveratrol treatment could improve the progression of CP via the downregulation of c-kit/SCF by activating Sirt1.

  17. Multifunction Sr, Co and F co-doped microporous coating on titanium of antibacterial, angiogenic and osteogenic activities

    PubMed Central

    Zhou, Jianhong; Zhao, Lingzhou

    2016-01-01

    Advanced multifunction titanium (Ti) based bone implant with antibacterial, angiogenic and osteogenic activities is stringently needed in clinic, which may be accomplished via incorporation of proper inorganic bioactive elements. In this work, microporous TiO2/calcium-phosphate coating on Ti doped with strontium, cobalt and fluorine (SCF-TiCP) was developed, which had a hierarchical micro/nano-structure with a microporous structure evenly covered with nano-grains. SCF-TiCP greatly inhibited the colonization and growth of both gram-positive and gram-negative bacteria. No cytotoxicity appeared for SCF-TiCP. Furthermore, SCF-TiCP stimulated the expression of key angiogenic factors in rat bone marrow stem cells (MSCs) and dramatically enhanced MSC osteogenic differentiation. The in vivo animal test displayed that SCF-TiCP induced more new bone and tighter implant/bone bonding. In conclusion, multifunction SCF-TiCP of antibacterial, angiogenic and osteogenic activities is a promising orthopedic and dental Ti implant coating for improved clinical performance. PMID:27353337

  18. Bone marrow adipocytes promote the regeneration of stem cells and hematopoiesis by secreting SCF

    PubMed Central

    Zhou, Bo O.; Yu, Hua; Yue, Rui; Zhao, Zhiyu; Rios, Jonathan J.; Naveiras, Olaia; Morrison, Sean J.

    2017-01-01

    Endothelial cells and Leptin Receptor+ (LepR+) stromal cells are critical sources of haematopoietic stem cell (HSC) niche factors, including Stem Cell Factor (SCF), in bone marrow. After irradiation or chemotherapy, these cells are depleted while adipocytes become abundant. We discovered that bone marrow adipocytes synthesize SCF. They arise from Adipoq-Cre/ER+ progenitors, which represent ~5% of LepR+ cells, and proliferate after irradiation. Scf deletion using Adipoq-Cre/ER inhibited hematopoietic regeneration after irradiation or 5-fluorouracil treatment, depleting HSCs and reducing mouse survival. Scf from LepR+ cells, but not endothelial, hematopoietic, or osteoblastic cells, also promoted regeneration. In non-irradiated mice, Scf deletion using Adipoq-Cre/ER did not affect HSC frequency in long bones, which have few adipocytes, but depleted HSCs in tail vertebrae, which have abundant adipocytes. A-ZIP/F1 ‘fatless” mice exhibited delayed hematopoietic regeneration in long bones but not in tail vertebrae, where adipocytes inhibited vascularization. Adipocytes are a niche component that promotes hematopoietic regeneration. PMID:28714970

  19. Natural chemical shielding analysis of nuclear magnetic resonance shielding tensors from gauge-including atomic orbital calculations

    NASA Astrophysics Data System (ADS)

    Bohmann, Jonathan A.; Weinhold, Frank; Farrar, Thomas C.

    1997-07-01

    Nuclear magnetic shielding tensors computed by the gauge including atomic orbital (GIAO) method in the Hartree-Fock self-consistent-field (HF-SCF) framework are partitioned into magnetic contributions from chemical bonds and lone pairs by means of natural chemical shielding (NCS) analysis, an extension of natural bond orbital (NBO) analysis. NCS analysis complements the description provided by alternative localized orbital methods by directly calculating chemical shieldings due to delocalized features in the electronic structure, such as bond conjugation and hyperconjugation. Examples of NCS tensor decomposition are reported for CH4, CO, and H2CO, for which a graphical mnemonic due to Cornwell is used to illustrate the effect of hyperconjugative delocalization on the carbon shielding.

  20. Immediate estimation of correlation energy for molecular systems from the partial charges on atoms in the molecule

    NASA Astrophysics Data System (ADS)

    Kristyán, Sándor

    1997-11-01

    In the author's previous work (Chem. Phys. Lett. 247 (1995) 101 and Chem. Phys. Lett. 256 (1996) 229) a simple quasi-linear relationship was introduced between the number of electrons, N, participating in any molecular system and the correlation energy: -0.035 ( N - 1) > Ecorr[hartree] > - 0.045( N -1). This relationship was developed to estimate more accurately correlation energy immediately in ab initio calculations by using the partial charges of atoms in the molecule, easily obtained after Hartree-Fock self-consistent field (HF-SCF) calculations. The method is compared to the well-known B3LYP, MP2, CCSD and G2M methods. Correlation energy estimations for negatively (-1) charged atomic ions are also reported.

  1. Integral processing in beyond-Hartree-Fock calculations

    NASA Technical Reports Server (NTRS)

    Taylor, P. R.

    1986-01-01

    The increasing rate at which improvements in processing capacity outstrip improvements in input/output performance of large computers has led to recent attempts to bypass generation of a disk-based integral file. The direct self-consistent field (SCF) method of Almlof and co-workers represents a very successful implementation of this approach. This paper is concerned with the extension of this general approach to configuration interaction (CI) and multiconfiguration-self-consistent field (MCSCF) calculations. After a discussion of the particular types of molecular orbital (MO) integrals for which -- at least for most current generation machines -- disk-based storage seems unavoidable, it is shown how all the necessary integrals can be obtained as matrix elements of Coulomb and exchange operators that can be calculated using a direct approach. Computational implementations of such a scheme are discussed.

  2. 39 CFR 121.4 - Package Services.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Center Facility (SCF) turnaround Package Services mail accepted at the origin SCF before the day zero... origin before the day-zero Critical Entry Time is 3 days, for each remaining (non-intra-SCF) 3-digit ZIP... intra-Network Distribution Center (NDC) Package Services mail accepted at origin before the day-zero...

  3. 39 CFR 121.4 - Package Services.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Center Facility (SCF) turnaround Package Services mail accepted at the origin SCF before the day zero... origin before the day-zero Critical Entry Time is 3 days, for each remaining (non-intra-SCF) 3-digit ZIP... intra-Network Distribution Center (NDC) Package Services mail accepted at origin before the day-zero...

  4. Neuroprotection by stem cell factor in rat cortical neurons involves AKT and NFkappaB.

    PubMed

    Dhandapani, Krishnan M; Wade, F Marlene; Wakade, Chandramohan; Mahesh, Virendra B; Brann, Darrell W

    2005-10-01

    Stem cell factor (SCF) is a highly expressed cytokine in the central nervous system. In the present study, we demonstrate a neuroprotective role for SCF and its tyrosine kinase receptor, c-kit, against camptothecin-induced apoptosis and glutamate excitotoxicity in rat cortical neurons. This protection was blocked by pharmacological or molecular inhibition of either the MEK/ERK or PI3K/Akt signaling pathways. The importance of these pathways was further confirmed by the activation of both ERK, in a MEK-dependent manner, and Akt, via PI3K. Activation of Akt increased the binding of the p50 and p65 subunits of NFkappaB, which was also important for neuroprotection. Akt inhibition prevented NFkappaB binding, suggesting a role for Akt in SCF-induced NFkappaB. Pharmacological inhibition of NFkappaB or dominant negative IkappaB also prevented neuroprotection by SCF. SCF up-regulated the anti-apoptotic genes, bcl-2 and bcl-xL in an NFkappaB-dependent manner. Together, these findings demonstrate a neuroprotective role for SCF in cortical neurons, an effect that was mediated by Akt and ERK, as well as NFkappaB-mediated gene transcription. SCF represents a novel therapeutic target in the treatment of neurodegenerative disease.

  5. New insights into the negative thermal expansion: Direct experimental evidence for the “guitar-string” effect in cubic ScF 3

    DOE PAGES

    Hu, Lei; Chen, Jun; Sanson, Andrea; ...

    2016-06-23

    The understanding of the negative thermal expansion (NTE) mechanism remains challenging but critical for the development of NTE materials. This study sheds light on NTE of ScF 3, one of the most outstanding materials with NTE. The local dynamics of ScF 3 has been investigated by a combined analysis of synchrotron-based X-ray total scattering, ex-tended X-ray absorption fine structure and neutron powder diffraction. Very interestingly, we observe that i) the Sc-F nearest-neighbor distance strongly expands with increasing temperature while the Sc-Sc next-nearest-neighbor distance contracts, ii) the thermal ellipsoids of relative vibrations be-tween Sc-F nearest-neighbors are highly elongated in the directionmore » perpendicular to the Sc-F bond, indicating that the Sc-F bond is much softer to bend than to stretch, and iii) there is mainly dynamically transverse motion of fluorine atoms, rather than static shifts. Here, these results are the direct experimental evidence for the NTE mechanism, in which the rigid unit is not necessary for the occurrence of NTE, and the key role is played by the transverse thermal vibrations of fluorine atoms through the “guitar-string” effect.« less

  6. Tumor necrosis factor-alpha inhibits stem cell factor-induced proliferation of human bone marrow progenitor cells in vitro. Role of p55 and p75 tumor necrosis factor receptors.

    PubMed Central

    Rusten, L S; Smeland, E B; Jacobsen, F W; Lien, E; Lesslauer, W; Loetscher, H; Dubois, C M; Jacobsen, S E

    1994-01-01

    Stem cell factor (SCF), a key regulator of hematopoiesis, potently synergizes with a number of hematopoietic growth factors. However, little is known about growth factors capable of inhibiting the actions of SCF. TNF-alpha has been shown to act as a bidirectional regulator of myeloid cell proliferation and differentiation. This study was designed to examine interactions between TNF-alpha and SCF. Here, we demonstrate that TNF-alpha potently and directly inhibits SCF-stimulated proliferation of CD34+ hematopoietic progenitor cells. Furthermore, TNF-alpha blocked all colony formation stimulated by SCF in combination with granulocyte colony-stimulating factor (CSF) or CSF-1. The synergistic effect of SCF observed in combination with GM-CSF or IL-3 was also inhibited by TNF-alpha, resulting in colony numbers similar to those obtained in the absence of SCF. These effects of TNF-alpha were mediated through the p55 TNF receptor, whereas little or no inhibition was signaled through the p75 TNF receptor. Finally, TNF-alpha downregulated c-kit cell-surface expression on CD34+ bone marrow cells, and this was predominantly a p55 TNF receptor-mediated event as well. Images PMID:7518828

  7. Induction of mast cell proliferation, maturation, and heparin synthesis by the rat c-kit ligand, stem cell factor

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tsai, M.; Takeishi, Takashi; Geissler, E.N.

    1991-07-15

    The authors investigated the effects of a newly recognized multifunctional growth factor, the c-kit ligand stem cell factor (SCF), on mouse mast cell proliferation and phenotype. Recombinant rat SCF{sup 164} (rrSCF{sup 164}) induced the development of large numbers of dermal mast cells in normal mice in vivo. Many of these mast cells had features of connective tissue-type mast cells (CTMC), in that they were reactive both with the heparin-binding fluorescent dye berberine sulfate and with safranin. In vitro, rrSCF{sup 164} induced the proliferation of cloned interleukin 3 (IL-3)-dependent mouse mast cells and primary populations of IL-3-dependent, bone marrow-derived cultured mastmore » cells (BMCMC), which represent immature mast cells, and purified peritoneal mast cells, which represent a type of mature CTMC> BMCMC maintained in rrSCF{sup 164} not only proliferated but also matured. These findings identify SCF as a single cytokine that can induce immature, IL-3-dependent mast cells to mature and to acquire multiple characteristics of CTMC. These findings also directly demonstrate that SCF can regulate the development of a cellular lineage expressing c-kit through effects on both proliferation and maturation.« less

  8. Turtle Bayou 1936-1983: case history of a major gas field in south Louisiana

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cronquist, C.

    1984-11-01

    Turtle Bayou field, located in the middle Miocene trend in south Louisiana, is nearing the end of a productive life spanning more than 30 years. Discovered by Shell Oil Co. in 1949 after unsuccessful attempts by two other companies, the field is a typical, low-relief, moderately faulted U.S. Gulf Coast structure, probably associated with deep salt movement. The productive interval includes 22 separate gas-bearing sands in a regressive sequence of sands and shales from approximately 6,500 to 12,000 ft (1980 to 3660 m). Now estimated to have contained about 1.2 trillion scf (34 X 10/sup 9/ std m/sup 3/) ofmore » gas in place, cumulative production through 1982 was 702 billion scf (20 X 10/sup 9/ std m/sup 3/). Cumulative condensate/gas ration (CGR) has been 20 bbl/MMcf (110 X 10/sup -6/ m/sup 3//m/sup 3/. Recovery mechanisms in individual reservoirs include strong bottomwater drive, partial edgewater drive, and pressure depletion. Recovery efficiencies in major reservoirs range form 40 to 83% of original gas in place (OGIP). On decline since 1973, it is anticipated the field will be essentially depleted in the next 5 years.« less

  9. A new fractional snow-covered area parameterization for the Community Land Model and its effect on the surface energy balance

    NASA Astrophysics Data System (ADS)

    Swenson, S. C.; Lawrence, D. M.

    2011-11-01

    One function of the Community Land Model (CLM4) is the determination of surface albedo in the Community Earth System Model (CESM1). Because the typical spatial scales of CESM1 simulations are large compared to the scales of variability of surface properties such as snow cover and vegetation, unresolved surface heterogeneity is parameterized. Fractional snow-covered area, or snow-covered fraction (SCF), within a CLM4 grid cell is parameterized as a function of grid cell mean snow depth and snow density. This parameterization is based on an analysis of monthly averaged SCF and snow depth that showed a seasonal shift in the snow depth-SCF relationship. In this paper, we show that this shift is an artifact of the monthly sampling and that the current parameterization does not reflect the relationship observed between snow depth and SCF at the daily time scale. We demonstrate that the snow depth analysis used in the original study exhibits a bias toward early melt when compared to satellite-observed SCF. This bias results in a tendency to overestimate SCF as a function of snow depth. Using a more consistent, higher spatial and temporal resolution snow depth analysis reveals a clear hysteresis between snow accumulation and melt seasons. Here, a new SCF parameterization based on snow water equivalent is developed to capture the observed seasonal snow depth-SCF evolution. The effects of the new SCF parameterization on the surface energy budget are described. In CLM4, surface energy fluxes are calculated assuming a uniform snow cover. To more realistically simulate environments having patchy snow cover, we modify the model by computing the surface fluxes separately for snow-free and snow-covered fractions of a grid cell. In this configuration, the form of the parameterized snow depth-SCF relationship is shown to greatly affect the surface energy budget. The direct exposure of the snow-free surfaces to the atmosphere leads to greater heat loss from the ground during autumn and greater heat gain during spring. The net effect is to reduce annual mean soil temperatures by up to 3°C in snow-affected regions.

  10. A new fractional snow-covered area parameterization for the Community Land Model and its effect on the surface energy balance

    NASA Astrophysics Data System (ADS)

    Swenson, S. C.; Lawrence, D. M.

    2012-11-01

    One function of the Community Land Model (CLM4) is the determination of surface albedo in the Community Earth System Model (CESM1). Because the typical spatial scales of CESM1 simulations are large compared to the scales of variability of surface properties such as snow cover and vegetation, unresolved surface heterogeneity is parameterized. Fractional snow-covered area, or snow-covered fraction (SCF), within a CLM4 grid cell is parameterized as a function of grid cell mean snow depth and snow density. This parameterization is based on an analysis of monthly averaged SCF and snow depth that showed a seasonal shift in the snow depth-SCF relationship. In this paper, we show that this shift is an artifact of the monthly sampling and that the current parameterization does not reflect the relationship observed between snow depth and SCF at the daily time scale. We demonstrate that the snow depth analysis used in the original study exhibits a bias toward early melt when compared to satellite-observed SCF. This bias results in a tendency to overestimate SCF as a function of snow depth. Using a more consistent, higher spatial and temporal resolution snow depth analysis reveals a clear hysteresis between snow accumulation and melt seasons. Here, a new SCF parameterization based on snow water equivalent is developed to capture the observed seasonal snow depth-SCF evolution. The effects of the new SCF parameterization on the surface energy budget are described. In CLM4, surface energy fluxes are calculated assuming a uniform snow cover. To more realistically simulate environments having patchy snow cover, we modify the model by computing the surface fluxes separately for snow-free and snow-covered fractions of a grid cell. In this configuration, the form of the parameterized snow depth-SCF relationship is shown to greatly affect the surface energy budget. The direct exposure of the snow-free surfaces to the atmosphere leads to greater heat loss from the ground during autumn and greater heat gain during spring. The net effect is to reduce annual mean soil temperatures by up to 3°C in snow-affected regions.

  11. Bone marrow adipocytes promote the regeneration of stem cells and haematopoiesis by secreting SCF.

    PubMed

    Zhou, Bo O; Yu, Hua; Yue, Rui; Zhao, Zhiyu; Rios, Jonathan J; Naveiras, Olaia; Morrison, Sean J

    2017-08-01

    Endothelial cells and leptin receptor + (LepR + ) stromal cells are critical sources of haematopoietic stem cell (HSC) niche factors, including stem cell factor (SCF), in bone marrow. After irradiation or chemotherapy, these cells are depleted while adipocytes become abundant. We discovered that bone marrow adipocytes synthesize SCF. They arise from Adipoq-Cre/ER + progenitors, which represent ∼5% of LepR + cells, and proliferate after irradiation. Scf deletion using Adipoq-Cre/ER inhibited haematopoietic regeneration after irradiation or 5-fluorouracil treatment, depleting HSCs and reducing mouse survival. Scf from LepR + cells, but not endothelial, haematopoietic or osteoblastic cells, also promoted regeneration. In non-irradiated mice, Scf deletion using Adipoq-Cre/ER did not affect HSC frequency in long bones, which have few adipocytes, but depleted HSCs in tail vertebrae, which have abundant adipocytes. A-ZIP/F1 'fatless' mice exhibited delayed haematopoietic regeneration in long bones but not in tail vertebrae, where adipocytes inhibited vascularization. Adipocytes are a niche component that promotes haematopoietic regeneration.

  12. Effects of dietary fibers on weight gain, carbohydrate metabolism, and gastric ghrelin gene expression in mice fed a high-fat diet.

    PubMed

    Wang, Zhong Q; Zuberi, Aamir R; Zhang, Xian H; Macgowan, Jacalyn; Qin, Jianhua; Ye, Xin; Son, Leslie; Wu, Qinglin; Lian, Kun; Cefalu, William T

    2007-12-01

    Diets that are high in dietary fiber are reported to have substantial health benefits. We sought to compare the metabolic effects of 3 types of dietary fibers -- sugarcane fiber (SCF), psyllium (PSY), and cellulose (CEL) -- on body weight, carbohydrate metabolism, and stomach ghrelin gene expression in a high-fat diet-fed mouse model. Thirty-six male mice (C57BL/6) were randomly divided into 4 groups that consumed high-fat diet alone (HFD) or high-fat diet containing 10% SCF, PSY, and CEL, respectively. After baseline measurements were assessed for body weight, plasma insulin, glucose, leptin, and glucagon-like peptide 1 (GLP-1), animals were treated for 12 weeks. Parameters were reevaluated at the end of study. Whereas there was no difference at the baseline, body weight gains in the PSY and SCF groups were significantly lower than in the CEL group at the end of study. No difference in body weight was observed between the PSY and SCF animals. Body composition analysis demonstrated that fat mass in the SCF group was considerably lower than in the CEL and HFD groups. In addition, fasting plasma glucose and insulin and areas under the curve of intraperitoneal glucose tolerance test were also significantly lower in the SCF and PSY groups than in the CEL and HFD groups. Moreover, fasting plasma concentrations of leptin were significantly lower and GLP-1 level was 2-fold higher in the SCF and PSY mice than in the HFD and CEL mice. Ghrelin messenger RNA levels of stomach in the SCF group were significantly lower than in the CEL and HFD groups as well. These results suggest differences in response to dietary fiber intake in this animal model because high-fat diets incorporating dietary fibers such as SCF and PSY appeared to attenuate weight gain, enhance insulin sensitivity, and modulate leptin and GLP-1 secretion and gastric ghrelin gene expression.

  13. Effects of Dietary Fibers on Weight Gain, Carbohydrate Metabolism and Gastric Ghrelin Gene Expression in High Fat Diet Fed Mice

    PubMed Central

    Wang, Zhong Q.; Zuberi, Aamir; Zhang, Xian H.; Macgowan, Jacalyn; Qin, Jianhua; Ye, Xin; Son, Leslie; Wu, Qinglin; Lian, Kun; Cefalu, William T.

    2009-01-01

    Diets that are high in dietary fiber are reported to have substantial health benefits. We sought to compare the metabolic effects for three types of dietary fibers, i.e. sugar cane fiber (SCF), psyllium (PSY) and cellulose (CEL) on body weight, carbohydrate metabolism and stomach ghrelin gene expression in a high-fat diet fed mouse model. Thirty-six male mice (C57BL/6) were randomly divided into four groups that consumed high fat-diets or high fat diet containing 10% SCF, PSY, and CEL respectively. After baseline measurements were assessed for body weight, plasma insulin, glucose, leptin and glucagon-like peptide-1 (GLP-1), animals were treated for 12 weeks. Parameters were re-evaluated at end of study. Whereas there was no difference at the baseline, body weight gains in the PSY and SCF groups were significantly lower than in CEL group at end of study, No difference in body weight was observed between the PSY and SCF animals. Body composition analysis demonstrated that fat mass in the SCF group was considerably lower than in the CEL and HFD groups. In addition, fasting plasma glucose and insulin and areas under curve of IPGTT were also significantly lower in the SCF and PSY groups than in the CEL and HFD groups. Moreover, fasting plasma concentrations of leptin were significantly lower and GLP-1 level was two-fold higher in the SCF and PSY mice than in the HFD and CEL mice. Ghrelin mRNA levels of stomach in SCF groups were significantly lower than in CEL and HFD groups as well. These results suggest differences in response to dietary fiber intake in this animal model as high fat diets incorporating dietary fibers such as SCF and PSY appeared to attenuate weight gain, enhance insulin sensitivity, and modulate leptin and GLP-1 secretion and gastric ghrelin gene expression. PMID:17998014

  14. ADM guidance-Ceramics: Fracture toughness testing and method selection.

    PubMed

    Cesar, Paulo Francisco; Della Bona, Alvaro; Scherrer, Susanne S; Tholey, Michael; van Noort, Richard; Vichi, Alessandro; Kelly, Robert; Lohbauer, Ulrich

    2017-06-01

    The objective is within the scope of the Academy of Dental Materials Guidance Project, which is to provide dental materials researchers with a critical analysis of fracture toughness (FT) tests such that the assessment of the FT of dental ceramics is conducted in a reliable, repeatable and reproducible way. Fracture mechanics theory and FT methodologies were critically reviewed to introduce basic fracture principles and determine the main advantages and disadvantages of existing FT methods from the standpoint of the dental researcher. The recommended methods for FT determination of dental ceramics were the Single Edge "V" Notch Beam (SEVNB), Single Edge Precracked Beam (SEPB), Chevron Notch Beam (CNB), and Surface Crack in Flexure (SCF). SEVNB's main advantage is the ease of producing the notch via a cutting disk, SEPB allows for production of an atomically sharp crack generated by a specific precracking device, CNB is technically difficult, but based on solid fracture mechanics solutions, and SCF involves fracture from a clinically sized precrack. The IF test should be avoided due to heavy criticism that has arisen in the engineering field regarding the empirical nature of the calculations used for FT determination. Dental researchers interested in FT measurement of dental ceramics should start with a broad review of fracture mechanics theory to understand the underlying principles involved in fast fracture of ceramics. The choice of FT methodology should be based on the pros and cons of each test, as described in this literature review. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

  15. On the photoisomerization of 5-hydroxytropolone: An ab initio and nuclear wave function study

    NASA Astrophysics Data System (ADS)

    Paz, Juan J.; Moreno, Miquel; Lluch, José M.

    1997-10-01

    In this paper we perform ab initio calculations for the stable conformations and the transition states for the isomerization processes in 5-hydroxytropolone in both the ground (S0) and first excited (S1) singlet electronic states. The Hartree-Fock self-consistent field (SCF) level and a complete active space SCF (CASSCF) level for S0 are considered, whereas the configuration interaction all single excitation method (CIS) and the CASSCF levels are used to deal with the S1 state. Energies are reevaluated at all levels through perturbation theory up to second order: Møller-Plesset for the Hartree-Fock and CIS methods, and the CASPT2 method for CAS results. The ab initio results are then used to perform different monodimensional fits to the potential energy surfaces in order to analyze the wave functions for the nuclear motions in both electronic states. Our best results predict that for the S0 state two stable conformers, syn and anti, can exist in thermal equilibrium. In accordance with experimental expectations the syn isomer is the most stable. As for the S1 state, and again in accord with experimental spectroscopical data, the order of stability reverses, the anti being the most stable. A more interesting result is that analysis of the nuclear wave functions shows an important syn-anti mixing in the S1 state that does not appear in S0. This result explains the appearance of syn-anti and anti-syn crossover transitions observed in the electronic spectra of 5-hydroxytropolone so that syn-anti reaction may take place through photoisomerization.

  16. A Theoretical Study of the Conformational Landscape of Serotonin

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mourik, Van Tonja; Emson, Laura E.

    2002-10-25

    The conformational landscape of neutral serotonin has been investigated by several theoretical methods. The potential energy surface was scanned by systematically varying the three dihedral angles that determine the conformation of the alkyl side chain. In addition, the two possible conformations of the phenol hydroxyl group (anti and syn with respect to the indole NH) were considered. The OH-anti stationary points located with SCF/6-31G* have been re-optimized with B3LYP/6-31+G*, which resulted in twelve true minima. Eleven of these have a corresponding OH-syn conformer that is 1-4 kJ/mol higher in energy. IR vibrational spectra of all twenty-three serotonin conformers, computed atmore » the B3LYP/6-31+G* level f theory, are presented. The initial scan of the serotonin potential energy surface has been repeated with several computationally cheaper methods, to assess their reliability for locating the correct serotonin conformers. It is found that the semi-empirical methods AM1 and PM3 do no t yield sufficiently accurate results, due to their inability to account for subtle intramolecular interactions within the serotonin molecule. On the other hand, SCF in combination with the 3-21G* basis set is ascertained to be a good alternative to SCF/6-31G* for performing the initial scan of the potential energy surface of flexible molecules.« less

  17. Pharmacologic induction of epidermal melanin and protection against sunburn in a humanized mouse model.

    PubMed

    Amaro-Ortiz, Alexandra; Vanover, Jillian C; Scott, Timothy L; D'Orazio, John A

    2013-09-07

    Fairness of skin, UV sensitivity and skin cancer risk all correlate with the physiologic function of the melanocortin 1 receptor, a Gs-coupled signaling protein found on the surface of melanocytes. Mc1r stimulates adenylyl cyclase and cAMP production which, in turn, up-regulates melanocytic production of melanin in the skin. In order to study the mechanisms by which Mc1r signaling protects the skin against UV injury, this study relies on a mouse model with "humanized skin" based on epidermal expression of stem cell factor (Scf). K14-Scf transgenic mice retain melanocytes in the epidermis and therefore have the ability to deposit melanin in the epidermis. In this animal model, wild type Mc1r status results in robust deposition of black eumelanin pigment and a UV-protected phenotype. In contrast, K14-Scf animals with defective Mc1r signaling ability exhibit a red/blonde pigmentation, very little eumelanin in the skin and a UV-sensitive phenotype. Reasoning that eumelanin deposition might be enhanced by topical agents that mimic Mc1r signaling, we found that direct application of forskolin extract to the skin of Mc1r-defective fair-skinned mice resulted in robust eumelanin induction and UV protection (1). Here we describe the method for preparing and applying a forskolin-containing natural root extract to K14-Scf fair-skinned mice and report a method for measuring UV sensitivity by determining minimal erythematous dose (MED). Using this animal model, it is possible to study how epidermal cAMP induction and melanization of the skin affect physiologic responses to UV exposure.

  18. Comparing the effects of nano-sized sugarcane fiber with cellulose and psyllium on hepatic cellular signaling in mice

    PubMed Central

    Wang, Zhong Q; Yu, Yongmei; Zhang, Xian H; Floyd, Z Elizabeth; Boudreau, Anik; Lian, Kun; Cefalu, William T

    2012-01-01

    Aim To compare the effects of dietary fibers on hepatic cellular signaling in mice. Methods Mice were randomly divided into four groups (n = 9/group): high-fat diet (HFD) control, cellulose, psyllium, and sugarcane fiber (SCF) groups. All mice were fed a HFD with or without 10% dietary fiber (w/w) for 12 weeks. Body weight, food intake, fasting glucose, and fasting insulin levels were measured. At the end of the study, hepatic fibroblast growth factor (FGF) 21, AMP-activated protein kinase (AMPK) and insulin signaling protein content were determined. Results Hepatic FGF21 content was significantly lowered, but βKlotho, fibroblast growth factor receptor 1, fibroblast growth factor receptor 3, and peroxisome proliferator-activated receptor alpha proteins were significantly increased in the SCF group compared with those in the HFD group (P < 0.01). SCF supplementation also significantly enhanced insulin and AMPK signaling, as well as decreased hepatic triglyceride and cholesterol in comparison with the HFD mice. The study has shown that dietary fiber, especially SCF, significantly attenuates lipid accumulation in the liver by enhancing hepatic FGF21, insulin, and AMPK signaling in mice fed a HFD. Conclusion This study suggests that the modulation of gastrointestinal factors by dietary fibers may play a key role in both enhancing hepatic multiple cellular signaling and reducing lipid accumulation. PMID:22787396

  19. SCF-Xα-SW electron densities with the overlapping sphere approximation

    NASA Astrophysics Data System (ADS)

    McMaster, Blair N.; Smith, Vedene H., Jr.; Salahub, Dennis R.

    Self consistent field-Xα-scattered wave (SCF-Xα-SW) calculations have been performed for a series of eight first and second row homonuclear diatomic molecules using both the touching (TS) and 25 per cent overlapping sphere (OS) versions. The OS deformation density maps exhibit much better quantitative agreement with those from other Xα methods, which do not employ the spherical muffin-tin (MT) potential approximation, than do the TS maps. The OS version thus compensates very effectively for the errors involved in the MT approximation in computing electron densities. A detailed comparison between the TS- and OS-Xα-SW orbitals reveals that the reasons for this improvement are surprisingly specific. The dominant effect of the OS approximation is to increase substantially the electron density near the midpoint of bonding σ orbitals, with a consequent reduction of the density behind the atoms. A similar effect occurs for the bonding π orbitals but is less pronounced. These effects are due to a change in hybridization of the orbitals, with the OS approximation increasing the proportion of the subdominant partial waves and hence changing the shapes of the orbitals. It is this increased orbital polarization which so effectively compensates for the lack of (non-spherically symmetric) polarization components in the MT potential, when overlapping spheres are used.

  20. Soluble fiber dextrin and soluble corn fiber supplementation modify indices of health in cecum and colon of Sprague-Dawley rats.

    PubMed

    Knapp, Brenda K; Bauer, Laura L; Swanson, Kelly S; Tappenden, Kelly A; Fahey, George C; de Godoy, Maria R C

    2013-02-04

    The objective of this study was to evaluate health outcomes resulting from dietary supplementation of novel, low-digestible carbohydrates in the cecum and colon of Sprague-Dawley rats randomly assigned to one of four treatment groups for 21 days: 5% cellulose (Control), Pectin, soluble fiber dextrin (SFD), or soluble corn fiber (SCF). Rats fed Pectin had a higher average daily food intake, but no differences in final body weights or rates of weight gain among treatments were observed. No differences were observed in total short-chain fatty acid (SCFA) or branched-chain fatty acid (BCFA) concentrations in the cecum and colon of rats fed either SFD or SCF. The SFD and SCF treatments increased cecal propionate and decreased butyrate concentrations compared to Control or Pectin. Pectin resulted in increased BCFA in the cecum and colon. Supplementation of SFD and SCF had no effect on cecal microbial populations compared to Control. Consumption of SFD and SCF increased total and empty cecal weight but not colon weight. Gut histomorphology was positively affected by SFD and SCF. Increased crypt depth, goblet cell numbers, and acidic mucin were observed in both the cecum and colon of rats supplemented with SFD, SCF, and Pectin. These novel, low-digestible carbohydrates appear to be beneficial in modulating indices of hindgut morphology when supplemented in the diet of the rat.

  1. TNF-α inhibits SCF, ghrelin, and substance P expressions through the NF-κB pathway activation in interstitial cells of Cajal.

    PubMed

    Ren, Keyu; Yong, Chunming; Yuan, Hao; Cao, Bin; Zhao, Kun; Wang, Jin

    2018-01-01

    Ulcerative colitis is a chronic inflammatory disease of the colon where intestinal motility is disturbed. Interstitial cells of Cajal (ICC) are required to maintain normal intestinal motility. In the present study, we assessed the effect of tumor necrosis factor-alpha (TNF-α) on viability and apoptosis of ICC, as well as on the expression of stem cell factor (SCF), ghrelin, and substance P. ICC were derived from the small intestines of Swiss albino mice. Cell viability and apoptosis were measured using CCK-8 assay and flow cytometry, respectively. ELISA was used to measure the concentrations of IL-1β, IL-6, ghrelin, substance P, and endothelin-1. Quantitative RT-PCR was used to measure the expression of SCF. Western blotting was used to measure the expression of apoptosis-related proteins, interleukins, SCF, and NF-κB signaling pathway proteins. TNF-α induced inflammatory injury in ICC by decreasing cell viability and increasing apoptosis and levels of IL-1β and IL-6. TNF-α decreased the levels of SCF, ghrelin, and substance P, but had no effect on endothelin-1. TNF-α down-regulated expressions of SCF, ghrelin, and substance P by activating the NF-κB pathway in ICC. In conclusion, TNF-α down-regulated the expressions of SCF, ghrelin, and substance P via the activation of the NF-κB pathway in ICC.

  2. Soluble corn fiber increases bone calcium retention in postmenopausal women in a dose-dependent manner: a randomized crossover trial.

    PubMed

    Jakeman, Steven A; Henry, Courtney N; Martin, Berdine R; McCabe, George P; McCabe, Linda D; Jackson, George S; Peacock, Munro; Weaver, Connie M

    2016-09-01

    Dietary soluble corn fiber (SCF) significantly improves calcium absorption in adolescents and the bone strength and architecture in rodent models. In this study, we aimed to determine the skeletal benefits of SCF in postmenopausal women. We used our novel technology of determining bone calcium retention by following the urinary appearance of (41)Ca, a rare long-lived radioisotope, from prelabeled bone to rapidly and sensitively evaluate the effectiveness of SCF in reducing bone loss. A randomized-order, crossover, double-blinded trial was performed in 14 healthy postmenopausal women to compare doses of 0, 10, and 20 g fiber from SCF/d for 50 d. A dose-response effect was shown with 10 and 20 g fiber from SCF/d, whereby bone calcium retention was improved by 4.8% (P < 0.05) and 7% (P < 0.04), respectively. The bone turnover biomarkers N-terminal telopeptide and osteocalcin were not changed by the interventions; however, a significant increase in bone-specific alkaline phosphatase, which is a bone-formation marker, was detected between 0 and 20 g fiber from SCF/d (8%; P = 0.035). Daily SCF consumption significantly increased bone calcium retention in postmenopausal women, which improved the bone calcium balance by an estimated 50 mg/d. This study was registered at clinicaltrials.gov as NCT02416947. © 2016 American Society for Nutrition.

  3. SCF increases in utero-labeled stem cells migration and improves wound healing.

    PubMed

    Zgheib, Carlos; Xu, Junwang; Mallette, Andrew C; Caskey, Robert C; Zhang, Liping; Hu, Junyi; Liechty, Kenneth W

    2015-01-01

    Diabetic skin wounds lack the ability to heal properly and constitute a major and significant complication of diabetes. Nontraumatic lower extremity amputations are the number one complication of diabetic skin wounds. The complexity of their pathophysiology requires an intervention at many levels to enhance healing and wound closure. Stem cells are a promising treatment for diabetic skin wounds as they have the ability to correct abnormal healing. Stem cell factor (SCF), a chemokine expressed in the skin, can induce stem cells migration, however the role of SCF in diabetic skin wound healing is still unknown. We hypothesize that SCF would correct the impairment and promote the healing of diabetic skin wounds. Our results show that SCF improved wound closure in diabetic mice and increased HIF-1α and vascular endothelial growth factor (VEGF) expression levels in these wounds. SCF treatment also enhanced the migration of red fluorescent protein (RFP)-labeled skin stem cells via in utero intra-amniotic injection of lenti-RFP at E8. Interestingly these RFP+ cells are present in the epidermis, stain negative for K15, and appear to be distinct from the already known hair follicle stem cells. These results demonstrate that SCF improves diabetic wound healing in part by increasing the recruitment of a unique stem cell population present in the skin. © 2015 by the Wound Healing Society.

  4. The applicability of PEEK-based abutment screws.

    PubMed

    Schwitalla, Andreas Dominik; Abou-Emara, Mohamed; Zimmermann, Tycho; Spintig, Tobias; Beuer, Florian; Lackmann, Justus; Müller, Wolf-Dieter

    2016-10-01

    The high-performance polymer PEEK (poly-ether-ether-ketone) is more and more being used in the field of dentistry, mainly for removable and fixed prostheses. In cases of screw-retained implant-supported reconstructions of PEEK, an abutment screw made of PEEK might be advantageous over a conventional metal screw due to its similar elasticity. Also in case of abutment screw fracture, a screw of PEEK could be removed more easily. M1.6-abutment screws of four different PEEK compounds were subjected to tensile tests to set their maximum tensile strengths in relation to an equivalent stress of 186MPa, which is aused by a tightening torque of 15Ncm. Two screw types were manufactured via injection molding and contained 15% short carbon fibers (sCF-15) and 40% (sCF-40), respectively. Two screw types were manufactured via milling and contained 20% TiO2 powder (TiO2-20) and >50% parallel orientated, continuous carbon fibers (cCF-50). A conventional abutments screw of Ti6Al4V (Ti; CAMLOG(®) abutment screw, CAMLOG, Wimsheim, Germany) served as control. The maximum tensile strength was 76.08±5.50MPa for TiO2-20, 152.67±15.83MPa for sCF-15, 157.29±20.11MPa for sCF-40 and 191.69±36.33MPa for cCF-50. The maximum tensile strength of the Ti-screws amounted 1196.29±21.4MPa. The results of the TiO2-20 and the Ti screws were significantly different from the results of the other samples, respectively. For the manufacturing of PEEK abutment screws, PEEK reinforced by >50% continuous carbon fibers would be the material of choice. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. 454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber.

    PubMed

    Hooda, Seema; Boler, Brittany M Vester; Serao, Mariana C Rossoni; Brulc, Jennifer M; Staeger, Michael A; Boileau, Thomas W; Dowd, Scot E; Fahey, George C; Swanson, Kelly S

    2012-07-01

    The relative contribution of novel fibers such as polydextrose and soluble corn fiber (SCF) to the human gut microbiome and its association with host physiology has not been well studied. This study was conducted to test the impact of polydextrose and SCF on the composition of the human gut microbiota using 454 pyrosequencing and to identify associations among fecal microbiota and fermentative end-products. Healthy adult men (n = 20) with a mean dietary fiber (DF) intake of 14 g/d were enrolled in a randomized, double-blind, placebo-controlled crossover study. Participants consumed 3 treatment snack bars/d during each 21-d period that contained no supplemental fiber (NFC), polydextrose (PDX; 21 g/d), or SCF (21 g/d) for 21 d. There were no washout periods. Fecal samples were collected on d 16-21 of each period; DNA was extracted, followed by amplification of the V4-V6 region of the 16S rRNA gene using barcoded primers. PDX and SCF significantly affected the relative abundance of bacteria at the class, genus, and species level. The consumption of PDX and SCF led to greater fecal Clostridiaceae and Veillonellaceae and lower Eubacteriaceae compared with a NFC. The abundance of Faecalibacterium, Phascolarctobacterium, and Dialister was greater (P < 0.05) in response to PDX and SCF intake, whereas Lactobacillus was greater (P < 0.05) only after SCF intake. Faecalibacterium prausnitzii, well known for its antiinflammatory properties, was greater (P < 0.05) after fiber consumption. Principal component analysis clearly indicated a distinct clustering of individuals consuming supplemental fibers. Our data demonstrate a beneficial shift in the gut microbiome of adults consuming PDX and SCF, with potential application as prebiotics.

  6. Genetically engineered mouse models for functional studies of SKP1-CUL1-F-box-protein (SCF) E3 ubiquitin ligases.

    PubMed

    Zhou, Weihua; Wei, Wenyi; Sun, Yi

    2013-05-01

    The SCF (SKP1 (S-phase-kinase-associated protein 1), Cullin-1, F-box protein) E3 ubiquitin ligases, the founding member of Cullin-RING ligases (CRLs), are the largest family of E3 ubiquitin ligases in mammals. Each individual SCF E3 ligase consists of one adaptor protein SKP1, one scaffold protein cullin-1 (the first family member of the eight cullins), one F-box protein out of 69 family members, and one out of two RING (Really Interesting New Gene) family proteins RBX1/ROC1 or RBX2/ROC2/SAG/RNF7. Various combinations of these four components construct a large number of SCF E3s that promote the degradation of many key regulatory proteins in cell-context, temporally, and spatially dependent manners, thus controlling precisely numerous important cellular processes, including cell cycle progression, apoptosis, gene transcription, signal transduction, DNA replication, maintenance of genome integrity, and tumorigenesis. To understand how the SCF E3 ligases regulate these cellular processes and embryonic development under in vivo physiological conditions, a number of mouse models with transgenic (Tg) expression or targeted deletion of components of SCF have been established and characterized. In this review, we will provide a brief introduction to the ubiquitin-proteasome system (UPS) and the SCF E3 ubiquitin ligases, followed by a comprehensive overview on the existing Tg and knockout (KO) mouse models of the SCF E3s, and discuss the role of each component in mouse embryogenesis, cell proliferation, apoptosis, carcinogenesis, as well as other pathogenic processes associated with human diseases. We will end with a brief discussion on the future directions of this research area and the potential applications of the knowledge gained to more effective therapeutic interventions of human diseases.

  7. Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women: a randomized, double-blind placebo-controlled study.

    PubMed

    Song, Mi-young; Wang, Jing-hua; Eom, Taewoong; Kim, Hojun

    2015-08-01

    Schisandra chinensis fruit (SCF) is known to have beneficial effects on metabolic diseases, including obesity, and to affect gut microbiota in in vivo studies. However, in human research, there have been a few studies in terms of its clinical roles in lipid metabolism and modulation of gut microbiota. A double-blind, placebo-controlled study with 28 obese women with SCF or placebo was conducted for 12 weeks. Anthropometry and blood and fecal sampling were performed before and after treatment. Analysis of the gut microbiota in feces was performed using denaturing gradient gel electrophoresis and quantitative polymerase chain reaction. Although the values did not differ significantly between the 2 groups, the SCF group tended to show a greater decrease in waist circumference, fat mass, fasting blood glucose, triglycerides, aspartate aminotransferase, and alanine aminotransferase than the placebo group. Clustering of the denaturing gradient gel electrophoresis fingerprints for total bacteria before and after treatment indicated more separate clustering in SCF group than placebo. In correlation analysis, Bacteroides and Bacteroidetes (both increased by SCF) showed significant negative correlation with fat mass, aspartate aminotransferase, and/or alanine aminotransferase, respectively. Ruminococcus (decreased by SCF) showed negative correlation with high-density lipoprotein cholesterol and fasting blood glucose. In conclusion, administration of SCF for 12 weeks resulted in modulation of the gut microbiota composition in Korean obese women, and significant correlations with some bacterial genera and metabolic parameters were noted. However, in general, SCF was not sufficient to induce significant changes in obesity-related parameters compared with placebo. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Miniature optical fiber temperature sensor based on FMF-SCF structure

    NASA Astrophysics Data System (ADS)

    Zhang, Chuanbiao; Ning, Tigang; Zheng, Jingjing; Gao, Xuekai; Lin, Heng; Li, Jing; Pei, Li; Wen, Xiaodong

    2018-03-01

    We proposed and experimentally demonstrated a miniature optical fiber temperature sensor consisting of a seven core fiber (SCF) and a few mode fiber (FMF). The device is fabricated by splicing a section of FMF with a segment of SCF to form a FMF-SCF based sensing structure, and during the FMF region, few modes can be excited and will propagate within the SCF. In experiment, the proposed device has good quality interferometric spectra, and the highest extinction ratio of 27 dB was achieved. When the temperature increases from room temperature to 110 °C, the temperature response properties of the sensor have been investigated, the wavelength sensitivity of about 91.8 pm/°C and the amplitude sensitivity of about 1.57 × 10-2 a.u./°C are obtained, respectively. Due to its easy and controllable fabrication, the sensor can be a suitable candidate in temperature sensing applications.

  9. Generation of plasmas in supercritical xenon inside microcapillaries for synthesis of diamondoid

    NASA Astrophysics Data System (ADS)

    Oshima, Fumito; Ishii, Chikako; Stauss, Sven; Terashima, Kazuo

    2012-10-01

    Diamondoids are series of sp^3 hybridized carbon nanomaterials that could be applied in various fields such as pharmacy and optoelectronics. In our previous studies, higher order diamondoids were synthesized in supercritical fluid (SCF) plasmas in a batch-type reactor using adamantane (C10H16), the smallest diamondoid, as a precursor and seed. However the yield was low and the selectivity was difficult to control. We have developed a continuous flow SCF microplasma reactor that allows discharge volume and residence time to be adjusted. The electrodes consist of a tungsten wire inserted into a fused silica capillary and a sputtered silver outside of the capillary. We dissolved adamantane in supercritical xenon near critical point, and then generated DBDs inside the capillary using a nominal constant xenon flow rate of 0˜2.3 mL min-1. Micro-Raman spectra of the synthesized products show peaks that are characteristic of hydrocarbons possessing sp^3 hybridized bonds while gas-chromatography/mass spectrometry spectra indicate the synthesis of diamantane (C14H20) and possibly isomers of diamondoids consisting of up to nine cages, nonamantane. It is suggested that this type of SCF microplasma reactor might be effective not only for synthesis of diamondoids, but also other nanomaterials.

  10. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

    PubMed

    Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

    2015-04-21

    Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

  11. Vibrational modes in thymine molecule from an ab initio MO calculation

    NASA Astrophysics Data System (ADS)

    Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ueda, Toyotoshi; Ushizawa, Koichi; Ito, Gen; Kumakura, Akiko; Tsuboi, Masamichi

    1997-03-01

    Ab initio self-consistent field molecular orbital (SCF MO) calculations have been made of the thymine molecule for the equilibrium geometry, harmonic force constants, vibrational frequencies, vibrational modes, infrared intensities, and Raman intensities. The results have been correlated with the observed Raman and infrared spectra of thymine crystalline powder.

  12. Baryon anomaly and strong color fields in Pb + Pb collisions at 2.76A TeV at the CERN Large Hadron Collider

    NASA Astrophysics Data System (ADS)

    Topor Pop, V.; Gyulassy, M.; Barrette, J.; Gale, C.

    2011-10-01

    With the HIJING/B¯B v2.0 heavy ion event generator, we explore the phenomenological consequences of several high parton density dynamical effects predicted in central Pb+Pb collisions at the Large Hadron Collider (LHC) energies. These include (1) jet quenching due to parton energy loss (dE/dx), (2) strangeness and hyperon enhancement due to strong longitudinal color field (SCF), and (3) enhancement of baryon-to-meson ratios due to baryon-antibaryon junction (J¯J) loops and SCF effects. The saturation/minijet cutoff scale p0(s,A) and effective string tension κ(s,A) are constrained by our previous analysis of LHC p+p data and recent data on the charged multiplicity for Pb+Pb collisions reported by the ALICE collaboration. We predict the hadron flavor dependence (mesons and baryons) of the nuclear modification factor RAA(pT) and emphasize the possibility that the baryon anomaly could persist at the LHC up to pT˜10 GeV, well beyond the range observed in central Au+Au collisions at RHIC energies.

  13. Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations.

    PubMed

    De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe

    2014-12-09

    A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.

  14. The unrestricted Hartree-Fock self consistent field calculation for spin density wave state in metallic carbon nanotube

    NASA Astrophysics Data System (ADS)

    Kobayashi, Katsushi

    1997-06-01

    The possibility of a spin density wave (SDW) state in a metallic carbon nanotube (CN) and its electronic properties are investigated within the Hartree-Fock self consistent field (SCF) energy-band calculation. Two kinds of spatial SDW states are assumed in this study. Each assumed SDW on the wave function is constructed with the degenerate π orbital in the metallic CN system. The results calculated for the one SDW model of CN always have a relative stability (˜ 0.1 eV/cell) in SCF total energy compared with the original model in which no SDW is assumed. All the results calculated for another SDW model are completely equal to the original one. Moreover, in the energy dispersion of the former stable SDW model, the degenerate π level found in the original model disappears and the band gap (3-5 eV) occurs around at the Fermi level. The energetic stability and the band gap are also found in the π-electron band calculation within the Hubbard Hamiltonian.

  15. Higher-order micro-fiber modes for Escherichia coli manipulation using a tapered seven-core fiber

    PubMed Central

    Rong, Qiangzhou; Zhou, Yi; Yin, Xunli; Shao, Zhihua; Qiao, Xueguang

    2017-01-01

    Optical manipulation using optical micro- and nano-fibers has shown potential for controlling bacterial activities such as E. coli trapping, propelling, and binding. Most of these manipulations have been performed using the propagation of the fundamental mode through the fiber. However, along the maximum mode-intensity axis, the higher-order modes have longer evanescent field extensions and larger field amplitudes at the fiber waist than the fundamental mode, opening up new possibilities for manipulating E. coli bacteria. In this work, a compact seven-core fiber (SCF)-based micro-fiber/optical tweezers was demonstrated for trapping, propelling, and rotating E. coli bacteria using the excitation of higher-order modes. The diameter of the SCF taper was 4 µm at the taper waist, which was much larger than that of previous nano-fiber tweezers. The laser wavelength was tunable from 1500 nm to 1600 nm, simultaneously causing photophoretic force, gradient force, and scattering force. This work provides a new opportunity for better understanding optical manipulation using higher-order modes at the single-cell level. PMID:28966849

  16. Higher-order micro-fiber modes for Escherichia coli manipulation using a tapered seven-core fiber.

    PubMed

    Rong, Qiangzhou; Zhou, Yi; Yin, Xunli; Shao, Zhihua; Qiao, Xueguang

    2017-09-01

    Optical manipulation using optical micro- and nano-fibers has shown potential for controlling bacterial activities such as E. coli trapping, propelling, and binding. Most of these manipulations have been performed using the propagation of the fundamental mode through the fiber. However, along the maximum mode-intensity axis, the higher-order modes have longer evanescent field extensions and larger field amplitudes at the fiber waist than the fundamental mode, opening up new possibilities for manipulating E. coli bacteria. In this work, a compact seven-core fiber (SCF)-based micro-fiber/optical tweezers was demonstrated for trapping, propelling, and rotating E. coli bacteria using the excitation of higher-order modes. The diameter of the SCF taper was 4 µm at the taper waist, which was much larger than that of previous nano-fiber tweezers. The laser wavelength was tunable from 1500 nm to 1600 nm, simultaneously causing photophoretic force, gradient force, and scattering force. This work provides a new opportunity for better understanding optical manipulation using higher-order modes at the single-cell level.

  17. Fractography and the Surface Crack in Flexure (SCF) method for evaluating fracture toughness of ceramics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Quinn, G.D.; Gettings, R.J.; Kuebler, J.J.

    1996-12-31

    The surface crack in flexure (SCF) method, also known as the controlled surface flaw method, has been used to measure fracture toughness of ceramics and glasses for almost 20 years. New fracture toughness results for a range of ceramics and glasses including alumina, boron carbide, silicon carbide, silicon nitride, titanium diboride, zirconia, glass ceramic, borosilicate crown glass, and a whisker-reinforced alumina are presented in this paper. Some materials are conducive to precrack measurements, while others are not. New techniques for detecting the precracks are presented. A surprising outcome from a recently concluded Versailles Advanced Materials and Standards (VAMAS) round robinmore » project was that the computed toughness is often not sensitive to the exact precrack size measurement. Consistent results were obtained by many laboratories despite different viewing modes and magnifications. The reasons for this consistency and why toughness is insensitive to precrack size is presented.« less

  18. Collision for Li++He System. I. Potential Curves and Non-Adiabatic Coupling Matrix Elements

    NASA Astrophysics Data System (ADS)

    Yoshida, Junichi; O-Ohata, Kiyosi

    1984-02-01

    The potential curves and the non-adiabatic coupling matrix elements for the Li++He collision system were computed. The SCF molecular orbitals were constructed with the CGTO atomic bases centered on each nucleus and the center of mass of two nuclei. The SCF and CI calculations were done at various internuclear distances in the range of 0.1˜25.0 a.u. The potential energies and the wavefunctions were calculated with good approximation over whole internuclear distance. The non-adiabatic coupling matrix elements were calculated with the tentative method in which the ETF are approximately taken into account.

  19. A comparison of the coupled cluster and internally contracted averaged coupled-pair functional levels of theory for the calculation of the MCH2(+) binding energies for M = Sc to Cu

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Scuseria, Gustavo E.

    1992-01-01

    The correlation contribution to the M-C binding energy for the MCH2(+) systems can exceed 100 kcal/mol. At the self-consistent field (SCF) level, these systems can be more than 50 kcal/mol above the fragment energies. In spite of the poor zeroth-order reference, the coupled cluster single and double excitation method with a perturbational estimate of triple excitations, CCSD(T), method is shown to provide an accurate description of these systems. The maximum difference between the CCSD(T) and internally contracted averaged coupled-pair functional binding energies is 1.5 kcal/mol for CrCH2(+), with the remaining systems agreeing to within 1.0 kcal/mol.

  20. The Complex Economic System of Supply Chain Financing

    NASA Astrophysics Data System (ADS)

    Zhang, Lili; Yan, Guangle

    Supply Chain Financing (SCF) refers to a series of innovative and complicated financial services based on supply chain. The SCF set-up is a complex system, where the supply chain management and Small and Medium Enterprises (SMEs) financing services interpenetrate systematically. This paper establishes the organization structure of SCF System, and presents two financing models respectively, with or without the participation of the third-party logistic provider (3PL). Using Information Economics and Game Theory, the interrelationship among diverse economic sectors is analyzed, and the economic mechanism of development and existent for SCF system is demonstrated. New thoughts and approaches to solve SMEs financing problem are given.

  1. Cloud-based Computing and Applications of New Snow Metrics for Societal Benefit

    NASA Astrophysics Data System (ADS)

    Nolin, A. W.; Sproles, E. A.; Crumley, R. L.; Wilson, A.; Mar, E.; van de Kerk, M.; Prugh, L.

    2017-12-01

    Seasonal and interannual variability in snow cover affects socio-environmental systems including water resources, forest ecology, freshwater and terrestrial habitat, and winter recreation. We have developed two new seasonal snow metrics: snow cover frequency (SCF) and snow disappearance date (SDD). These metrics are calculated at 500-m resolution using NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) snow cover data (MOD10A1). SCF is the number of times snow is observed in a pixel over the user-defined observation period. SDD is the last date of observed snow in a water year. These pixel-level metrics are calculated rapidly and globally in the Google Earth Engine cloud-based environment. SCF and SDD can be interactively visualized in a map-based interface, allowing users to explore spatial and temporal snowcover patterns from 2000-present. These metrics are especially valuable in regions where snow data are sparse or non-existent. We have used these metrics in several ongoing projects. When SCF was linked with a simple hydrologic model in the La Laguna watershed in northern Chile, it successfully predicted summer low flows with a Nash-Sutcliffe value of 0.86. SCF has also been used to help explain changes in Dall sheep populations in Alaska where sheep populations are negatively impacted by late snow cover and low snowline elevation during the spring lambing season. In forest management, SCF and SDD appear to be valuable predictors of post-wildfire vegetation growth. We see a positive relationship between winter SCF and subsequent summer greening for several years post-fire. For western US winter recreation, we are exploring trends in SDD and SCF for regions where snow sports are economically important. In a world with declining snowpacks and increasing uncertainty, these metrics extend across elevations and fill data gaps to provide valuable information for decision-making. SCF and SDD are being produced so that anyone with Internet access and a Google account can access, visualize, and download the data with a minimum of technical expertise and no need for proprietary software.

  2. Simultaneous transcranial direct current stimulation (tDCS) and whole-head magnetoencephalography (MEG): assessing the impact of tDCS on slow cortical magnetic fields.

    PubMed

    Garcia-Cossio, Eliana; Witkowski, Matthias; Robinson, Stephen E; Cohen, Leonardo G; Birbaumer, Niels; Soekadar, Surjo R

    2016-10-15

    Transcranial direct current stimulation (tDCS) can influence cognitive, affective or motor brain functions. Whereas previous imaging studies demonstrated widespread tDCS effects on brain metabolism, direct impact of tDCS on electric or magnetic source activity in task-related brain areas could not be confirmed due to the difficulty to record such activity simultaneously during tDCS. The aim of this proof-of-principal study was to demonstrate the feasibility of whole-head source localization and reconstruction of neuromagnetic brain activity during tDCS and to confirm the direct effect of tDCS on ongoing neuromagnetic activity in task-related brain areas. Here we show for the first time that tDCS has an immediate impact on slow cortical magnetic fields (SCF, 0-4Hz) of task-related areas that are identical with brain regions previously described in metabolic neuroimaging studies. 14 healthy volunteers performed a choice reaction time (RT) task while whole-head magnetoencephalography (MEG) was recorded. Task-related source-activity of SCFs was calculated using synthetic aperture magnetometry (SAM) in absence of stimulation and while anodal, cathodal or sham tDCS was delivered over the right primary motor cortex (M1). Source reconstruction revealed task-related SCF modulations in brain regions that precisely matched prior metabolic neuroimaging studies. Anodal and cathodal tDCS had a polarity-dependent impact on RT and SCF in primary sensorimotor and medial centro-parietal cortices. Combining tDCS and whole-head MEG is a powerful approach to investigate the direct effects of transcranial electric currents on ongoing neuromagnetic source activity, brain function and behavior. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Simultaneous transcranial direct current stimulation (tDCS) and whole-head magnetoencephalography (MEG): assessing the impact of tDCS on slow cortical magnetic fields

    PubMed Central

    Garcia-Cossio, Eliana; Witkowski, Matthias; Robinson, Stephen E.; Cohen, Leonardo G.; Birbaumer, Niels; Soekadar, Surjo R.

    2016-01-01

    Transcranial direct current stimulation (tDCS) can influence cognitive, affective or motor brain functions. Whereas previous imaging studies demonstrated widespread tDCS effects on brain metabolism, direct impact of tDCS on electric or magnetic source activity in task-related brain areas could not be confirmed due to the difficulty to record such activity simultaneously during tDCS. The aim of this proof-of-principal study was to demonstrate the feasibility of whole-head source localization and reconstruction of neuromagnetic brain activity during tDCS and to confirm the direct effect of tDCS on ongoing neuromagnetic activity in task-related brain areas. Here we show for the first time that tDCS has an immediate impact on slow cortical magnetic fields (SCF, 0–4 Hz) of task-related areas that are identical with brain regions previously described in metabolic neuroimaging studies. 14 healthy volunteers performed a choice reaction time (RT) task while whole-head magnetoencephalography (MEG) was recorded. Task-related source-activity of SCFs was calculated using synthetic aperture magnetometry (SAM) in absence of stimulation and while anodal, cathodal or sham tDCS was delivered over the right primary motor cortex (M1). Source reconstruction revealed task-related SCF modulations in brain regions that precisely matched prior metabolic neuroimaging studies. Anodal and cathodal tDCS had a polarity-dependent impact on RT and SCF in primary sensorimotor and medial centro-parietal cortices. Combining tDCS and whole-head MEG is a powerful approach to investigate the direct effects of transcranial electric currents on ongoing neuromagnetic source activity, brain function and behavior. PMID:26455796

  4. Parallel SCF adaptor capture proteomics reveals a role for SCFFBXL17 in NRF2 activation via BACH1 repressor turnover.

    PubMed

    Tan, Meng-Kwang Marcus; Lim, Hui-Jun; Bennett, Eric J; Shi, Yang; Harper, J Wade

    2013-10-10

    Modular cullin-RING E3 ubiquitin ligases (CRLs) use substrate binding adaptor proteins to specify target ubiquitylation. Many of the ~200 human CRL adaptor proteins remain poorly studied due to a shortage of efficient methods to identify biologically relevant substrates. Here, we report the development of parallel adaptor capture (PAC) proteomics and its use to systematically identify candidate targets for the leucine-rich repeat family of F-box proteins (FBXLs) that function with SKP1-CUL1-F-box protein (SCF) E3s. In validation experiments, we identify the unstudied F-box protein FBXL17 as a regulator of the NFR2 oxidative stress pathway. We demonstrate that FBXL17 controls the transcription of the NRF2 target HMOX1 via turnover of the transcriptional repressor BACH1 in the absence or presence of extrinsic oxidative stress. This work identifies a role for SCF(FBXL17) in controlling the threshold for NRF2-dependent gene activation and provides a framework for elucidating the functions of CRL adaptor proteins. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Characterization of Neem (Azadirachta indica A. Juss) seed volatile compounds obtained by supercritical carbon dioxide process.

    PubMed

    Swapna Sonale, R; Ramalakshmi, K; Udaya Sankar, K

    2018-04-01

    Extraction process employing Supercritical fluid carbon dioxide (SCF) yields bioactive compounds near natural forms without any artifact formation. Neem seed was subjected to SCF at different temperatures and pressure conditions. These extracts were partitioned to separate volatile fraction and were analyzed by Gas Chromatography-Mass spectroscopy along with the volatiles extracted by the hydro-distillation method. Experimental results show that there is a significant effect of pressure and temperature on isolation of a number of volatile compounds as well as retention of biologically active compounds. Twenty-five volatile compounds were isolated in the Hydro-distillate compare to the SCF extract of 100 bar, 40 °C which showed forty volatile compounds corresponds to 76.38 and 92.39% of total volatiles respectively. The majority of bioactive compounds such as Terpinen-4-ol, 1,2,4-Trithiolane, 3,5-diethyl, allyl isopropyl sulphide, Cycloisolongifolene, á-Bisabolene, (-)-α-Panasinsen, Isocaryophyllene, trans-Sesquisabinene hydrate, 1-Naphthalenol, were identified in the extract when isolated at 100 bar and 40 °C.

  6. Supercritical fluid particle design for poorly water-soluble drugs (review).

    PubMed

    Sun, Yongda

    2014-01-01

    Supercritical fluid particle design (SCF PD) offers a number of routes to improve solubility and dissolution rate for enhancing the bioavailability of poorly water-soluble drugs, which can be adopted through an in-depth knowledge of SCF PD processes and the molecular properties of active pharmaceutical ingredients (API) and drug delivery system (DDS). Combining with research experiences in our laboratory, this review focuses on the most recent development of different routes (nano-micron particles, polymorphic particles, composite particles and bio-drug particles) to improve solubility and dissolution rate of poorly water-soluble drugs, covering the fundamental concept of SCF and the principle of SCF PD processes which are typically used to control particle size, shape, morphology and particle form and hence enable notable improvement in the dissolution rate of the poorly water-soluble drugs. The progress of the industrialization of SCF PD processes in pharmaceutical manufacturing environment with scaled-up plant under current good manufacturing process (GMP) specification is also considered in this review.

  7. Decoupling the Functional Pleiotropy of Stem Cell Factor by Tuning c-Kit Signaling

    PubMed Central

    Ho, Chia Chi M.; Chhabra, Akanksha; Starkl, Philipp; Schnorr, Peter-John; Wilmes, Stephan; Moraga, Ignacio; Kwon, Hye-Sook; Gaudenzio, Nicolas; Sibilano, Riccardo; Wehrman, Tom S.; Gakovic, Milica; Sockolosky, Jonathan T.; Tiffany, Matthew R.; Ring, Aaron M.; Piehler, Jacob; Weissman, Irving L.; Galli, Stephen J.; Shizuru, Judith A.; Garcia, K. Christopher

    2017-01-01

    SUMMARY Most secreted growth factors and cytokines are functionally pleiotropic because their receptors are expressed on diverse cell types. While important for normal mammalian physiology, pleiotropy limits the efficacy of cytokines and growth factors as therapeutics. Stem cell factor (SCF) is a growth factor that acts through the c-Kit receptor tyrosine kinase to elicit hematopoietic progenitor expansion, but can be toxic when administered in vivo because it concurrently activates mast cells. We engineered a mechanism-based SCF partial agonist that impaired c-Kit dimerization, truncating downstream signaling amplitude. This SCF variant elicited biased activation of hematopoietic progenitors over mast cells in vitro and in vivo. Mouse models of SCF-mediated anaphylaxis, radioprotection, and hematopoietic expansion revealed that this SCF partial agonist retained therapeutic efficacy while exhibiting virtually no anaphylactic off-target effects. The approach of biasing cell activation by tuning signaling thresholds and outputs has applications to many dimeric receptor-ligand systems. PMID:28283060

  8. Rat Stem-Cell Factor Induces Splenocytes Capable Of Regenerating The Thymus

    PubMed Central

    Migita, Russell T.; Trebasky, Lisa D.; Housman, Jerry M.; Elliott, Gary S.; Hendren, R. Wayne; Deprince, Randolph B.; Greiner, Dale L.

    1992-01-01

    Cytokine regulation of prethymic T-lymphoid progenitor-cell proliferation and/or differentiation has not been well-defined, although much is known of cytokine regulation of hemopoietic stem- and progenitor-cell development. Here we use a recently identified hemopoietic growth factor, stem-cell factor (SCF) (a form of the c-kit ligand), and a transplant model of thymocyte regeneration to assess the effect of SCF on the in vivo generation of prethymic, thymocyte progenitor-cell activity. We show that recombinant rat SCF (rrSCF164 administered to weanling rats selectively induces an increase in thymocyte progenitor activity in the spleens of treated rats as compared to rats treated with vehicle, polyethylene glycol (PEG)-conjugated rat albumin, or recombinant human granulocyte colony-stimulating factor (rhG-CSF). These data demonstrate that administration of SCF in vivo affects extrathymic-origin thymocyte regenerating cells and may influence, directly or indirectly, early prethymic stages of T-cell lymphopoiesis in addition to its known effect on early stages of myelopoiesis and erythropoiesis. PMID:1285280

  9. Increased c-kit and stem cell factor expression in the pulmonary vasculature of nitrofen-induced congenital diaphragmatic hernia.

    PubMed

    Takahashi, Toshiaki; Friedmacher, Florian; Zimmer, Julia; Puri, Prem

    2016-05-01

    Persistent pulmonary hypertension(PPH) in congenital diaphragmatic hernia (CDH) is caused by increased vascular cell proliferation and endothelial cell (EC) dysfunction, thus leading to obstructive changes in the pulmonary vasculature. C-Kit and its ligand, stem cell factor(SCF), are expressed by ECs in the developing lung mesenchyme, suggesting an important role during lung vascular formation. Conversely, absence of c-Kit expression has been demonstrated in ECs of dysplastic alveolar capillaries. We hypothesized that c-Kit and SCF expression is increased in the pulmonary vasculature of nitrofen-induced CDH. Timed-pregnant rats received nitrofen or vehicle on gestational day 9(D9). Fetuses were sacrificed on D15, D18, and D21, and divided into control and CDH group. Pulmonary gene expression levels of c-Kit and SCF were analyzed by qRT-PCR. Immunofluorescence double staining for c-Kit and SCF was combined with CD34 to evaluate protein expression in ECs of the pulmonary vasculature. Relative mRNA levels of c-Kit and SCF were significantly increased in lungs of CDH fetuses on D15, D18, and D21 compared to controls. Confocal laser scanning microscopy confirmed markedly increased vascular c-Kit and SCF expression in mesenchymal ECs of CDH lungs on D15, D18, and D21 compared to controls. Increased expression of c-Kit and SCF in the pulmonary vasculature of nitrofen-induced CDH lungs suggest that increased c-Kit signaling during lung vascular formation may contribute to vascular remodeling and thus to PPH. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Protein kinase C-δ-mediated recycling of active KIT in colon cancer.

    PubMed

    Park, Misun; Kim, Won Kyu; Song, Meiying; Park, Minhee; Kim, Hyunki; Nam, Hye Jin; Baek, Sung Hee; Kim, Hoguen

    2013-09-15

    Abnormal signaling through receptor tyrosine kinase (RTK) moieties is important in tumorigenesis and drug targeting of colorectal cancers. Wild-type KIT (WT-KIT), a RTK that is activated upon binding with stem cell factor (SCF), is highly expressed in some colon cancers; however, little is known about the functional role of SCF-dependent KIT activation in colon cancer pathogenesis. We aimed to elucidate the conditions and roles of WT-KIT activation in colon cancer tumorigenesis. Colorectal cancers with KIT expression were characterized by immunoblotting and immunohistochemistry. The biologic alterations after KIT-SCF binding were analyzed with or without protein kinase C (PKC) activation. We found that WT-KIT was expressed in a subset of colon cancer cell lines and was activated by SCF, leading to activation of downstream AKT and extracellular signal-regulated kinase (ERK) signaling pathways. We also showed that KIT expression gradually decreased, after prolonged SCF stimulation, due to lysosomal degradation. Degradation of WT-KIT after SCF binding was significantly rescued when PKC was activated. We also showed the involvement of activated PKC-δ in the recycling of WT-KIT. We further showed that a subset of colorectal cancers exhibit expressions of both WT-KIT and activated PKC-δ and that expression of KIT is correlated with poor patient survival (P = 0.004). Continuous downstream signal activation after KIT-SCF binding is accomplished through PKC-δ-mediated recycling of KIT. This sustained KIT activation may contribute to tumor progression in a subset of colon cancers with KIT expression and might provide the rationale for a therapeutic approach targeting KIT. ©2013 AACR.

  11. Tribal implementation of a patient-centred medical home model in Alaska accompanied by decreased hospital use

    PubMed Central

    Johnston, Janet M.; Smith, Julia J.; Hiratsuka, Vanessa Y.; Dillard, Denise A.; Szafran, Quenna N.; Driscoll, David L.

    2013-01-01

    Background Between 1995 and 1998, tribally owned Southcentral Foundation (SCF) incrementally assumed responsibility from the Indian Health Service (IHS) for primary care services on the Alaska Native Medical Center (ANMC) campus in Anchorage, Alaska. In 1999, SCF began implementing components of a Patient-Centered Medical Home (PCMH) model to improve access and continuity of care. Objective To evaluate hospitalisation trends before, during and after PCMH implementation. Design Time series analysis of aggregated medical record data. Methods Regression analysis with correlated errors was used to estimate trends over time for the percent of customer-owners hospitalised overall and for specific conditions during 4 time periods (March 1996–July 1999: SCF assumes responsibility for primary care; August 1999–July 2000: PCMH implementation starts; August 2000–April 2005: early post-PCMH implementation; May 2005–December 2009: later post-PCMH implementation). Analysis was restricted to individuals residing in Southcentral Alaska and receiving health care at ANMC. Results The percent of SCF customer-owners hospitalised per month for any reason was steady before and during PCMH implementation, declined steadily immediately following implementation and subsequently stabilised. The percent hospitalised per month for unintentional injury or poisoning also declined during and after the PCMH implementation. Among adult asthma patients, the percent hospitalised annually for asthma declined prior to and during implementation and remained lower thereafter. The percent of heart failure patients hospitalised annually for heart failure remained relatively constant throughout the study period while the percent of hypertension patients hospitalised for hypertension shifted higher between 1999 and 2002 compared to earlier and later years. Conclusion Implementation of PCMH at SCF was accompanied by decreases in the percent of customer-owners hospitalised monthly for any reason and for unintentional injury and in the percent of asthma patients hospitalised annually for asthma. Increased accessibility to empanelled care teams may have contributed to decreased need for hospitalisation. PMID:23984283

  12. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.

    Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

  13. Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics

    DOE PAGES

    Martínez, Enrique; Cawkwell, Marc J.; Voter, Arthur F.; ...

    2015-04-21

    Here, Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached atmore » each time step. Lastly, the thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.« less

  14. SCF-KIT signaling induces endothelin-3 synthesis and secretion: Thereby activates and regulates endothelin-B-receptor for generating temporally- and spatially-precise nitric oxide to modulate SCF- and or KIT-expressing cell functions.

    PubMed

    Chen, Lei L; Zhu, Jing; Schumacher, Jonathan; Wei, Chongjuan; Ramdas, Latha; Prieto, Victor G; Jimenez, Arnie; Velasco, Marco A; Tripp, Sheryl R; Andtbacka, Robert H I; Gouw, Launce; Rodgers, George M; Zhang, Liansheng; Chan, Benjamin K; Cassidy, Pamela B; Benjamin, Robert S; Leachman, Sancy A; Frazier, Marsha L

    2017-01-01

    We demonstrate that SCF-KIT signaling induces synthesis and secretion of endothelin-3 (ET3) in human umbilical vein endothelial cells and melanoma cells in vitro, gastrointestinal stromal tumors, human sun-exposed skin, and myenteric plexus of human colon post-fasting in vivo. This is the first report of a physiological mechanism of ET3 induction. Integrating our finding with supporting data from literature leads us to discover a previously unreported pathway of nitric oxide (NO) generation derived from physiological endothelial NO synthase (eNOS) or neuronal NOS (nNOS) activation (referred to as the KIT-ET3-NO pathway). It involves: (1) SCF-expressing cells communicate with neighboring KIT-expressing cells directly or indirectly (cleaved soluble SCF). (2) SCF-KIT signaling induces timely local ET3 synthesis and secretion. (3) ET3 binds to ETBR on both sides of intercellular space. (4) ET3-binding-initiated-ETBR activation increases cytosolic Ca2+, activates cell-specific eNOS or nNOS. (5) Temporally- and spatially-precise NO generation. NO diffuses into neighboring cells, thus acts in both SCF- and KIT-expressing cells. (6) NO modulates diverse cell-specific functions by NO/cGMP pathway, controlling transcriptional factors, or other mechanisms. We demonstrate the critical physiological role of the KIT-ET3-NO pathway in fulfilling high demand (exceeding basal level) of endothelium-dependent NO generation for coping with atherosclerosis, pregnancy, and aging. The KIT-ET3-NO pathway most likely also play critical roles in other cell functions that involve dual requirement of SCF-KIT signaling and NO. New strategies (e.g. enhancing the KIT-ET3-NO pathway) to harness the benefit of endogenous eNOS and nNOS activation and precise NO generation for correcting pathophysiology and restoring functions warrant investigation.

  15. SCF-KIT signaling induces endothelin-3 synthesis and secretion: Thereby activates and regulates endothelin-B-receptor for generating temporally- and spatially-precise nitric oxide to modulate SCF- and or KIT-expressing cell functions

    PubMed Central

    Zhu, Jing; Schumacher, Jonathan; Wei, Chongjuan; Ramdas, Latha; Prieto, Victor G.; Jimenez, Arnie; Velasco, Marco A.; Tripp, Sheryl R.; Andtbacka, Robert H. I.; Gouw, Launce; Rodgers, George M.; Zhang, Liansheng; Chan, Benjamin K.; Cassidy, Pamela B.; Benjamin, Robert S.; Leachman, Sancy A.; Frazier, Marsha L.

    2017-01-01

    We demonstrate that SCF-KIT signaling induces synthesis and secretion of endothelin-3 (ET3) in human umbilical vein endothelial cells and melanoma cells in vitro, gastrointestinal stromal tumors, human sun-exposed skin, and myenteric plexus of human colon post-fasting in vivo. This is the first report of a physiological mechanism of ET3 induction. Integrating our finding with supporting data from literature leads us to discover a previously unreported pathway of nitric oxide (NO) generation derived from physiological endothelial NO synthase (eNOS) or neuronal NOS (nNOS) activation (referred to as the KIT-ET3-NO pathway). It involves: (1) SCF-expressing cells communicate with neighboring KIT-expressing cells directly or indirectly (cleaved soluble SCF). (2) SCF-KIT signaling induces timely local ET3 synthesis and secretion. (3) ET3 binds to ETBR on both sides of intercellular space. (4) ET3-binding-initiated-ETBR activation increases cytosolic Ca2+, activates cell-specific eNOS or nNOS. (5) Temporally- and spatially-precise NO generation. NO diffuses into neighboring cells, thus acts in both SCF- and KIT-expressing cells. (6) NO modulates diverse cell-specific functions by NO/cGMP pathway, controlling transcriptional factors, or other mechanisms. We demonstrate the critical physiological role of the KIT-ET3-NO pathway in fulfilling high demand (exceeding basal level) of endothelium-dependent NO generation for coping with atherosclerosis, pregnancy, and aging. The KIT-ET3-NO pathway most likely also play critical roles in other cell functions that involve dual requirement of SCF-KIT signaling and NO. New strategies (e.g. enhancing the KIT-ET3-NO pathway) to harness the benefit of endogenous eNOS and nNOS activation and precise NO generation for correcting pathophysiology and restoring functions warrant investigation. PMID:28880927

  16. A novel gene, MdSSK1, as a component of the SCF complex rather than MdSBP1 can mediate the ubiquitination of S-RNase in apple.

    PubMed

    Yuan, Hui; Meng, Dong; Gu, Zhaoyu; Li, Wei; Wang, Aide; Yang, Qing; Zhu, Yuandi; Li, Tianzhong

    2014-07-01

    As a core factor in S-RNase-based gametophytic self-incompatibility (GSI), the SCF (SKP1-Cullin1-F-box-Rbx1) complex (including pollen determinant SLF, S-locus-F-box) functions as an E3 ubiquitin ligase on non-self S-RNase. The SCF complex is formed by SKP1 bridging between SLF, CUL1, and Rbx1; however, it is not known whether an SCF complex lacking SKP1 can mediate the ubiquitination of S-RNase. Three SKP1-like genes from pollen were cloned based on the structural features of the SLF-interacting-SKP1-like (SSK) gene and the 'Golden Delicious' apple genome. These genes have a motif of five amino acids following the standard 'WAFE' at the C terminal and, in addition, contain eight sheets and two helices. All three genes were expressed exclusively in pollen. In the yeast two-hybrid and pull-down assays only one was found to interact with MdSFBB and MdCUL1, suggesting it is the SLF-interacting SKP1-like gene in apple which was named MdSSK1. In vitro experiments using MdSSK1, S2-MdSFBB1 (S2-Malus domestica S-locus-F-box brother) and MdCUL1 proteins incubated with S 2-RNase and ubiquitin revealed that the SCF complex ubiquitinylates S-RNase in vitro, while MdSBP1 (Malus domestica S-RNase binding protein 1) could not functionally replace MdSSK1 in the SCF complex in ubiquitinylating S-RNase. According to the above experiments, MdSBP1 is probably the only factor responsible for recognition with S-RNase, while not a component of the SCF complex, and an SCF complex containing MdSSK1 is required for mediating the ubiquitination of S-RNase. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  17. Creation of the new industry-standard space test of laser retroreflectors for the GNSS and LAGEOS

    NASA Astrophysics Data System (ADS)

    Dell'Agnello, S.; Delle Monache, G. O.; Currie, D. G.; Vittori, R.; Cantone, C.; Garattini, M.; Boni, A.; Martini, M.; Lops, C.; Intaglietta, N.; Tauraso, R.; Arnold, D. A.; Pearlman, M. R.; Bianco, G.; Zerbini, S.; Maiello, M.; Berardi, S.; Porcelli, L.; Alley, C. O.; McGarry, J. F.; Sciarretta, C.; Luceri, V.; Zagwodzki, T. W.

    2011-03-01

    We built a new experimental apparatus (the “Satellite/lunar laser ranging Characterization Facility”, SCF) and created a new test procedure (the SCF-Test) to characterize and model the detailed thermal behavior and the optical performance of cube corner laser retroreflectors in space for industrial and scientific applications. The primary goal of these innovative tools is to provide critical design and diagnostic capabilities for Satellites Laser Ranging (SLR) to Galileo and other GNSS (Global Navigation Satellite System) constellations. The capability will allow us to optimize the design of GNSS laser retroreflector payloads to maximize ranging efficiency, to improve signal-to-noise conditions in daylight and to provide pre-launch validation of retroreflector performance under laboratory-simulated space conditions. Implementation of new retroreflector designs being studied will help to improve GNSS orbits, which will then increase the accuracy, stability, and distribution of the International Terrestrial Reference Frame (ITRF), to provide better definition of the geocenter (origin) and the scale (length unit).Our key experimental innovation is the concurrent measurement and modeling of the optical Far Field Diffraction Pattern (FFDP) and the temperature distribution of the SLR retroreflector payload under thermal conditions produced with a close-match solar simulator. The apparatus includes infrared cameras for non-invasive thermometry, thermal control and real-time movement of the payload to experimentally simulate satellite orientation on orbit with respect to both solar illumination and laser interrogation beams. These unique capabilities provide experimental validation of the space segment for SLR and Lunar Laser Ranging (LLR).We used the SCF facility and the SCF-Test to perform a comprehensive, non-invasive space characterization of older generation, back-coated retroreflectors of the GIOVE-A and -B (Galileo In-Orbit Validation Elements) and the GPS-35 and -36 designs. First, using a full GPS flight model at laser wavelengths of 532 and 632 nm, we found its “effective optical cross section” in air, under isothermal conditions, to be six times lower than the Retroreflector Standard for GNSS satellites (100 × 106 m2 at 20,000 km altitude for GPS and 180 × 106 m2 for Galileo at 23,200 km altitude), issued by the International Laser Ranging Service (ILRS). Under the simulated thermal and space conditions of the SCF, we also showed that in some space configurations the “effective optical cross section” is further reduced, by the thermal degradation of the FFDP. Using the same SCF-Test configuration on an individual GIOVE prototype cube, we measured severe thermal degradation in optical performance, which appears to be caused by the retroreflector metal coating and the non-optimized thermal conductance of the mounting.Uncoated retroreflectors with proper mounting can minimize thermal degradation and significantly increase the optical performance, and as such, are emerging as the recommended design for modern GNSS satellites. The COMPASS-M1, GLONASS-115 GNSS satellites use uncoated cubes. They provide better efficiency than those on GPS and GIOVE, including better daylight ranging performance. However, these retroreflectors were not characterized in the laboratory under space conditions prior to launch, so we have no basis to evaluate how well they were optimized for future GNSS satellites. SCF-Testing, under a non-disclosure agreement between INFN-LNF and the European Space Agency (ESA), of prototype uncoated cubes for the first four Galileo satellites to be launched (named “IOV”, In-Orbit Validation satellites) is a major step forward. An SCF-Test performed on a LAGEOS (LAser GEOdynamics Satellite) engineering model retroreflector array provided by NASA, showed the good space performance on what is now a reference ILRS payload standard. The IOV and LAGEOS measurements demonstrated the effectiveness of the SCF-Test as an LRA diagnostic, optimization and validation tool in use by NASA, ESA and ASI.

  18. Non-linear eigensolver-based alternative to traditional SCF methods

    NASA Astrophysics Data System (ADS)

    Gavin, B.; Polizzi, E.

    2013-05-01

    The self-consistent procedure in electronic structure calculations is revisited using a highly efficient and robust algorithm for solving the non-linear eigenvector problem, i.e., H({ψ})ψ = Eψ. This new scheme is derived from a generalization of the FEAST eigenvalue algorithm to account for the non-linearity of the Hamiltonian with the occupied eigenvectors. Using a series of numerical examples and the density functional theory-Kohn/Sham model, it will be shown that our approach can outperform the traditional SCF mixing-scheme techniques by providing a higher converge rate, convergence to the correct solution regardless of the choice of the initial guess, and a significant reduction of the eigenvalue solve time in simulations.

  19. Effects of intermolecular forces and backbone architecture on the phase behavior of fluorocopolymer-supercritical fluid mixtures

    NASA Astrophysics Data System (ADS)

    Mertdogan, Cynthia Asli

    The impact of polymer backbone architecture on fluorocopolymer solubility in supercritical fluid (SCF) solvents is studied by systematically varying the chemical type of the repeat units in the main chain. The fluorocopolymers investigated include nonpolar copolymers of tetrafluoroethylene with 19 mol% hexafluoropropylene (FEPsb{19}) and 48 mol% hexafluoropropylene (FEPsb{48}) and a polar copolymer of vinylidene fluoride with 22 mol% hexafluoropropylene (Fluorelsp°ler ). The solvents are methodically varied from nonpolar perfluoroalkanes and SFsb6 to polar fluorocarbons and COsb2. Low molecular weight solvents are used to facilitate in interpreting the intermolecular forces that control fluorocopolymer solubility, although pressures in excess of 2,500 bar are sometimes needed to dissolve the fluorocopolymers in these simple solvents. Polarity effects, which vary inversely with temperature, are moderated by operating over a large temperature range from 0 to 300sp° C. A variable-volume view cell, capable of operating to high temperatures and high pressures, was designed and implemented to meet these extreme operating conditions. Increasing the polarizability of nonpolar solvents reduces the pressures required to dissolve FEPsb{19} by as much as 1,500 bar going from perfluoromethane to perfluoropropane. However, in polar solvents, the pressures required for FEPsb{19} solubility rise dramatically as the temperature is decreased due to the increase in polar, solvent-solvent interactions that do not favor the solubility of a nonpolar copolymer. Replacing semi-crystalline FEPsb{19} with amorphous FEPsb{48} yields the same trends in phase behavior. Therefore, crystallinity does not control the shape of these fluorocopolymer-SCF cloud-point curves. Adding a cosolvent to the solution can dramatically lower the pressures needed to dissolve the copolymer. Introducing the "cosolvent" directly into the polymer backbone by changing copolymer architecture is another method of modifying fluorocopolymer solubility as seen with the results for Fluorel-SCF mixtures compared to those for FEPsb{19}-SCF mixtures. A supercritical fractionation of FEPsb{19} provides information on the impact of molecular weight and end-group content on fluorocopolymer solubility. Challenges remain for modeling fluorocopolymer-solvent mixtures. The Sanchez-Lacombe equation cannot capture the characteristics of FEPsb{19}-SCF solvent phase behavior unless two empirical mixture parameters, one of which varies with temperature, are used.

  20. Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

    1997-07-01

    Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

  1. Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Du; Yang, Weitao

    An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly smaller active-space ppRPA matrix while keeping the error to within 0.05 eV from the corresponding full ppRPA excitation energies. The resulting computational cost is significantly reduced and becomes less than the construction of the non-local Fock exchange potential matrix in the self-consistent-field (SCF) procedure. With only a modest number of active orbitals, the original ppRPA singlet-triplet (ST) gaps as well as the low-lying single and doublemore » excitation energies can be accurately reproduced at much reduced computational costs, up to 100 times faster than the iterative Davidson diagonalization of the original full ppRPA matrix. For high-lying Rydberg excitations where the Davidson algorithm fails, the computational savings of active-space ppRPA with respect to the direct diagonalization is even more dramatic. The virtues of the underlying full ppRPA combined with the significantly lower computational cost of the active-space approach will significantly expand the applicability of the ppRPA method to calculate excitation energies at a cost of O(K^{4}), with a prefactor much smaller than a single SCF Hartree-Fock (HF)/hybrid functional calculation, thus opening up new possibilities for the quantum mechanical study of excited state electronic structure of large systems.« less

  2. Accurate and efficient calculation of excitation energies with the active-space particle-particle random phase approximation

    DOE PAGES

    Zhang, Du; Yang, Weitao

    2016-10-13

    An efficient method for calculating excitation energies based on the particle-particle random phase approximation (ppRPA) is presented. Neglecting the contributions from the high-lying virtual states and the low-lying core states leads to the significantly smaller active-space ppRPA matrix while keeping the error to within 0.05 eV from the corresponding full ppRPA excitation energies. The resulting computational cost is significantly reduced and becomes less than the construction of the non-local Fock exchange potential matrix in the self-consistent-field (SCF) procedure. With only a modest number of active orbitals, the original ppRPA singlet-triplet (ST) gaps as well as the low-lying single and doublemore » excitation energies can be accurately reproduced at much reduced computational costs, up to 100 times faster than the iterative Davidson diagonalization of the original full ppRPA matrix. For high-lying Rydberg excitations where the Davidson algorithm fails, the computational savings of active-space ppRPA with respect to the direct diagonalization is even more dramatic. The virtues of the underlying full ppRPA combined with the significantly lower computational cost of the active-space approach will significantly expand the applicability of the ppRPA method to calculate excitation energies at a cost of O(K^{4}), with a prefactor much smaller than a single SCF Hartree-Fock (HF)/hybrid functional calculation, thus opening up new possibilities for the quantum mechanical study of excited state electronic structure of large systems.« less

  3. GM-CSF Inhibits c-Kit and SCF Expression by Bone Marrow-Derived Dendritic Cells

    PubMed Central

    Barroeta Seijas, Amairelys Belen; Simonetti, Sonia; Vitale, Sara; Runci, Daniele; Quinci, Angela Caterina; Soriani, Alessandra; Criscuoli, Mattia; Filippi, Irene; Naldini, Antonella; Sacchetti, Federico Maria; Tarantino, Umberto; Oliva, Francesco; Piccirilli, Eleonora; Santoni, Angela; Di Rosa, Francesca

    2017-01-01

    Stem cell factor (SCF), the ligand of c-kit, is a key cytokine for hematopoiesis. Hematopoietic precursors express c-kit, whereas differentiated cells of hematopoietic lineage are negative for this receptor, with the exception of NK cells, mast cells, and a few others. While it has long been recognized that dendritic cells (DCs) can express c-kit, several questions remain concerning the SCF/c-kit axis in DCs. This is particularly relevant for DCs found in those organs wherein SCF is highly expressed, including the bone marrow (BM). We characterized c-kit expression by conventional DCs (cDCs) from BM and demonstrated a higher proportion of c-kit+ cells among type 1 cDC subsets (cDC1s) than type 2 cDC subsets (cDC2s) in both humans and mice, whereas similar levels of c-kit expression were observed in cDC1s and cDC2s from mouse spleen. To further study c-kit regulation, DCs were generated with granulocyte-macrophage colony-stimulating factor (GM-CSF) from mouse BM, a widely used protocol. CD11c+ cells were purified from pooled non-adherent and slightly adherent cells collected after 7 days of culture, thus obtaining highly purified BM-derived DCs (BMdDCs). BMdDCs contained a small fraction of c-kit+ cells, and by replating them for 2 days with GM-CSF, we obtained a homogeneous population of c-kit+ CD40hi MHCIIhi cells. Not only did BMdDCs express c-kit but they also produced SCF, and both were striking upregulated if GM-CSF was omitted after replating. Furthermore, a small but significant reduction in BMdDC survival was observed upon SCF silencing. Incubation of BMdDCs with SCF did not modulate antigen presentation ability of these cells, nor it did regulate their membrane expression of the chemokine receptor CXCR4. We conclude that the SCF/c-kit-mediated prosurvival circuit may have been overlooked because of the prominent use of GM-CSF in DC cultures in vitro, including those human DC cultures destined for the clinics. We speculate that DCs more prominently rely on SCF in vivo in some microenvironments, with potential implications for graft-versus-host disease and antitumor immunity. PMID:28261209

  4. Kit signaling inhibits the sphingomyelin-ceramide pathway through PLC gamma 1: implication in stem cell factor radioprotective effect.

    PubMed

    Maddens, Stéphane; Charruyer, Alexandra; Plo, Isabelle; Dubreuil, Patrice; Berger, Stuart; Salles, Bernard; Laurent, Guy; Jaffrézou, Jean-Pierre

    2002-08-15

    Previous studies demonstrated that Kit activation confers radioprotection. However, the mechanism by which Kit signaling interferes with cellular response to ionizing radiation (IR) has not been firmly established. Based on the role of the sphingomyelin (SM) cycle apoptotic pathway in IR-induced apoptosis, we hypothesized that one of the Kit signaling components might inhibit IR-induced ceramide production or ceramide-induced apoptosis. Results show that, in both Ba/F3 and 32D murine cell lines transfected with wild-type c-kit, stem cell factor (SCF) stimulation resulted in a significant reduction of IR-induced apoptosis and cytotoxicity, whereas DNA repair remained unaffected. Moreover, SCF stimulation inhibited IR-induced neutral sphingomyelinase (N-SMase) stimulation and ceramide production. The SCF inhibitory effect on SM cycle was not influenced by wortmannin, a phosphoinositide-3 kinase (PI3K) inhibitor. The SCF protective effect was maintained in 32D-KitYF719 cells in which the PI3K/Akt signaling pathway is abolished due to mutation in Kit docking site for PI3K. In contrast, phospholipase C gamma (PLC gamma) inhibition by U73122 totally restored IR-induced N-SMase stimulation, ceramide production, and apoptosis in Kit-activated cells. Moreover, SCF did not protect 32D-KitYF728 cells (lacking a functional docking site for PLC gamma 1), from IR-induced SM cycle. Finally, SCF-induced radioprotection of human CD34(+) bone marrow cells was also inhibited by U73122. Altogether, these results suggest that SCF radioprotection is due to PLC gamma 1-dependent negative regulation of IR-induced N-SMase stimulation. Beyond the scope of Kit-expressing cells, it suggests that PLC gamma 1 status could greatly influence the post-DNA damage cellular response to IR, and perhaps, to other genotoxic agents.

  5. Polydextrose and soluble corn fiber increase five-day fecal wet weight in healthy men and women.

    PubMed

    Timm, Derek A; Thomas, William; Boileau, Thomas W; Williamson-Hughes, Patricia S; Slavin, Joanne L

    2013-04-01

    Dietary fiber has well-established beneficial effects on laxation. Many fibers have been developed with positive sensory properties and 2 such fibers are polydextrose (PDX) and soluble corn fiber (SCF), which can be added to many commercially produced products. We conducted a randomized, double-blind, placebo-controlled, crossover study comparing the laxative effects of PDX and SCF at a dose of 20 g/d with a low fiber control (LFC) eaten daily as a muffin and cereal in 36 healthy men and women. Each treatment period was 10 d with a 2-wk washout period between. Participants collected fecal samples during the last 5 d of each treatment and completed food diaries and gastrointestinal tolerance questionnaires on d 1, 2, and 10 of each treatment period. Five-day fecal wet weight was higher after the PDX and SCF treatments than the LFC treatment (P ≤ 0.0007). The number of stools per day and daily fecal output also were significantly greater during the PDX treatment compared with the LFC treatment. The whole gut transit time did not differ among treatments. The PDX treatment resulted in a softer stool (P = 0.002) than the SCF and LFC treatments. Fecal pH was lowered by the PDX treatment (P = 0.02), whereas SCF tended to lower it compared with the LFC treatment (P = 0.07). When the participants consumed PDX and SCF, they reported significantly more flatulence and borborygmi compared with when they consumed the LFC. Consumption of PDX and SCF at a dose of 20 g/d results in a mild laxative effect with nominal gastrointestinal tolerance issues.

  6. Role of SKP1-CUL1-F-Box-Protein (SCF) E3 Ubiquitin Ligases in Skin Cancer

    PubMed Central

    Xie, Chuan-Ming; Wei, Wenyi; Sun, Yi

    2013-01-01

    Many biological processes such as cell proliferation, differentiation, and cell death depend precisely on the timely synthesis and degradation of key regulatory proteins. While protein synthesis can be regulated at multiple levels, protein degradation is mainly controlled by the ubiquitin—proteasome system (UPS), which consists of two distinct steps: (1) ubiquitylation of targeted protein by E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme and E3 ubiquitin ligase, and (2) subsequent degradation by the 26S proteasome. Among all E3 ubiquitin ligases, the SCF (SKP1-CUL1-F-box protein) E3 ligases are the largest family and are responsible for the turnover of many key regulatory proteins. Aberrant regulation of SCF E3 ligases is associated with various human diseases, such as cancers, including skin cancer. In this review, we provide a comprehensive overview of all currently published data to define a promoting role of SCF E3 ligases in the development of skin cancer. The future directions in this area of research are also discussed with an ultimate goal to develop small molecule inhibitors of SCF E3 ligases as a novel approach for the treatment of human skin cancer. Furthermore, altered components or substrates of SCF E3 ligases may also be developed as the biomarkers for early diagnosis or predicting prognosis. PMID:23522382

  7. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pedersen, Malin; Loefstedt, Tobias; Sun Jianmin

    Signaling by the receptor for stem cell factor (SCF), c-Kit, is of major importance for hematopoiesis, melanogenesis and reproduction, and the biological responses are commonly proliferation and cell survival. Thus, constitutive activation due to c-Kit mutations is involved in the pathogenesis of several forms of cancer, e.g. leukemias, gastrointestinal stromal tumors and testicular tumors. Tumor survival requires oxygen supply through induced neovascularization, a process largely mediated by the vascular endothelial growth factor (VEGF), a prominent target of the transcription factors hypoxia-inducible factor-1 (HIF-1) and HIF-2. Using Affymetrix microarrays we have identified genes that are upregulated following SCF stimulation. Interestingly, manymore » of the genes induced were found to be related to a hypoxic response. These findings were corroborated by our observation that SCF stimulation of the hematopoietic cell lines M-07e induces HIF-1{alpha} and HIF-2{alpha} protein accumulation at normoxia. In addition, SCF-induced HIF-1{alpha} was transcriptionally active, and transcribed HIF-1 target genes such as VEGF, BNIP3, GLUT1 and DEC1, an effect that could be reversed by siRNA against HIF-1{alpha}. We also show that SCF-induced accumulation of HIF-1{alpha} is dependent on both the PI-3-kinase and Ras/MEK/Erk pathways. Our data suggest a novel mechanism of SCF/c-Kit signaling in angiogenesis and tumor progression.« less

  8. Presence of supercooling-facilitating (anti-ice nucleation) hydrolyzable tannins in deep supercooling xylem parenchyma cells in Cercidiphyllum japonicum.

    PubMed

    Wang, Donghui; Kasuga, Jun; Kuwabara, Chikako; Endoh, Keita; Fukushi, Yukiharu; Fujikawa, Seizo; Arakawa, Keita

    2012-04-01

    Xylem parenchyma cells (XPCs) in trees adapt to subzero temperatures by deep supercooling. Our previous study indicated the possibility of the presence of diverse kinds of supercooling-facilitating (SCF; anti-ice nucleation) substances in XPCs of katsura tree (Cercidiphyllum japonicum), all of which might have an important role in deep supercooling of XPCs. In the previous study, a few kinds of SCF flavonol glycosides were identified. Thus, in the present study, we tried to identify other kinds of SCF substances in XPCs of katsura tree. SCF substances were purified from xylem extracts by silica gel column chromatography and Sephadex LH-20 column chromatography. Then, four SCF substances isolated were identified by UV, mass and nuclear magnetic resonance analyses. The results showed that the four kinds of hydrolyzable gallotannins, 2,2',5-tri-O-galloyl-α,β-D-hamamelose (trigalloyl Ham or kurigalin), 1,2,6-tri-O-galloyl-β-D-glucopyranoside (trigalloyl Glc), 1,2,3,6-tetra-O-galloyl-β-D-glucopyranoside (tetragalloyl Glc) and 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranoside (pentagalloyl Glc), in XPCs exhibited supercooling capabilities in the range of 1.5-4.5°C, at a concentration of 1 mg mL⁻¹. These SCF substances, including flavonol glycosides and hydrolyzable gallotannins, may contribute to the supercooling in XPCs of katsura tree.

  9. The AB Initio Mia Method: Theoretical Development and Practical Applications

    NASA Astrophysics Data System (ADS)

    Peeters, Anik

    The bottleneck in conventional ab initio Hartree -Fock calculations is the storage of the electron repulsion integrals because their number increases with the fourth power of the number of basis functions. This problem can be solved by a combination of the multiplicative integral approximation (MIA) and the direct SCF method. The MIA approach was successfully applied in the geometry optimisation of some biologically interesting compounds like the neurolepticum Haloperidol and two TIBO derivatives, inactivators of HIV1. In this thesis the potency of the MIA-method is shown by the application of this method in the calculation of the forces on the nuclei. In addition, the MIA method enabled the development of a new model for performing crystal field studies: the supermolecule model. The results for this model are in better agreement with experimental data than the results for the point charge model. This is illustrated by the study of some small molecules in the solid state: 2,3-diketopiperazine, formamide oxime and two polymorphic forms of glycine, alpha-glycine and beta-glycine.

  10. 40 CFR 60.64 - Test methods and procedures.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... than kilns (including associated alkali bypass and clinker cooler) that are subject to the 10 percent... Qi are on the same basis (either wet or dry), scf/hr. P = 30 days of clinker production during the...

  11. 40 CFR 60.64 - Test methods and procedures.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... than kilns (including associated alkali bypass and clinker cooler) that are subject to the 10 percent... Qi are on the same basis (either wet or dry), scf/hr. P = 30 days of clinker production during the...

  12. Quantum-chemical study of model chemisorption structures on copper-containing catalysts. Communicat ion 1. ab-initio calculations of CuCo and CuCo/sup +/

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kuzminskii, M.B.; Bagator'yants, A.A.; Kazanskii, V.B.

    1986-08-01

    The authors perform ab-initio calculations, by the SCF MO LCAO method, of the electronic and geometric structure of the systems CuCO /SUP n+/ (n=0, 1) and potential curves of CO, depending on the charge state of the copper, with variation of all geometric parameters. The calculations of open-shell electronic states were performed by the unrestricted SCF method in a minimal basis set (I, STO-3G for the C and O, and MINI-1' for the Cu) and in a valence two-exponential basis set (II, MIDI-1 for the C and O, and MIDI'2' for the Cu). The principal results from the calculation inmore » the more flexible basis II are presented and the agreement between the results obtained in the minimal basis I and these data is then analyzed qualitatively.« less

  13. Static Thrust and Vectoring Performance of a Spherical Convergent Flap Nozzle with a Nonrectangular Divergent Duct

    NASA Technical Reports Server (NTRS)

    Wing, David J.

    1998-01-01

    The static internal performance of a multiaxis-thrust-vectoring, spherical convergent flap (SCF) nozzle with a non-rectangular divergent duct was obtained in the model preparation area of the Langley 16-Foot Transonic Tunnel. Duct cross sections of hexagonal and bowtie shapes were tested. Additional geometric parameters included throat area (power setting), pitch flap deflection angle, and yaw gimbal angle. Nozzle pressure ratio was varied from 2 to 12 for dry power configurations and from 2 to 6 for afterburning power configurations. Approximately a 1-percent loss in thrust efficiency from SCF nozzles with a rectangular divergent duct was incurred as a result of internal oblique shocks in the flow field. The internal oblique shocks were the result of cross flow generated by the vee-shaped geometric throat. The hexagonal and bowtie nozzles had mirror-imaged flow fields and therefore similar thrust performance. Thrust vectoring was not hampered by the three-dimensional internal geometry of the nozzles. Flow visualization indicates pitch thrust-vector angles larger than 10' may be achievable with minimal adverse effect on or a possible gain in resultant thrust efficiency as compared with the performance at a pitch thrust-vector angle of 10 deg.

  14. A perisinusoidal niche for extramedullary haematopoiesis in the spleen.

    PubMed

    Inra, Christopher N; Zhou, Bo O; Acar, Melih; Murphy, Malea M; Richardson, James; Zhao, Zhiyu; Morrison, Sean J

    2015-11-26

    Haematopoietic stresses mobilize haematopoietic stem cells (HSCs) from the bone marrow to the spleen and induce extramedullary haematopoiesis (EMH). However, the cellular nature of the EMH niche is unknown. Here we assessed the sources of the key niche factors, SCF (also known as KITL) and CXCL12, in the mouse spleen after EMH induction by myeloablation, blood loss, or pregnancy. In each case, Scf was expressed by endothelial cells and Tcf21(+) stromal cells, primarily around sinusoids in the red pulp, while Cxcl12 was expressed by a subset of Tcf21(+) stromal cells. EMH induction markedly expanded the Scf-expressing endothelial cells and stromal cells by inducing proliferation. Most splenic HSCs were adjacent to Tcf21(+) stromal cells in red pulp. Conditional deletion of Scf from spleen endothelial cells, or of Scf or Cxcl12 from Tcf21+ stromal cells, severely reduced spleen EMH and reduced blood cell counts without affecting bone marrow haematopoiesis. Endothelial cells and Tcf21(+) stromal cells thus create a perisinusoidal EMH niche in the spleen, which is necessary for the physiological response to diverse haematopoietic stresses.

  15. High-level expression of human stem cell factor fused with erythropoietin mimetic peptide in Escherichia coli.

    PubMed

    Su, Lin; Chen, Song-Sen; Yang, Ke-Gong; Liu, Chang-Zheng; Zhang, Yan-Li; Liang, Zhi-Quan

    2006-06-01

    Stem cell factor (SCF) and erythropoietin are essential for normal erythropoiesis and induce proliferation and differentiation synergistically for erythroid progenitor cells. Here, we report our work on construction of SCF/erythropoietin mimetic peptide (EMP) fusion protein gene, in which human SCF cDNA (1-165aa) and EMP sequence (20aa) were connected using a short (GGGGS) or long (GGGGSGGGGGS) linker sequence. The SCF/EMP gene was cloned into the pBV220 vector and expressed in the Escherichia coli DH5alpha strain. The expression level of the fusion protein was about 30% of total cell protein. The resulting inclusion bodies were solubilized with 8 M urea, followed by dilution refolding. The renatured protein was subsequently purified by Q-Sepharose FF column. The final product was >95% pure by SDS-PAGE and the yield of fusion protein was about 40 mg/L of culture. UT-7 cell proliferation and human cord blood cell colony-forming assays showed that the fusion proteins exhibited more potent activity than recombinant human SCF, suggesting a new strategy to enhance biological activities of growth factors.

  16. Complex interactions in EML cell stimulation by stem cell factor and IL-3.

    PubMed

    Ye, Zhi-jia; Gulcicek, Erol; Stone, Kathryn; Lam, Tukiet; Schulz, Vincent; Weissman, Sherman M

    2011-03-22

    Erythroid myeloid lymphoid (EML) cells are an established multipotent hematopoietic precursor cell line that can be maintained in medium including stem cell factor (SCF). EML cultures contain a heterogeneous mixture of cells, including a lineage-negative, CD34+ subset of cells that propagate rapidly in SCF and can clonally regenerate the mixed population. A second major subset of EML cells consists of lineage-negative. CD34- cells that can be propagated in IL-3 but grow slowly, if at all, in SCF, although they express the SCF receptor (c-kit). The response of these cells to IL-3 is stimulated synergistically by SCF, and we present evidence that both the synergy and the inhibition of c-kit responses may be mediated by direct interaction with IL-3 receptor. Further, the relative level of tyrosine phosphorylation of various substrates by either cytokine alone differs from that produced by the combination of the two cytokines, suggesting that cell signaling by the combination of the two cytokines differs from that produced by either alone.

  17. Complex interactions in EML cell stimulation by stem cell factor and IL-3

    PubMed Central

    Ye, Zhi-jia; Gulcicek, Erol; Stone, Kathryn; Lam, Tukiet; Schulz, Vincent; Weissman, Sherman M.

    2011-01-01

    Erythroid myeloid lymphoid (EML) cells are an established multipotent hematopoietic precursor cell line that can be maintained in medium including stem cell factor (SCF). EML cultures contain a heterogeneous mixture of cells, including a lineage-negative, CD34+ subset of cells that propagate rapidly in SCF and can clonally regenerate the mixed population. A second major subset of EML cells consists of lineage-negative. CD34− cells that can be propagated in IL-3 but grow slowly, if at all, in SCF, although they express the SCF receptor (c-kit). The response of these cells to IL-3 is stimulated synergistically by SCF, and we present evidence that both the synergy and the inhibition of c-kit responses may be mediated by direct interaction with IL-3 receptor. Further, the relative level of tyrosine phosphorylation of various substrates by either cytokine alone differs from that produced by the combination of the two cytokines, suggesting that cell signaling by the combination of the two cytokines differs from that produced by either alone. PMID:21383156

  18. MoonLIGHT: A USA-Italy lunar laser ranging retroreflector array for the 21st century

    NASA Astrophysics Data System (ADS)

    Martini, M.; Dell'Agnello, S.; Currie, D.; Delle Monache, G.; Vittori, R.; Chandler, J. F.; Cantone, C.; Boni, A.; Berardi, S.; Patrizi, G.; Maiello, M.; Garattini, M.; Lops, C.; March, R.; Bellettini, G.; Tauraso, R.; Intaglietta, N.; Tibuzzi, M.; Murphy, T. W.; Bianco, G.; Ciocci, E.

    2012-12-01

    Since the 1970s Lunar Laser Ranging (LLR) to the Apollo Cube Corner Retroreflector (CCR) arrays (developed by the University of Maryland, UMD) have supplied significant tests of General Relativity: possible changes in the gravitational constant, gravitational self-energy, weak equivalence principle, geodetic precession, inverse-square force-law. LLR has also provided significant information on the composition and origin of the Moon. This is the only Apollo experiment still in operation. In the 1970s Apollo LLR arrays contributed a negligible fraction of the ranging error budget. Since the ranging capabilities of ground stations improved by more than two orders of magnitude, now, because of the lunar librations, Apollo CCR arrays dominate the error budget. With the project MoonLIGHT (Moon Laser Instrumentation for General relativity High-accuracy Tests), in 2006 INFN-LNF joined UMD in the development and test of a new-generation LLR payload made by a single, large CCR (100 mm diameter) unaffected by librations. In particular, INFN-LNF built and is operating a new experimental apparatus (Satellite/lunar laser ranging Characterization Facility, SCF) and created a new industry-standard test procedure (SCF-Test) to characterize and model the detailed thermal behavior and the optical performance of CCRs in laboratory-simulated space conditions, for industrial and scientific applications. Our key experimental innovation is the concurrent measurement and modeling of the optical Far Field Diffraction Pattern (FFDP) and the temperature distribution of retroreflector payloads under thermal conditions produced with a solar simulator. The apparatus includes infrared cameras for non-invasive thermometry, thermal control and real-time payload movement to simulate satellite orientation on orbit with respect to solar illumination and laser interrogation beams. These capabilities provide: unique pre-launch performance validation of the space segment of LLR/SLR (Satellite Laser Ranging); retroreflector design optimization to maximize ranging efficiency and signal-to-noise conditions in daylight. Results of the SCF-Test of our CCR payload will be presented. Negotiations are underway to propose our payload and SCF-Test services for precision gravity and lunar science measurements with next robotic lunar landing missions. We will describe the addition of the CCR optical Wavefront Fizeau Interferogram (WFI) concurrently to FFDP/temperature measurements in the framework of an ASI-INFN project, ETRUSCO-2. The main goals of the latter are: development of a standard GNSS (Global Navigation Satellite System) laser Retroreflector Array; a second SCF; SCF-Test of Galileo, GPS and other 'as-built' GNSS retroreflector payloads. Results on analysis of Apollo LLR data and search of new gravitational physics with LLR, Mercury Radar Ranging will be presented.

  19. Optical fiber curvature sensor based on MMF-SCF-MMF structure

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Liu, Yu

    2018-07-01

    A sensitive curvature sensor based on MMF-SCF-MMF (MMF: multimode fiber; SCF: seven core fiber) structure is proposed. The multimode fiber (MMF) are used to improve the light coupling efficiency between the input singlemode fiber (SMF) and the seven-core fiber (SCF), and the seven-core fiber is used as the main element for curvature measurement. Experimental results show that the best curvature sensitivity reaches 41.46453 nm/m-1 in the range of 0.094 m-1-0.567 m-1. The temperature sensitivity is up to 59.02 pm/°C in the range of 20 °C-55 °C. The optical curvature sensors are widely used for buildings structure health monitoring and mechanical engineering due to the advantages of compact structure, anti-electromagnetic interference, and low cost.

  20. Efficient secure-channel free public key encryption with keyword search for EMRs in cloud storage.

    PubMed

    Guo, Lifeng; Yau, Wei-Chuen

    2015-02-01

    Searchable encryption is an important cryptographic primitive that enables privacy-preserving keyword search on encrypted electronic medical records (EMRs) in cloud storage. Efficiency of such searchable encryption in a medical cloud storage system is very crucial as it involves client platforms such as smartphones or tablets that only have constrained computing power and resources. In this paper, we propose an efficient secure-channel free public key encryption with keyword search (SCF-PEKS) scheme that is proven secure in the standard model. We show that our SCF-PEKS scheme is not only secure against chosen keyword and ciphertext attacks (IND-SCF-CKCA), but also secure against keyword guessing attacks (IND-KGA). Furthermore, our proposed scheme is more efficient than other recent SCF-PEKS schemes in the literature.

  1. Next-generation laser retroreflectors for GNSS, solar system exploration, geodesy, gravitational physics and earth observation

    NASA Astrophysics Data System (ADS)

    Dell'Agnello, S.; Boni, A.; Cantone, C.; Ciocci, E.; Martini, M.; Patrizi, G.; Tibuzzi, M.; Delle Monache, G.; Vittori, R.; Bianco, G.; Currie, D.; Intaglietta, N.; Salvatori, L.; Lops, C.; Contessa, S.; Porcelli, L.; Mondaini, C.; Tuscano, P.; Maiello, M.

    2017-11-01

    The SCF_Lab (Satellite/lunar/gnss laser ranging and altimetry Characterization Facility Laboratory) of INFNLNF is designed to cover virtually LRAs (Laser Retroreflector Arrays) of CCRs (Cube Corner Retroreflectors) for missions in the whole solar system, with a modular organization of its instrumentation, two redundant SCF (SCF_Lab Characterization Facilities), and an evolutionary measurement approach, including customization and potentially upgrade on-demand. See http://www.lnf.infn.it/esperimenti/etrusco/ for a general description.

  2. Non-linear eigensolver-based alternative to traditional SCF methods

    NASA Astrophysics Data System (ADS)

    Gavin, Brendan; Polizzi, Eric

    2013-03-01

    The self-consistent iterative procedure in Density Functional Theory calculations is revisited using a new, highly efficient and robust algorithm for solving the non-linear eigenvector problem (i.e. H(X)X = EX;) of the Kohn-Sham equations. This new scheme is derived from a generalization of the FEAST eigenvalue algorithm, and provides a fundamental and practical numerical solution for addressing the non-linearity of the Hamiltonian with the occupied eigenvectors. In contrast to SCF techniques, the traditional outer iterations are replaced by subspace iterations that are intrinsic to the FEAST algorithm, while the non-linearity is handled at the level of a projected reduced system which is orders of magnitude smaller than the original one. Using a series of numerical examples, it will be shown that our approach can outperform the traditional SCF mixing techniques such as Pulay-DIIS by providing a high converge rate and by converging to the correct solution regardless of the choice of the initial guess. We also discuss a practical implementation of the technique that can be achieved effectively using the FEAST solver package. This research is supported by NSF under Grant #ECCS-0846457 and Intel Corporation.

  3. Highly Regular, Uniform K3ScF6:Mn4+ Phosphors: Facile Synthesis, Microstructures, Photoluminescence Properties, and Application in Light-Emitting Diode Devices.

    PubMed

    Ming, Hong; Liu, Shuifu; Liu, Lili; Peng, Jiaqing; Fu, Junxiang; Du, Fu; Ye, Xinyu

    2018-06-13

    A new generation of red phosphors of complex fluoride matrices activated with Mn 4+ has gained a broad interest in getting high color quality and low color temperature of solid-state white light-emitting diodes (WLEDs). However, besides their instability toward moisture, the extremely irregular and nonuniform morphologies of these phosphors have limited their practical industry applications. In the present study, a novel type of K 3 ScF 6 :Mn 4+ red phosphor with highly regular, uniform, and high color purity was obtained successfully through a facile coprecipitation route under mild conditions. The crystal structure was identified with aids of the powder X-ray diffraction, Rietveld refinement, and density functional theory calculations. The prototype crystallizes in the space group Fm3 m with a cubic structure, and the lattice parameters are fitted well to be a = b = c = 8.4859(8) Å and V = 611.074(2) Å 3 . The Mn 4+ ions occupy Sc 3+ sites and locate at the centers of the distorted ScF 6 octahedrons. A wide band gap of approximately 6.15 eV can provide sufficient space to accommodate impurity energy levels. Unlike most other Mn 4+ ion-activated fluoride phosphors, the as-prepared K 3 ScF 6 :Mn 4+ phosphors demonstrate highly uniform and regular morphologies with shapes transforming from cube to octahedron with increasing Mn 4+ ion concentration. Under blue light excitation, the as-prepared K 3 ScF 6 :Mn 4+ sample exhibits intense sharp-line red fluorescence (the strongest peak located at 631 nm) with high color purity. An excellent recovery in luminescence upon heating and cooling processes implies high stability of K 3 ScF 6 :Mn 4+ . Furthermore, a warm WLED fabricated with blue GaN chips merged with the mixture of K 3 ScF 6 :Mn 4+ and the well-known commercial YAG:Ce 3+ yellow phosphors exhibits wonderful color quality with lower correlated color temperature (3250 K) and higher color-rendering index ( R a = 86.4). These results suggest that the K 3 ScF 6 :Mn 4+ phosphor possesses stupendous potentiality for practical applications.

  4. Biostratigraphic reappraisal of the Lower Triassic Sanga do Cabral Supersequence from South America, with a description of new material attributable to the parareptile genus Procolophon

    NASA Astrophysics Data System (ADS)

    Dias-da-Silva, Sérgio; Pinheiro, Felipe L.; Stock Da-Rosa, Átila Augusto; Martinelli, Agustín G.; Schultz, Cesar L.; Silva-Neves, Eduardo; Modesto, Sean P.

    2017-11-01

    The Sanga do Cabral Supersequence (SCS), comprises the Brazilian Sanga do Cabral Formation (SCF) and the Uruguayan Buena Vista Formation (BVF). So far, the SCS has yielded temnospondyls, parareptiles, archosauromorphs, putative synapsids, and a number of indeterminate specimens. In the absence of absolute dates for these rocks, a biostratigraphic approach is necessary to establish the ages of the SCF and the BVF. It is well established that the SCF is Early Triassic mainly due to the presence of the widespread Gondwanan reptile Procolophon trigoniceps. Conversely, the age of the BVF is subject of great controversy, being regarded alternatively as Permian, Permo-Triassic, and Early Triassic. The BVF has yielded the definite procolophonid Pintosaurus magnidentis. Procolophonoidea is one of the most diverse and conspicuous terrestrial tetrapod groups of the Lower Triassic Lystrosaurus Assemblage Zone in the Karoo Basin of South Africa, which preserves tetrapods from the aftermath of the end-Permian extinction event. Based on a previous interpretation that the fauna of the BVF is Permian, and in the reinterpretation of disarticulated vertebrae from SCF with 'swollen' neural arches as belonging to either seymouriamorphs or diadectomorphs, it was recently suggested that at least part of the SCF is Permian in age, which prompted this comprehensive reevaluation of both SCS's faunal content and geology. Moreoever, new, strikingly large procolophonid specimens (skull, vertebra, and a mandibular fragment) from the SCF are described and referred to the genus Procolophon. The large procolophonid vertebra described here contradicts the recent hypothesis that similar specimens from the SCF belong to seymouriamorphs or diadectomorphs, because its morphology is consistent with that found in Procolophon. There is not a single diagnostic specimen that supports the inference of Permian levels in the SCS. Accordingly, because all diagnostic and biostratigraphically informative fossils from the SCF and the BVF are either Early Triassic or restricted to the Triassic, we conclude that the available biostratigraphic data reinforce an Early Triassic age assignment to the SCS.

  5. New algorithms for field-theoretic block copolymer simulations: Progress on using adaptive-mesh refinement and sparse matrix solvers in SCFT calculations

    NASA Astrophysics Data System (ADS)

    Sides, Scott; Jamroz, Ben; Crockett, Robert; Pletzer, Alexander

    2012-02-01

    Self-consistent field theory (SCFT) for dense polymer melts has been highly successful in describing complex morphologies in block copolymers. Field-theoretic simulations such as these are able to access large length and time scales that are difficult or impossible for particle-based simulations such as molecular dynamics. The modified diffusion equations that arise as a consequence of the coarse-graining procedure in the SCF theory can be efficiently solved with a pseudo-spectral (PS) method that uses fast-Fourier transforms on uniform Cartesian grids. However, PS methods can be difficult to apply in many block copolymer SCFT simulations (eg. confinement, interface adsorption) in which small spatial regions might require finer resolution than most of the simulation grid. Progress on using new solver algorithms to address these problems will be presented. The Tech-X Chompst project aims at marrying the best of adaptive mesh refinement with linear matrix solver algorithms. The Tech-X code PolySwift++ is an SCFT simulation platform that leverages ongoing development in coupling Chombo, a package for solving PDEs via block-structured AMR calculations and embedded boundaries, with PETSc, a toolkit that includes a large assortment of sparse linear solvers.

  6. Analysis-Driven Design Optimization of a SMA-Based Slat-Cove Filler for Aeroacoustic Noise Reduction

    NASA Technical Reports Server (NTRS)

    Scholten, William; Hartl, Darren; Turner, Travis

    2013-01-01

    Airframe noise is a significant component of environmental noise in the vicinity of airports. The noise associated with the leading-edge slat of typical transport aircraft is a prominent source of airframe noise. Previous work suggests that a slat-cove filler (SCF) may be an effective noise treatment. Hence, development and optimization of a practical slat-cove-filler structure is a priority. The objectives of this work are to optimize the design of a functioning SCF which incorporates superelastic shape memory alloy (SMA) materials as flexures that permit the deformations involved in the configuration change. The goal of the optimization is to minimize the actuation force needed to retract the slat-SCF assembly while satisfying constraints on the maximum SMA stress and on the SCF deflection under static aerodynamic pressure loads, while also satisfying the condition that the SCF self-deploy during slat extension. A finite element analysis model based on a physical bench-top model is created in Abaqus such that automated iterative analysis of the design could be performed. In order to achieve an optimized design, several design variables associated with the current SCF configuration are considered, such as the thicknesses of SMA flexures and the dimensions of various components, SMA and conventional. Designs of experiment (DOE) are performed to investigate structural response to an aerodynamic pressure load and to slat retraction and deployment. DOE results are then used to inform the optimization process, which determines a design minimizing actuator forces while satisfying the required constraints.

  7. Unremitting Cell Proliferation in the Secretory Phase of Eutopic Endometriosis

    PubMed Central

    Franco-Murillo, Yanira; Miranda-Rodríguez, José Antonio; Rendón-Huerta, Erika; Montaño, Luis F.; Cornejo, Gerardo Velázquez; Gómez, Lucila Poblano; Valdez-Morales, Francisco Javier; Gonzalez-Sanchez, Ignacio

    2014-01-01

    Objective: Endometriosis is linked to altered cell proliferation and stem cell markers c-kit/stem cell factor (SCF) in ectopic endometrium. Our aim was to investigate whether c-kit/SCF also plays a role in eutopic endometrium. Design: Eutopic endometrium obtained from 35 women with endometriosis and 25 fertile eumenorrheic women was analyzed for in situ expression of SCF/c-kit, Ki67, RAC-alpha serine/threonine-protein kinase (Akt), phosphorylated RAC-alpha serine/threonin-protein kinase (pAkt), Glycogen synthase kinase 3 beta (GSK3β), and phosphorylated glycogen synthase kinase 3 beta (pGSK3β), throughout the menstrual cycle. Results: Expression of Ki67 and SCF was higher in endometriosis than in control tissue (P < .05) and greater in secretory rather than proliferative (P < .01) endometrium in endometriosis. Expression of c-kit was also higher in endometriosis although similar in both phases. Expression of Akt and GSK3β was identical in all samples and cycle phases, whereas pAkt and pGSK3β, opposed to control tissue, remained overexpressed in the secretory phase in endometriosis. Conclusion: Unceasing cell proliferation in the secretory phase of eutopic endometriosis is linked to deregulation of c-kit/SCF-associated signaling pathways. PMID:25194152

  8. Effect of a soluble cocoa fiber-enriched diet in Zucker fatty rats.

    PubMed

    Sánchez, David; Moulay, Leila; Muguerza, Begoña; Quiñones, Mar; Miguel, Marta; Aleixandre, Amaya

    2010-06-01

    The effects of a soluble cocoa fiber (SCF) were studied in Zucker fatty rats. Two groups of Zucker fatty rats were fed the following diets: standard diet and 5% SCF-enriched diet. A group of Zucker lean rats fed the standard diet was used for results comparison with obese Zucker animals. Solid and liquid intakes, body weight, plasma glucose, lipid profile, and systolic (SBP) and diastolic (DBP) blood pressure were recorded weekly. At the end of the experimental period insulin was determined, and fat apparent digestibility (FAD) and insulin resistance were calculated. The Zucker fatty rats fed 5% SCF-enriched diet showed less weight gain and food intake than those fed the standard diet. The group fed the fiber-enriched diet showed lower values of the total cholesterol/high-density lipoprotein cholesterol ratio and triglyceride levels than the standard group. FAD was also lower in the fiber group. Both SBP and DBP were decreased. In addition, SCF reduced plasma glucose and insulin, and as a consequence the insulin resistance was also decreased. Our data demonstrate that SCF resulted in an improvement of the studied risk factors associated with cardiometabolic disorders.

  9. Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1–F-box interface

    DOE PAGES

    Gorelik, Maryna; Orlicky, Stephen; Sartori, Maria A.; ...

    2016-03-14

    Skp1–Cul1–F-box (SCF) E3 ligases play key roles in multiple cellular processes through ubiquitination and subsequent degradation of substrate proteins. Although Skp1 and Cul1 are invariant components of all SCF complexes, the 69 different human F-box proteins are variable substrate binding modules that determine specificity. SCF E3 ligases are activated in many cancers and inhibitors could have therapeutic potential. Here, we used phage display to develop specific ubiquitin-based inhibitors against two F-box proteins, Fbw7 and Fbw11. Unexpectedly, the ubiquitin variants bind at the interface of Skp1 and F-box proteins and inhibit ligase activity by preventing Cul1 binding to the same surface.more » Using structure-based design and phage display, we modified the initial inhibitors to generate broad-spectrum inhibitors that targeted many SCF ligases, or conversely, a highly specific inhibitor that discriminated between even the close homologs Fbw11 and Fbw1. We propose that most F-box proteins can be targeted by this approach for basic research and for potential cancer therapies.« less

  10. Low NO sub x heavy fuel combustor concept program phase 1A gas tests

    NASA Technical Reports Server (NTRS)

    Cutrone, M. B.; Beebe, K. W.; Cutrone, M. B.

    1982-01-01

    The emissions performance of a rich lean combustor (developed for liquid fuels) for combustion of simulated coal gases ranging in heating value from 167 to 244 Btu/scf were assessed. The 244 Btu/scf gas is typical of the product gas from an oxygen blown gasifier, while the 167 Btu/scf gas is similar to that from an air blown gasifier. Although meeting NOx goals for the 167 Btu/scf gas, NOx performance of the rich lean combustor did not meet program goals with the 244 Btu/scf gas because of high thermal NOx, similar to levels expected from conventional lean burning combustors. The NOx emissions are attributed to inadequate fuel air mixing in the rich stage resulting from the design of the large central fuel nozzle delivering 71% of the total gas flow. NOx generation from NH3 was significant at ammonia concentrations significantly less tha 0.5%. These levels occur depending on fuel gas cleanup system design, However, NOx yield from ammonia injected into the fuel gas decreased rapidly with increasing ammonia level, and is projected to be less than 10% at NH3 levels of 0.5% or higher.

  11. Static bending deflection and free vibration analysis of moderate thick symmetric laminated plates using multidimensional wave digital filters

    NASA Astrophysics Data System (ADS)

    Tseng, Chien-Hsun

    2018-06-01

    This paper aims to develop a multidimensional wave digital filtering network for predicting static and dynamic behaviors of composite laminate based on the FSDT. The resultant network is, thus, an integrated platform that can perform not only the free vibration but also the bending deflection of moderate thick symmetric laminated plates with low plate side-to-thickness ratios (< = 20). Safeguarded by the Courant-Friedrichs-Levy stability condition with the least restriction in terms of optimization technique, the present method offers numerically high accuracy, stability and efficiency to proceed a wide range of modulus ratios for the FSDT laminated plates. Instead of using a constant shear correction factor (SCF) with a limited numerical accuracy for the bending deflection, an optimum SCF is particularly sought by looking for a minimum ratio of change in the transverse shear energy. This way, it can predict as good results in terms of accuracy for certain cases of bending deflection. Extensive simulation results carried out for the prediction of maximum bending deflection have demonstratively proven that the present method outperforms those based on the higher-order shear deformation and layerwise plate theories. To the best of our knowledge, this is the first work that shows an optimal selection of SCF can significantly increase the accuracy of FSDT-based laminates especially compared to the higher order theory disclaiming any correction. The highest accuracy of overall solution is compared to the 3D elasticity equilibrium one.

  12. A spin column-free approach to sodium hydroxide-based glycan permethylation.

    PubMed

    Hu, Yueming; Borges, Chad R

    2017-07-24

    Glycan permethylation was introduced as a tool to facilitate the study of glycans in 1903. Since that time, permethylation procedures have been continually modified to improve permethylation efficiency and qualitative applicability. Typically, however, either laborious preparation steps or cumbersome and uneconomical spin columns have been needed to obtain decent permethylation yields on small glycan samples. Here we describe a spin column-free (SCF) glycan permethylation procedure that is applicable to both O- and N-linked glycans and can be employed upstream to intact glycan analysis by MALDI-MS, ESI-MS, or glycan linkage analysis by GC-MS. The SCF procedure involves neutralization of NaOH beads by acidified phosphate buffer, which eliminates the risk of glycan oxidative degradation and avoids the use of spin columns. Optimization of the new permethylation procedure provided high permethylation efficiency for both hexose (>98%) and HexNAc (>99%) residues-yields which were comparable to (or better than) those of some widely-used spin column-based procedures. A light vs. heavy labelling approach was employed to compare intact glycan yields from a popular spin-column based approach to the SCF approach. Recovery of intact N-glycans was significantly better with the SCF procedure (p < 0.05), but overall yield of O-glycans was similar or slightly diminished (p < 0.05 for tetrasaccharides or smaller). When the SCF procedure was employed upstream to hydrolysis, reduction and acetylation for glycan linkage analysis of pooled glycans from unfractionated blood plasma, analytical reproducibility was on par with that from previous spin column-based "glycan node" analysis results. When applied to blood plasma samples from stage III-IV breast cancer patients (n = 20) and age-matched controls (n = 20), the SCF procedure facilitated identification of three glycan nodes with significantly different distributions between the cases and controls (ROC c-statistics > 0.75; p < 0.01). In summary, the SCF permethylation procedure expedites and economizes both intact glycan analysis and linkage analysis of glycans from whole biospecimens.

  13. A spin column-free approach to sodium hydroxide-based glycan permethylation†

    PubMed Central

    Hu, Yueming; Borges, Chad R.

    2018-01-01

    Glycan permethylation was introduced as a tool to facilitate the study of glycans in 1903. Since that time, permethylation procedures have been continually modified to improve permethylation efficiency and qualitative applicability. Typically, however, either laborious preparation steps or cumbersome and uneconomical spin columns have been needed to obtain decent permethylation yields on small glycan samples. Here we describe a spin column-free (SCF) glycan permethylation procedure that is applicable to both O- and N-linked glycans and can be employed upstream to intact glycan analysis by MALDI-MS, ESI-MS, or glycan linkage analysis by GC-MS. The SCF procedure involves neutralization of NaOH beads by acidified phosphate buffer, which eliminates the risk of glycan oxidative degradation and avoids the use of spin columns. Optimization of the new permethylation procedure provided high permethylation efficiency for both hexose (>98%) and HexNAc (>99%) residues—yields which were comparable to (or better than) those of some widely-used spin column-based procedures. A light vs. heavy labelling approach was employed to compare intact glycan yields from a popular spin-column based approach to the SCF approach. Recovery of intact N-glycans was significantly better with the SCF procedure (p < 0.05), but overall yield of O-glycans was similar or slightly diminished (p < 0.05 for tetrasaccharides or smaller). When the SCF procedure was employed upstream to hydrolysis, reduction and acetylation for glycan linkage analysis of pooled glycans from unfractionated blood plasma, analytical reproducibility was on par with that from previous spin column-based “glycan node” analysis results. When applied to blood plasma samples from stage III–IV breast cancer patients (n = 20) and age-matched controls (n = 20), the SCF procedure facilitated identification of three glycan nodes with significantly different distributions between the cases and controls (ROC c-statistics > 0.75; p < 0.01). In summary, the SCF permethylation procedure expedites and economizes both intact glycan analysis and linkage analysis of glycans from whole biospecimens. PMID:28635997

  14. Nociceptive tuning by stem cell factor/c-Kit signaling.

    PubMed

    Milenkovic, Nevena; Frahm, Christina; Gassmann, Max; Griffel, Carola; Erdmann, Bettina; Birchmeier, Carmen; Lewin, Gary R; Garratt, Alistair N

    2007-12-06

    The molecular mechanisms regulating the sensitivity of sensory circuits to environmental stimuli are poorly understood. We demonstrate here a central role for stem cell factor (SCF) and its receptor, c-Kit, in tuning the responsiveness of sensory neurons to natural stimuli. Mice lacking SCF/c-Kit signaling displayed profound thermal hypoalgesia, attributable to a marked elevation in the thermal threshold and reduction in spiking rate of heat-sensitive nociceptors. Acute activation of c-Kit by its ligand, SCF, resulted in a reduced thermal threshold and potentiation of heat-activated currents in isolated small-diameter neurons and thermal hyperalgesia in mice. SCF-induced thermal hyperalgesia required the TRP family cation channel TRPV1. Lack of c-Kit signaling during development resulted in hypersensitivity of discrete mechanoreceptive neuronal subtypes. Thus, c-Kit can now be grouped with a small family of receptor tyrosine kinases, including c-Ret and TrkA, that control the transduction properties of sensory neurons.

  15. A poly-epoxy surface explored by Hartree-Fock ΔSCF simulations of C1s XPS spectra

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gavrielides, A.; Duguet, T., E-mail: thomas.duguet@ensiacet.fr, E-mail: Paul.Bagus@unt.edu; Esvan, J.

    Whereas poly-epoxy polymers represent a class of materials with a wide range of applications, the structural disorder makes them difficult to model. In the present work, we use good experimental model samples in the sense that they are pure, fully polymerized, flat and smooth, defect-free, and suitable for ultrahigh vacuum x-ray photoelectron spectroscopy, XPS, experiments. In parallel, we perform Hartree-Fock, HF, calculations of the binding energies, BEs, of the C1s electrons in a model molecule composed of the two constituents of the poly-epoxy sample. These C1s BEs were determined using the HF ΔSCF method, which is known to yield accuratemore » values, especially for the shifts of the BEs, ΔBEs. We demonstrate the benefits of combining rigorous theory with careful XPS measurements in order to obtain correct assignments of the C1s XPS spectra of the polymer sample. Both the relative binding energies—by the ΔSCF method—and relative intensities—in the sudden approximation, SA, are calculated. It results in an excellent match with the experimental spectra. We are able to identify 9 different chemical environments under the C1s peak, where an exclusively experimental work would have found only 3 contributions. In addition, we observe that some contributions are localized at discrete binding energies, whereas others allow a much wider range because of the variation of their second neighbor bound polarization. Therefore, HF-ΔSCF simulations significantly increase the spectral resolution of XPS and thus offer a new avenue for the exploration of the surface of polymers.« less

  16. Formation of indomethacin-saccharin cocrystals using supercritical fluid technology.

    PubMed

    Padrela, Luis; Rodrigues, Miguel A; Velaga, Sitaram P; Matos, Henrique A; de Azevedo, Edmundo Gomes

    2009-08-12

    The main objective of the present work is to check the feasibility of supercritical fluid (SCF) technologies in the screening and design of cocrystals (novel crystalline solids). The cocrystal formation tendencies in three different SCF techniques, focusing on distinct supercritical fluid properties - solvent, anti-solvent and atomization enhancer - were investigated. The effect of processing parameters on the cocrystal formation behaviour and particle properties in these techniques was also studied. A recently reported indomethacin-saccharin (IND-SAC) cocrystalline system was our model system. A 1:1 molar ratio of indomethacin (gamma-form) and saccharin was used as a starting material. The SCF techniques employed in the study include the CSS technique (cocrystallization with supercritical solvent), the SAS technique (supercritical anti-solvent), and the AAS technique (atomization and anti-solvent). The resulting cocrystalline phase was identified using differential scanning calorimetry (DSC), powder X-ray diffraction (PXRD), and Fourier transform-Raman (FT-Raman). The particle morphologies and size distributions were determined using scanning electron microscopy (SEM) and aerosizer, respectively. The pure IND-SAC cocrystals were obtained from SAS and AAS processes, whilst partial to no cocrystal formation occurred in the CSS process. However, no remarkable differences were observed in terms of cocrystal formation at different processing conditions in SAS and AAS processes. Particles from CSS processes were agglomerated and large, whilst needle-to-block-shaped and spherical particles were obtained from SAS and AAS processes, respectively. The particle size distribution of these particles was 0.2-5microm. Particulate IND-SAC cocrystals with different morphologies and sizes (nano-to-micron) were produced using supercritical fluid techniques. This work demonstrates the potential of SCF technologies as screening methods for cocrystals with possibilities for particle engineering.

  17. Measurement of generation-dependent proliferation rates and death rates during mouse erythroid progenitor cell differentiation.

    PubMed

    Akbarian, Vahe; Wang, Weijia; Audet, Julie

    2012-05-01

    Herein, we describe an experimental and computational approach to perform quantitative carboxyfluorescein diacetate succinimidyl ester (CFSE) cell-division tracking in cultures of primary colony-forming unit-erythroid (CFU-E) cells, a hematopoietic progenitor cell type, which is an important target for the treatment of blood disorders and for the manufacture of red blood cells. CFSE labeling of CFU-Es isolated from mouse fetal livers was performed to examine the effects of stem cell factor (SCF) and erythropoietin (EPO) in culture. We used a dynamic model of proliferation based on the Smith-Martin representation of the cell cycle to extract proliferation rates and death rates from CFSE time-series. However, we found that to accurately represent the cell population dynamics in differentiation cultures of CFU-Es, it was necessary to develop a model with generation-specific rate parameters. The generation-specific rates of proliferation and death were extracted for six generations (G(0) -G(5) ) and they revealed that, although SCF alone or EPO alone supported similar total cell outputs in culture, stimulation with EPO resulted in significantly higher proliferation rates from G(2) to G(5) and higher death rates in G(2) , G(3) , and G(5) compared with SCF. In addition, proliferation rates tended to increase from G(1) to G(5) in cultures supplemented with EPO and EPO + SCF, while they remained lower and more constant across generations with SCF. The results are consistent with the notion that SCF promotes CFU-E self-renewal while EPO promotes CFU-E differentiation in culture. Copyright © 2012 International Society for Advancement of Cytometry.

  18. Toroidal figures of equilibrium from a second-order accurate, accelerated SCF method with subgrid approach

    NASA Astrophysics Data System (ADS)

    Huré, J.-M.; Hersant, F.

    2017-02-01

    We compute the structure of a self-gravitating torus with polytropic equation of state (EOS) rotating in an imposed centrifugal potential. The Poisson solver is based on isotropic multigrid with optimal covering factor (fluid section-to-grid area ratio). We work at second order in the grid resolution for both finite difference and quadrature schemes. For soft EOS (I.e. polytropic index n ≥ 1), the underlying second order is naturally recovered for boundary values and any other integrated quantity sensitive to the mass density (mass, angular momentum, volume, virial parameter, etc.), I.e. errors vary with the number N of nodes per direction as ˜1/N2. This is, however, not observed for purely geometrical quantities (surface area, meridional section area, volume), unless a subgrid approach is considered (I.e. boundary detection). Equilibrium sequences are also much better described, especially close to critical rotation. Yet another technical effort is required for hard EOS (n < 1), due to infinite mass density gradients at the fluid surface. We fix the problem by using kernel splitting. Finally, we propose an accelerated version of the self-consistent field (SCF) algorithm based on a node-by-node pre-conditioning of the mass density at each step. The computing time is reduced by a factor of 2 typically, regardless of the polytropic index. There is a priori no obstacle to applying these results and techniques to ellipsoidal configurations and even to 3D configurations.

  19. Theoretical studies of large water clusters: (H2O)28, (H2O)29, (H2O)30, and (H2O)31 hexakaidecahedral structures

    NASA Astrophysics Data System (ADS)

    Khan, Arshad

    1997-04-01

    The 28, 29, 30, and 31 mer hexakaidecahedral water clusters were studied by applying the intermediate neglect of differential overlap self-consistent field restricted Hartree-Fock method (INDO SCF RHF) after parametrization for H and O atoms. The most stable 29 and 30 mer clusters have one and two water molecules, respectively within the cavity of the distorted hexakaidecahedral cage with stabilization energy/monomer values of around 10.9 and 11.0 kcal, respectively. The 31 mer cluster with three water molecules within the cavity is less stable than the isomer with two molecules within the cavity and the third one bonded outside of the cage by around 3 kcal/mol.

  20. 75 FR 69088 - Proposed Information Collection Activity; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-10

    ... Strengthening Communities Fund and progress toward the objective of improving the capacity of organizations... Information Collection Activity; Comment Request Proposed Projects Title: Strengthening Communities Fund (SCF... information from participants in two Strengthening Communities Fund (SCF) programs: The Nonprofit Capacity...

  1. 75 FR 54342 - Submission for OMB Review; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-07

    ... the Strengthening Communities Fund in meeting its objective of improving the capacity of grantees that...-0376] Submission for OMB Review; Comment Request Title: Strengthening Communities Fund Program... from Strengthening Communities Fund (SCF) grantees. Grantees include participants in two SCF grant...

  2. 76 FR 9581 - Submission for OMB Review; Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-18

    ... the Strengthening Communities Fund and progress toward the objective of improving the capacity of... OMB Review; Comment Request Title: Strengthening Communities Fund (SCF) Performance Management and... obtain information from participants in two Strengthening Communities Fund (SCF) programs: The Nonprofit...

  3. 160 W 800 fs Yb:YAG single crystal fiber amplifier without CPA.

    PubMed

    Markovic, Vesna; Rohrbacher, Andreas; Hofmann, Peter; Pallmann, Wolfgang; Pierrot, Simonette; Resan, Bojan

    2015-10-05

    We demonstrate a compact and simple two-stage Yb:YAG single crystal fiber amplifier which delivers 160 W average power, 800 fs pulses without chirped pulse amplification. This is the highest average power of femtosecond laser based on SCF. Additionally, we demonstrate the highest small signal gain of 32.5 dB from the SCF in the first stage and the highest extraction efficiency of 42% in the second stage. The excellent performance of the second stage was obtained using the bidirectional pumping scheme, which is applied to SCF for the first time.

  4. Subjective cognitive complaints one year after ceasing adjuvant endocrine treatment for early-stage breast cancer.

    PubMed

    Ribi, K; Aldridge, J; Phillips, K-A; Thompson, A; Harvey, V; Thürlimann, B; Cardoso, F; Pagani, O; Coates, A S; Goldhirsch, A; Price, K N; Gelber, R D; Bernhard, J

    2012-05-08

    In the BIG 1-98 trial objective cognitive function improved in postmenopausal women 1 year after cessation of adjuvant endocrine therapy for breast cancer. This report evaluates changes in subjective cognitive function (SCF). One hundred postmenopausal women, randomised to receive 5 years of adjuvant tamoxifen, letrozole, or a sequence of the two, completed self-reported measures on SCF, psychological distress, fatigue, and quality of life during the fifth year of trial treatment (year 5) and 1 year after treatment completion (year 6). Changes between years 5 and 6 were evaluated using the Wilcoxon signed-rank test. Subjective cognitive function and its correlates were explored. Subjective cognitive function and the other patient-reported outcomes did not change significantly after cessation of endocrine therapy with the exception of improvement for hot flushes (P=0.0005). No difference in changes was found between women taking tamoxifen or letrozole. Subjective cognitive function was the only psychosocial outcome with a substantial correlation between year 5 and 6 (Spearman's R=0.80). Correlations between SCF and the other patient-reported outcomes were generally low. Improved objective cognitive function but not SCF occur following cessation of adjuvant endocrine therapy in the BIG 1-98 trial. The substantial correlation of SCF scores over time may represent a stable attribute.

  5. Satellite-observed snow cover variations over the Tibetan Plateau for the period 2001-2014

    NASA Astrophysics Data System (ADS)

    Long, D.; Chen, X.

    2016-12-01

    Snow is an integral component of the global climate system. Owing to its high albedo and thermal and water storage properties, snow has important linkages and feedbacks through its influence on surface energy and moisture fluxes, clouds, precipitation, hydrology, and atmospheric circulation. As the "Roof of the World" and the "Third Pole" with the highest mountains in middle latitudes, the Tibetan Plateau (TP) is one of the most hot spots in climate change and hydrological studies, in which seasonal snow cover is a critical aspect. Unlike large-scale snow cover and regional-scale glaciers over other cryospheric regions, changes in snow cover over the TP has been largely unknown due mostly to the quality of observations. Based on improved MODIS daily snow cover products, this study aims to quantify the distribution and changes in snow cover over the TP for the period 2001 to 2014. Results show that the spatial distribution of changes in snow cover fraction (SCF) over the 14-year study period exhibited a general negative trend over the TP driven primarily by increasing land surface temperature (LST), except some areas of the upper Golden-Sanded River and upper Brahmaputra River basins. However, decreased LST and increased precipitation in the accumulation season (September to the following February) resulted in increased SCF in the accumulation season, coinciding with large-scale cold snaps and heavy snowfall events at middle latitudes. Detailed analyses of the intra-annual variability of SCF in the TP regions show an increase in SCF in the accumulation season but a decrease in SCF in the melting season (March to August), indicating that the intra-annual amplitude of SCF increased during the study period and more snow cover was released as snowmelt in the spring season.

  6. Regulation of flower development in Arabidopsis by SCF complexes.

    PubMed

    Ni, Weimin; Xie, Daoxin; Hobbie, Lawrence; Feng, Baomin; Zhao, Dazhong; Akkara, Joseph; Ma, Hong

    2004-04-01

    SCF complexes are the largest and best studied family of E3 ubiquitin protein ligases that facilitate the ubiquitylation of proteins targeted for degradation. The SCF core components Skp1, Cul1, and Rbx1 serve in multiple SCF complexes involving different substrate-specific F-box proteins that are involved in diverse processes including cell cycle and development. In Arabidopsis, mutations in the F-box gene UNUSUAL FLORAL ORGANS (UFO) result in a number of defects in flower development. However, functions of the core components Cul1 and Rbx1 in flower development are poorly understood. In this study we analyzed floral phenotypes caused by altering function of Cul1 or Rbx1, as well as the effects of mutations in ASK1 and ASK2. Plants homozygous for a point mutation in the AtCUL1 gene showed reduced floral organ number and several defects in each of the four whorls. Similarly, plants with reduced AtRbx1 expression due to RNA interference also exhibited floral morphological defects. In addition, compared to the ask1 mutant, plants homozygous for ask1 and heterozygous for ask2 displayed enhanced reduction of B function, as well as other novel defects of flower development, including carpelloid sepals and an inhibition of petal development. Genetic analyses demonstrate that AGAMOUS (AG) is required for the novel phenotypes observed in the first and second whorls. Furthermore, the genetic interaction between UFO and AtCUL1 supports the idea that UFO regulates multiple aspects of flower development as a part of SCF complexes. These results suggest that SCF complexes regulate several aspects of floral development in Arabidopsis.

  7. The regulatory effect of SC-236 (4-[5-(4-chlorophenyl)-3-(trifluoromethyl)-1-pyrazol-1-l] benzenesulfonamide) on stem cell factor induced migration of mast cells

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, Su-Jin; College of Oriental Medicine, Kyung Hee University, 1 Hoegi-Dong, Dongdaemun-Gu, Seoul 130-701; Jeong, Hyun-Ja

    SC-236 (4-[5-(4-chlorophenyl)-3-(trifluoromethyl)-1-pyrazol-1-]benzenesulfonamide; C{sub 16}H{sub 11}ClF{sub 3}N{sub 3}O{sub 2}S), is a highly selective cyclooxygenase (COX)-2 inhibitor. Recently, there have been reports that SC-236 protects against cartilage damage in addition to reducing inflammation and pain in osteoarthritis. However, the mechanism involved in the inflammatory allergic reaction has not been examined. Mast cells accumulation can be related to inflammatory conditions, including allergic rhinitis, asthma, and rheumatoid arthritis. The aim of the present study is to investigate the effects of SC-236 on stem cell factor (SCF)-induced migration, morphological alteration, and cytokine production of rat peritoneal mast cells (RPMCs). We observed that SCF significantly inducedmore » the migration and morphological alteration. The ability of SCF to enhance migration and morphological alteration was abolished by treatment with SC-236. In addition, production of tumor necrosis factor (TNF)-{alpha}, interleukin (IL)-1{beta}, and vascular endothelial growth factor (VEGF) production induced by SCF was significantly inhibited by treatment with SC-236. Previous work has demonstrated that SCF-induced migration and cytokine production of mast cells require p38 MAPK activation. We also showed that SC-236 suppresses the SCF-induced p38 MAPK activation in RPMCs. These data suggest that SC-236 inhibits migration and cytokine production through suppression of p38 MAPK activation. These results provided new insight into the pharmacological actions of SC-236 and its potential therapeutic role in the treatment of inflammatory allergic diseases.« less

  8. Genome-wide discovery of novel M1T1 group A streptococcal determinants important for fitness and virulence during soft-tissue infection

    PubMed Central

    Sundar, Ganesh S.; Islam, Emrul; Shirtliff, Mark E.

    2017-01-01

    The Group A Streptococcus remains a significant human pathogen causing a wide array of disease ranging from self-limiting to life-threatening invasive infections. Epithelium (skin or throat) colonization with progression to the subepithelial tissues is the common step in all GAS infections. Here, we used transposon-sequencing (Tn-seq) to define the GAS 5448 genetic requirements for in vivo fitness in subepithelial tissue. A near-saturation transposon library of the M1T1 GAS 5448 strain was injected subcutaneously into mice, producing suppurative inflammation at 24 h that progressed to prominent abscesses with tissue necrosis at 48 h. The library composition was monitored en masse by Tn-seq and ratios of mutant abundance comparing the output (12, 24 and 48 h) versus input (T0) mutant pools were calculated for each gene. We identified a total of 273 subcutaneous fitness (scf) genes with 147 genes (55 of unknown function) critical for the M1T1 GAS 5448 fitness in vivo; and 126 genes (53 of unknown function) potentially linked to in vivo fitness advantage. Selected scf genes were validated in competitive subcutaneous infection with parental 5448. Two uncharacterized genes, scfA and scfB, encoding putative membrane-associated proteins and conserved among Gram-positive pathogens, were further characterized. Defined scfAB mutants in GAS were outcompeted by wild type 5448 in vivo, attenuated for lesion formation in the soft tissue infection model and dissemination to the bloodstream. We hypothesize that scfAB play an integral role in enhancing adaptation and fitness of GAS during localized skin infection, and potentially in propagation to other deeper host environments. PMID:28832676

  9. Testing stem cell therapy in a rat model of inflammatory bowel disease: role of bone marrow stem cells and stem cell factor in mucosal regeneration.

    PubMed

    Qu, Bo; Xin, Guo-Rong; Zhao, Li-Xia; Xing, Hui; Lian, Li-Ying; Jiang, Hai-Yan; Tong, Jia-Zhao; Wang, Bei-Bei; Jin, Shi-Zhu

    2014-01-01

    The gastrointestinal (GI) mucosal cells turnover regularly under physiological conditions, which may be stimulated in various pathological situations including inflammation. Local epithelial stem cells appear to play a major role in such mucosal renewal or pathological regeneration. Less is clear about the involvement of multipotent stem cells from blood in GI repair. We attempted to explore a role of bone marrow mesenchymal stromal cells (BMMSCs) and soluble stem cell factor (SCF) in GI mucosa regeneration in a rat model of inflammatory bowel diseases (IBD). BMMSCs labelled with the fluorescent dye PKH26 from donor rats were transfused into rats suffering indomethacin-induced GI injury. Experimental effects by BMMSCs transplant and SCF were determined by morphometry of intestinal mucosa, double labeling of PKH26 positive BMMSCs with endogenous proliferative and intestinal cell markers, and western blot and PCR analyses of the above molecular markers in the recipient rats relative to controls. PKH26 positive BMMSCs were found in the recipient mucosa, partially colocalizing with the proliferating cell nuclear antigen (PCNA), Lgr5, Musashi-1 and ephrin-B3. mRNA and protein levels of PCNA, Lgr5, Musashi-1 and ephrin-B3 were elevated in the intestine in BMMSCs-treated rats, most prominent in the BMMSCs-SCF co-treatment group. The mucosal layer and the crypt layer of the small intestine were thicker in BMMSCs-treated rats, more evident in the BMMSCs-SCF co-treatment group. BMMSCs and SCF participate in but may play a synergistic role in mucosal cell regeneration following experimentally induced intestinal injury. Bone marrow stem cell therapy and SCF administration may be of therapeutic value in IBD.

  10. C-Kit Promotes Growth and Migration of Human Cardiac Progenitor Cells via the PI3K-AKT and MEK-ERK Pathways

    PubMed Central

    Al-Maqtari, Tareq; Cao, Pengxiao; Keith, Matthew C. L.; Wysoczynski, Marcin; Zhao, John; Moore IV, Joseph B.; Bolli, Roberto

    2015-01-01

    A recent phase I clinical trial (SCIPIO) has shown that autologous c-kit+ cardiac progenitor cells (CPCs) improve cardiac function and quality of life when transplanted into patients with ischemic heart disease. Although c-kit is widely used as a marker of resident CPCs, its role in the regulation of the cellular characteristics of CPCs remains unknown. We hypothesized that c-kit plays a role in the survival, growth, and migration of CPCs. To test this hypothesis, human CPCs were grown under stress conditions in the presence or absence of SCF, and the effects of SCF-mediated activation of c-kit on CPC survival/growth and migration were measured. SCF treatment led to a significant increase in cell survival and a reduction in cell death under serum depletion conditions. In addition, SCF significantly promoted CPC migration in vitro. Furthermore, the pro-survival and pro-migratory effects of SCF were augmented by c-kit overexpression and abrogated by c-kit inhibition with imatinib. Mechanistically, c-kit activation in CPCs led to activation of the PI3K and the MAPK pathways. With the use of specific inhibitors, we confirmed that the SCF/c-kit-dependent survival and chemotaxis of CPCs are dependent on both pathways. Taken together, our findings suggest that c-kit promotes the survival/growth and migration of human CPCs cultured ex vivo via the activation of PI3K and MAPK pathways. These results imply that the efficiency of CPC homing to the injury site as well as their survival after transplantation may be improved by modulating the activity of c-kit. PMID:26474484

  11. Systematic Expansion of Active Spaces beyond the CASSCF Limit: A GASSCF/SplitGAS Benchmark Study.

    PubMed

    Vogiatzis, Konstantinos D; Li Manni, Giovanni; Stoneburner, Samuel J; Ma, Dongxia; Gagliardi, Laura

    2015-07-14

    The applicability and accuracy of the generalized active space self-consistent field, (GASSCF), and (SplitGAS) methods are presented. The GASSCF method enables the exploration of larger active spaces than with the conventional complete active space SCF, (CASSCF), by fragmentation of a large space into subspaces and by controlling the interspace excitations. In the SplitGAS method, the GAS configuration interaction, CI, expansion is further partitioned in two parts: the principal, which includes the most important configuration state functions, and an extended, containing less relevant but not negligible ones. An effective Hamiltonian is then generated, with the extended part acting as a perturbation to the principal space. Excitation energies of ozone, furan, pyrrole, nickel dioxide, and copper tetrachloride dianion are reported. Various partitioning schemes of the GASSCF and SplitGAS CI expansions are considered and compared with the complete active space followed by second-order perturbation theory, (CASPT2), and multireference CI method, (MRCI), or available experimental data. General guidelines for the optimum applicability of these methods are discussed together with their current limitations.

  12. Fixed-pattern noise correction method based on improved moment matching for a TDI CMOS image sensor.

    PubMed

    Xu, Jiangtao; Nie, Huafeng; Nie, Kaiming; Jin, Weimin

    2017-09-01

    In this paper, an improved moment matching method based on a spatial correlation filter (SCF) and bilateral filter (BF) is proposed to correct the fixed-pattern noise (FPN) of a time-delay-integration CMOS image sensor (TDI-CIS). First, the values of row FPN (RFPN) and column FPN (CFPN) are estimated and added to the original image through SCF and BF, respectively. Then the filtered image will be processed by an improved moment matching method with a moving window. Experimental results based on a 128-stage TDI-CIS show that, after correcting the FPN in the image captured under uniform illumination, the standard deviation of row mean vector (SDRMV) decreases from 5.6761 LSB to 0.1948 LSB, while the standard deviation of the column mean vector (SDCMV) decreases from 15.2005 LSB to 13.1949LSB. In addition, for different images captured by different TDI-CISs, the average decrease of SDRMV and SDCMV is 5.4922/2.0357 LSB, respectively. Comparative experimental results indicate that the proposed method can effectively correct the FPNs of different TDI-CISs while maintaining image details without any auxiliary equipment.

  13. Protein Kinase R Degradation Is Essential for Rift Valley Fever Virus Infection and Is Regulated by SKP1-CUL1-F-box (SCF)FBXW11-NSs E3 Ligase.

    PubMed

    Mudhasani, Rajini; Tran, Julie P; Retterer, Cary; Kota, Krishna P; Whitehouse, Chris A; Bavari, Sina

    2016-02-01

    Activated protein kinase R (PKR) plays a vital role in antiviral defense primarily by inhibiting protein synthesis and augmenting interferon responses. Many viral proteins have adopted unique strategies to counteract the deleterious effects of PKR. The NSs (Non-structural s) protein which is encoded by Rift Valley fever virus (RVFV) promotes early PKR proteasomal degradation through a previously undefined mechanism. In this study, we demonstrate that NSs carries out this activity by assembling the SCF (SKP1-CUL1-F-box)(FBXW11) E3 ligase. NSs binds to the F-box protein, FBXW11, via the six amino acid sequence DDGFVE called the degron sequence and recruits PKR through an alternate binding site to the SCF(FBXW11) E3 ligase. We further show that disrupting the assembly of the SCF(FBXW11-NSs) E3 ligase with MLN4924 (a small molecule inhibitor of SCF E3 ligase activity) or NSs degron viral mutants or siRNA knockdown of FBXW11 can block PKR degradation. Surprisingly, under these conditions when PKR degradation was blocked, NSs was essential and sufficient to activate PKR causing potent inhibition of RVFV infection by suppressing viral protein synthesis. These antiviral effects were antagonized by the loss of PKR expression or with a NSs deleted mutant virus. Therefore, early PKR activation by disassembly of SCF(FBXW11-NSs) E3 ligase is sufficient to inhibit RVFV infection. Furthermore, FBXW11 and BTRC are the two homologues of the βTrCP (Beta-transducin repeat containing protein) gene that were previously described to be functionally redundant. However, in RVFV infection, among the two homologues of βTrCP, FBXW11 plays a dominant role in PKR degradation and is the limiting factor in the assembly of the SCF(FBXW11) complex. Thus, FBXW11 serves as a master regulator of RVFV infection by promoting PKR degradation. Overall these findings provide new insights into NSs regulation of PKR activity and offer potential opportunities for therapeutic intervention of RVFV infection.

  14. Assimilation of MODIS Snow Cover Through the Data Assimilation Research Testbed and the Community Land Model Version 4

    NASA Technical Reports Server (NTRS)

    Zhang, Yong-Fei; Hoar, Tim J.; Yang, Zong-Liang; Anderson, Jeffrey L.; Toure, Ally M.; Rodell, Matthew

    2014-01-01

    To improve snowpack estimates in Community Land Model version 4 (CLM4), the Moderate Resolution Imaging Spectroradiometer (MODIS) snow cover fraction (SCF) was assimilated into the Community Land Model version 4 (CLM4) via the Data Assimilation Research Testbed (DART). The interface between CLM4 and DART is a flexible, extensible approach to land surface data assimilation. This data assimilation system has a large ensemble (80-member) atmospheric forcing that facilitates ensemble-based land data assimilation. We use 40 randomly chosen forcing members to drive 40 CLM members as a compromise between computational cost and the data assimilation performance. The localization distance, a parameter in DART, was tuned to optimize the data assimilation performance at the global scale. Snow water equivalent (SWE) and snow depth are adjusted via the ensemble adjustment Kalman filter, particularly in regions with large SCF variability. The root-mean-square error of the forecast SCF against MODIS SCF is largely reduced. In DJF (December-January-February), the discrepancy between MODIS and CLM4 is broadly ameliorated in the lower-middle latitudes (2345N). Only minimal modifications are made in the higher-middle (4566N) and high latitudes, part of which is due to the agreement between model and observation when snow cover is nearly 100. In some regions it also reveals that CLM4-modeled snow cover lacks heterogeneous features compared to MODIS. In MAM (March-April-May), adjustments to snowmove poleward mainly due to the northward movement of the snowline (i.e., where largest SCF uncertainty is and SCF assimilation has the greatest impact). The effectiveness of data assimilation also varies with vegetation types, with mixed performance over forest regions and consistently good performance over grass, which can partly be explained by the linearity of the relationship between SCF and SWE in the model ensembles. The updated snow depth was compared to the Canadian Meteorological Center (CMC) data. Differences between CMC and CLM4 are generally reduced in densely monitored regions.

  15. SCF and CI calculations of the dipole moment function of ozone. [Self-Consistent Field and Configuration-Interaction

    NASA Technical Reports Server (NTRS)

    Curtiss, L. A.; Langhoff, S. R.; Carney, G. D.

    1979-01-01

    The constant and linear terms in a Taylor series expansion of the dipole moment function of the ground state of ozone are calculated with Cartesian Gaussian basis sets ranging in quality from minimal to double zeta plus polarization. Results are presented at both the self-consistent field and configuration-interaction levels. Although the algebraic signs of the linear dipole moment derivatives are all established to be positive, the absolute magnitudes of these quantities, as well as the infrared intensities calculated from them, vary considerably with the level of theory.

  16. AmeriFlux US-SCf Southern California Climate Gradient - Oak/Pine Forest

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goulden, Mike

    This is the AmeriFlux version of the carbon flux data for the site US-SCf Southern California Climate Gradient - Oak/Pine Forest. Site Description - Half hourly data are available at https://www.ess.uci.edu/~california/. This site is one of six Southern California Climate Gradient flux towers operated along an elevation gradient (sites are US-SCg, US-SCs, US-SCf, US-SCw, US-SCc, US-SCd). This site is a mixed oak/pine forest. The site experiences episodic severe drought and mortality, and has also experienced occasional logging and wildfire. Drought and mortality was especially severe in the early 2000s.

  17. Processing of polyphenolic composites with supercritical fluid anti-solvent technology

    NASA Astrophysics Data System (ADS)

    Kurniawansyah, Firman; Mammucari, Raffaella; Foster, Neil R.

    2017-05-01

    Polyphenols have been developed, primarily exploiting their robust antioxidant properties, for medical and food applications. In spite of their advantages, polyphenolic compounds have drawbacks from their natural characteristics of being poorly soluble in aqueous solutions, thermo-labile and low oral bioavailaibility. In this article, strategy of processing with supercritical fluid (SCF) anti-solvent to improve the shortcomings is overviewed. Information obtained from the existing studies commonly confirms SCF technology applicability to produce composites of polyphenols with various morphology, size distributions and crystallinity. The application of SCF technology also enables to develop polyphenolic composites for alternative drug delivery such as in the pulmonary administrations.

  18. Visible-Light-Promoted Trifluoromethylthiolation of Styrenes by Dual Photoredox/Halide Catalysis.

    PubMed

    Honeker, Roman; Garza-Sanchez, R Aleyda; Hopkinson, Matthew N; Glorius, Frank

    2016-03-18

    Herein, we report a new visible-light-promoted strategy to access radical trifluoromethylthiolation reactions by combining halide and photoredox catalysis. This approach allows for the synthesis of vinyl-SCF3 compounds of relevance in pharmaceutical chemistry directly from alkenes under mild conditions with irradiation from household light sources. Furthermore, alkyl-SCF3-containing cyclic ketone and oxindole derivatives can be accessed by radical-polar crossover semi-pinacol and cyclization processes. Inexpensive halide salts play a crucial role in activating the trifluoromethylthiolating reagent towards photoredox catalysis and aid the formation of the SCF3 radical. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Functional requirements document for the Earth Observing System Data and Information System (EOSDIS) Scientific Computing Facilities (SCF) of the NASA/MSFC Earth Science and Applications Division, 1992

    NASA Technical Reports Server (NTRS)

    Botts, Michael E.; Phillips, Ron J.; Parker, John V.; Wright, Patrick D.

    1992-01-01

    Five scientists at MSFC/ESAD have EOS SCF investigator status. Each SCF has unique tasks which require the establishment of a computing facility dedicated to accomplishing those tasks. A SCF Working Group was established at ESAD with the charter of defining the computing requirements of the individual SCFs and recommending options for meeting these requirements. The primary goal of the working group was to determine which computing needs can be satisfied using either shared resources or separate but compatible resources, and which needs require unique individual resources. The requirements investigated included CPU-intensive vector and scalar processing, visualization, data storage, connectivity, and I/O peripherals. A review of computer industry directions and a market survey of computing hardware provided information regarding important industry standards and candidate computing platforms. It was determined that the total SCF computing requirements might be most effectively met using a hierarchy consisting of shared and individual resources. This hierarchy is composed of five major system types: (1) a supercomputer class vector processor; (2) a high-end scalar multiprocessor workstation; (3) a file server; (4) a few medium- to high-end visualization workstations; and (5) several low- to medium-range personal graphics workstations. Specific recommendations for meeting the needs of each of these types are presented.

  20. Decreased number of interstitial cells of Cajal play an important role in the declined intestinal transit during cholesterol gallstone formation in guinea pigs fed on high cholesterol diet

    PubMed Central

    Fan, Ying; Wu, Shuo-Dong; Fu, Bei-Bei; Weng, Chao; Wang, Xin-Peng

    2014-01-01

    To study the changes of interstitial cells of Cajal (ICCs) and expression of c-kt and scf mRNA in terminal ileum tissue during cholesterol gallstone formation in guinea pigs fed on high cholesterol diet, forty guinea pigs were divided into the gallstone group and the control group. The animals in the gallstone group were fed on a high cholesterol diet (HCD), while those in the control group fed on a standard diet (StD). The guinea pigs were sacrificed at the 8th week. The expression of c-kit and scf in terminal ileum were determined by RT-PCR and the morphological characteristics and number of ICCs were observed and calculated by using immunohistochemistry. RT-PCR showed that, compared with the control group, the c-kit and scf mRNA expression levels in the gallstone group were significantly declined. In the animal assay, the decreased number of ICCs was present obviously in the gallstone group. We concluded from the study that decreased number of ICCs, decreased expression of c-kit and scf in terminal ileum are present in guinea pigs fed on high cholesterol diet. The c-kit/scf pathway inhibition might be involved in the decline of intestinal transit function during cholesterol gallstone formation. PMID:24995081

  1. The stem cell factor (SCF)/c-KIT signalling in testis and prostate cancer.

    PubMed

    Cardoso, Henrique J; Figueira, Marília I; Socorro, Sílvia

    2017-12-01

    The stem cell factor (SCF) is a cytokine that specifically binds the tyrosine kinase receptor c-KIT. The SCF/c-KIT interaction leads to receptor dimerization, activation of kinase activity and initiation of several signal transduction pathways that control cell proliferation, apoptosis, differentiation and migration in several tissues. The activity of SCF/c-KIT system is linked with the phosphatidylinositol 3-kinase (PI3-K), the Src, the Janus kinase/signal transducers and activators of transcription (JAK/STAT), the phospholipase-C (PLC-γ) and the mitogen-activated protein kinase (MAPK) pathways. Moreover, it has been reported that cancer cases display an overactivation of c-KIT due to the presence of gain-of-function mutations or receptor overexpression, which renders c-KIT a tempting target for cancer treatment. In the case of male cancers the most documented activated pathways are the PI3-K and Src, both enhancing abnormal cell proliferation. It is also known that the Src activity in prostate cancer cases depends on the presence of tr-KIT, the cytoplasmic truncated variant of c-KIT that is specifically expressed in tumour tissues and, thus, a very interesting target for drug development. The present review provides an overview of the signalling pathways activated by SCF/c-KIT and discusses the potential application of c-KIT inhibitors for treatment of testicular and prostatic cancers.

  2. The AtRbx1 protein is part of plant SCF complexes, and its down-regulation causes severe growth and developmental defects.

    PubMed

    Lechner, Esther; Xie, Daoxin; Grava, Sandrine; Pigaglio, Emmanuelle; Planchais, Severine; Murray, James A H; Parmentier, Yves; Mutterer, Jerome; Dubreucq, Bertrand; Shen, Wen-Hui; Genschik, Pascal

    2002-12-20

    Recently in yeast and animal cells, one particular class of ubiquitin ligase (E3), called the SCF, was demonstrated to regulate diverse processes including cell cycle and development. In plants SCF-dependent proteolysis is also involved in different developmental and hormonal regulations. To further investigate the function of SCF, we characterized at the molecular level the Arabidopsis RING-H2 finger protein AtRbx1. We demonstrated that the plant gene is able to functionally complement a yeast knockout mutant strain and showed that AtRbx1 protein interacts physically with at least two members of the Arabidopsis cullin family (AtCul1 and AtCul4). AtRbx1 also associates with AtCul1 and the Arabidopsis SKP1-related proteins in planta, indicating that it is part of plant SCF complexes. AtRbx1 mRNAs accumulate in various tissues of the plant, but at higher levels in tissues containing actively dividing cells. Finally to study the function of the gene in planta, we either overexpressed AtRbx1 or reduced its expression by a dsRNA strategy. Down-regulation of AtRbx1 impaired seedling growth and development, indicating that the gene is essential in plants. Furthermore, the AtRbx1-silenced plants showed a reduced level of AtCul1 protein, but accumulated higher level of cyclin D3.

  3. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jafarzadeh, S.; Rutten, R. J.; Szydlarski, M.

    A dense forest of slender bright fibrils near a small solar active region is seen in high-quality narrowband Ca ii H images from the SuFI instrument onboard the Sunrise balloon-borne solar observatory. The orientation of these slender Ca ii H fibrils (SCF) overlaps with the magnetic field configuration in the low solar chromosphere derived by magnetostatic extrapolation of the photospheric field observed with Sunrise/IMaX and SDO/HMI. In addition, many observed SCFs are qualitatively aligned with small-scale loops computed from a novel inversion approach based on best-fit numerical MHD simulation. Such loops are organized in canopy-like arches over quiet areas thatmore » differ in height depending on the field strength near their roots.« less

  4. 39 CFR 121.4 - Package Services.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Center Facility (SCF) turnaround Package Services mail accepted at the origin SCF before the day-zero...) Package Services mail accepted at origin before the day-zero Critical Entry Time is 3 days, for each... Center (NDC) Package Services mail accepted at origin before the day-zero Critical Entry Time is 4 days...

  5. 75 FR 18846 - Agency Recordkeeping/Reporting Requirements Under Emergency Review by the Office of Management...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-13

    ...: Strengthening Communities Fund Program Evaluation. OMB No.: New Collection. Description: This proposed information collection activity is to obtain evaluation information from Strengthening Communities Fund (SCF... authorized in the American Recovery and Reinvestment Act of 2009 (ARRA). The SCF evaluation is an important...

  6. 75 FR 16138 - Agency Recordkeeping/Reporting Requirements Under Emergency Review by the Office of Management...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-31

    ...: Strengthening Communities Fund Program Evaluation. OMB No.: New collection. Description: This proposed information collection activity is to obtain evaluation information from Strengthening Communities Fund (SCF... authorized in the American Recovery and Reinvestment Act of 2009 (ARPA). The SCF evaluation is an important...

  7. A new analysis of charge transfer and polarization for ligand-metal bonding - Model studies of Al4CO and Al4NH3

    NASA Technical Reports Server (NTRS)

    Bagus, P. S.; Hermann, K.; Bauschlicher, C. W., Jr.

    1984-01-01

    The nature of the bonding of CO and NH3 ligands to Al is analyzed, and the intra-unit charge polarization and inter-unit donation for the interaction of ligands with metals are studied. The consequences of metal-to-ligand and ligand-to-metal charge transfer are separately considered by performing a constrained space orbital variation (CSOV) with the electrons of the metal member of the complex in the field of frozen ligand. The electrons of the metal atoms are then frozen in the relaxed distribution given by the CSOV SCF wave function and the ligand electrons are allowed to relax. Quantitative measures of the importance of inter-unit charge transfers and intra-unit polarization are obtained using results of SCF studies of Al4CO and Al4NH3 clusters chosen to simulate the adsorption of the ligands at an on-top side of the Al(111) surface. The electrostatic attraction of the effective dipole moments of the metal and ligand units makes an important contribution to the bond.

  8. Using tethered triblock copolymers to mediate the interaction between substrates

    NASA Astrophysics Data System (ADS)

    Chern, Shyh-Shi; Zhulina, Ekaterina B.; Pickett, Galen T.; Balazs, Anna C.

    1998-04-01

    Using scaling analysis and a self-consistent field (SCF) theory, we compress two copolymer-coated surfaces and isolate conditions that yield multiple, distinct minima in the interaction profile. We focus on planar surfaces that are coated with ABC triblock copolymers. Tethered to the surface by the last monomer in the C block, the copolymers are grafted at relatively low densities. The surrounding solution is a poor solvent for both the A and C blocks, and is a good solvent for the B blocks. Through scaling theory, we pinpoint the parameters that yield two minima in the interaction profile. The SCF calculations reveal the changes in the morphology of the polymers as the layers are compressed. Through both studies, we determine how the morphological changes give rise to the observed surface interactions. The results provide guidelines for creating polymer-coated colloidal systems that can form two stable crystal structures. Such systems could be used for bistable, optical switches. The findings also yield a prescription for creating systems that exhibit additional minima in the free energy of interaction.

  9. Acceleration of High Angular Momentum Electron Repulsion Integrals and Integral Derivatives on Graphics Processing Units.

    PubMed

    Miao, Yipu; Merz, Kenneth M

    2015-04-14

    We present an efficient implementation of ab initio self-consistent field (SCF) energy and gradient calculations that run on Compute Unified Device Architecture (CUDA) enabled graphical processing units (GPUs) using recurrence relations. We first discuss the machine-generated code that calculates the electron-repulsion integrals (ERIs) for different ERI types. Next we describe the porting of the SCF gradient calculation to GPUs, which results in an acceleration of the computation of the first-order derivative of the ERIs. However, only s, p, and d ERIs and s and p derivatives could be executed simultaneously on GPUs using the current version of CUDA and generation of NVidia GPUs using a previously described algorithm [Miao and Merz J. Chem. Theory Comput. 2013, 9, 965-976.]. Hence, we developed an algorithm to compute f type ERIs and d type ERI derivatives on GPUs. Our benchmarks shows the performance GPU enable ERI and ERI derivative computation yielded speedups of 10-18 times relative to traditional CPU execution. An accuracy analysis using double-precision calculations demonstrates that the overall accuracy is satisfactory for most applications.

  10. Localized Symmetry Breaking for Tuning Thermal Expansion in ScF 3 Nanoscale Frameworks

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hu, Lei; Qin, Feiyu; Sanson, Andrea

    The local symmetry, beyond the averaged crystallographic structure, tends to bring unu-sual performances. Negative thermal expansion is a peculiar physical property of solids. Here, we report the delicate design of the localized symmetry breaking to achieve the controllable thermal expansion in ScF3 nano-scale frameworks. Intriguingly, an isotropic zero thermal expansion is concurrently engi-neered by localized symmetry breaking, with a remarkably low coefficient of thermal expansion of about +4.0×10-8/K up to 675K. This mechanism is investigated by the joint analysis of atomic pair dis-tribution function of synchrotron X-ray total scattering and extended X-ray absorption fine structure spectra. A localized rhombohedral distortionmore » presumably plays a critical role in stiffening ScF3 nano-scale frameworks and concomitantly suppressing transverse thermal vibrations of fluorine atoms. This physical scenario is also theoretically corroborated by the extinction of phonon modes with negative Grüneisen parameters in the rhombohedral ScF3. The present work opens an untraditional chemical modification to achieve controllable thermal expansion by breaking local symmetries of materials.« less

  11. The Ubiquitin Ligase SCF(Ucc1) Acts as a Metabolic Switch for the Glyoxylate Cycle.

    PubMed

    Nakatsukasa, Kunio; Nishimura, Takashi; Byrne, Stuart D; Okamoto, Michiyo; Takahashi-Nakaguchi, Azusa; Chibana, Hiroji; Okumura, Fumihiko; Kamura, Takumi

    2015-07-02

    Despite the crucial role played by the glyoxylate cycle in the virulence of pathogens, seed germination in plants, and sexual development in fungi, we still have much to learn about its regulation. Here, we show that a previously uncharacterized SCF(Ucc1) ubiquitin ligase mediates proteasomal degradation of citrate synthase in the glyoxylate cycle to maintain metabolic homeostasis in glucose-grown cells. Conversely, transcription of the F box subunit Ucc1 is downregulated in C2-compound-grown cells, which require increased metabolic flux for gluconeogenesis. Moreover, in vitro analysis demonstrates that oxaloacetate regenerated through the glyoxylate cycle induces a conformational change in citrate synthase and inhibits its recognition and ubiquitination by SCF(Ucc1), suggesting the existence of an oxaloacetate-dependent positive feedback loop that stabilizes citrate synthase. We propose that SCF(Ucc1)-mediated regulation of citrate synthase acts as a metabolic switch for the glyoxylate cycle in response to changes in carbon source, thereby ensuring metabolic versatility and flexibility. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Study of aerosol effect on accelerated snow melting over the Tibetan Plateau during boreal spring

    NASA Astrophysics Data System (ADS)

    Lee, Woo-Seop; Bhawar, Rohini L.; Kim, Maeng-Ki; Sang, Jeong

    2013-08-01

    In the present study, a coupled atmosphere-ocean global climate model (CSIRO-Mk3.6) is used to investigate the role of aerosol forcing agents as drivers of snow melting trends in the Tibetan Plateau (TP) region. Anthropogenic aerosol-induced snow cover changes in a warming climate are calculated from the difference between historical run (HIST) and all forcing except anthropogenic aerosol (NoAA). Absorbing aerosols can influence snow cover by warming the atmosphere, reducing snow reflectance after deposition. The warming the rate of snow melt, exposing darker surfaces below to short-wave radiation sooner, and allowing them to heat up even faster in the Himalayas and TP. The results show a strong spring snow cover decrease over TP when absorbing anthropogenic aerosol forcing is considered, whereas snow cover fraction (SCF) trends in NoAA are weakly negative (but insignificant) during 1951-2005. The enhanced spring snow cover trends in HIST are due to overall effects of different forcing agents: When aerosol forcing (AERO) is considered, a significant reduction of SCF than average can be found over the western TP and Himalayas. The large decreasing trends in SCF over the TP, with the maximum reduction of SCF around 12-15% over the western TP and Himalayas slope. Also accelerated snow melting during spring is due to effects of aerosol on snow albedo, where aerosol deposition cause decreases snow albedo. However, the SCF change in the “NoAA” simulations was observed to be less.

  13. Association of stem cell factor and high-sensitivity C reactive protein concentrations in crevicular fluid and serum in patients with chronic periodontitis with and without type 2 diabetes.

    PubMed

    Kalra, Nitish; Pradeep, Avani R; Priyanka, Ningappa; Kumari, Minal

    2013-03-01

    The aim of the present study was to clarify whether there is any correlation between the levels of high-sensitivity C reactive protein (hs-CRP) and stem cell factor (SCF) in serum and gingival crevicular fluid (GCF) of patients with chronic periodontitis (CP) with and without type 2 diabetes mellitus (DM). A total of 40 subjects were divided into 3 groups: 10 periodontally healthy subjects (Group 1), 15 CP patients (Group 2), and 15 type 2 DM patients with CP (Group 3). Levels of hs-CRP and SCF in GCF and serum were quantified using different techniques. The clinical outcomes evaluated were gingival index (GI), probing depth (PD) and clinical attachment level (CAL), and the correlations of the two inflammatory mediators with clinical parameters were evaluated. The levels of these inflammatory mediators increased continuously from group 1 to group 2, and to group 3. The serum levels of both hs-CRP and SCF were correlated with PD in patients with CP (P < 0.05). SCF levels were correlated with PD in Group 3 (P < 0.05). The fact that the levels of hs-CRP and SCF were highest in DM patients with CP suggests that the presence of a systemic condition has a profound effect on the levels of inflammatory mediators, both locally at sites of periodontal disease, and elsewhere.

  14. Dissolution enhancement of glibenclamide by solid dispersion: solvent evaporation versus a supercritical fluid-based solvent -antisolvent technique

    PubMed Central

    Tabbakhian, M.; Hasanzadeh, F.; Tavakoli, N.; Jamshidian, Z.

    2014-01-01

    Glibenclamide (GLIB) is a poorly soluble drug with formulation-dependent bioavailability. Therefore, we attempted in this study to improve GLIB dissolution rate by preparing drug solid dispersions by solvent evaporation (SE) and supercritical fluid solvent-antisolvent techniques (SCF-SAS). A D-optimal mixture design was used to investigate the effects of different ratios of HPMCE5 (50-100%), PEG6000 (0-40%), and Poloxamer407 (0-20%) on drug dissolution from different solid dispersion (SD) formulations prepared by SE. The ratios of carriers used in SCF-SAS method were HPMCE5 (fixed at 60%), PEG6000 (20-40%), and Poloxamer407 (0-20%). A constant drug: carrier weight ratio of 1:10 was used in all experiments. The SDs obtained were physically characterized and subjected to the dissolution study. The major GLIB bands in FTIR spectra were indicative of drug integrity. The reduced intensity and the fewer number of peaks observed in X-ray diffractograms (XRD) of GLIB formulations was the indicative of at least partial transformation of crystalline to amorphous GLIB. This change and/or dilution of drug in much higher amounts of carriers present caused disappearance of distinctive endothermic peaks in differential scanning calorimetry thermograms of GLIB formulations. The model generated according to the results of the D-optimal mixture design indicated that GLIB formulations comprising HPMC (50%-60%), PEG (34-40%), and poloxamer (6-10%) had enhanced dissolution performances. As compared to SE method, the SCF-SAS technique produced formulations of higher dissolution performances, likely due to the effects of solution and the supercritical CO2 (SC-CO2) on enhanced plasticization of polymers and thus increased diffusion of the drug into the polymer matrix. PMID:25657806

  15. Changes in mast cell number and stem cell factor expression in human skin after radiotherapy for breast cancer.

    PubMed

    Westbury, Charlotte B; Freeman, Alex; Rashid, Mohammed; Pearson, Ann; Yarnold, John R; Short, Susan C

    2014-05-01

    Mast cells are involved in the pathogenesis of radiation fibrosis and may be a therapeutic target. The mechanism of increased mast cell number in relation to acute and late tissue responses in human skin was investigated. Punch biopsies of skin 1 and 15-18 months after breast radiotherapy and a contralateral control biopsy were collected. Mast cells were quantified by immunohistochemistry using the markers c-Kit and tryptase. Stem cell factor (SCF) and collagen-1 expression was analysed by qRT-PCR. Clinical photographic scores were performed at post-surgical baseline and 18 months and 5 years post-radiotherapy. Primary human dermal microvascular endothelial cell (HDMEC) cultures were exposed to 2Gy ionising radiation and p53 and SCF expression was analysed by Western blotting and ELISA. Dermal mast cell numbers were increased at 1 (p=0.047) and 18 months (p=0.040) using c-Kit, and at 18 months (p=0.024) using tryptase immunostaining. Collagen-1 mRNA in skin was increased at 1 month (p=0.047) and 18 months (p=0.032) and SCF mRNA increased at 1 month (p=0.003). None of 16 cases scored had a change in photographic appearance at 5 years, compared to baseline. SCF expression was not increased in HDMECs irradiated in vitro. Increased mast cell number was associated with up-regulated collagen-1 expression in human skin at early and late time points. This increase could be secondary to elevated SCF expression at 1 month after radiotherapy. Although mast cells accumulate around blood vessels, no endothelial cell secretion of SCF was seen after in vitro irradiation. Modification of mast cell number and collagen-1 expression may be observed in skin at 1 and 18 months after radiotherapy in breast cancer patients with no change in photographic breast appearance at 5 years. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  16. Cationic aza-macrocyclic complexes of germanium(II) and silicon(IV).

    PubMed

    Everett, Matthew; Jolleys, Andrew; Levason, William; Light, Mark E; Pugh, David; Reid, Gillian

    2015-12-28

    [GeCl2(dioxane)] reacts with the neutral aza-macrocyclic ligands L, L = Me3tacn (1,4,7-trimethyl-1,4,7-triazacyclononane), Me4cyclen (1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane) or Me4cyclam (1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) and two mol. equiv. of Me3SiO3SCF3 in thf solution to yield the unusual and hydrolytically very sensitive [Ge(L)][O3SCF3]2 as white solids in moderate yield. Using shorter reaction times [Ge(Me3tacn)]Cl2 and [Ge(Me3tacn)]Cl[O3SCF3] were also isolated; the preparation of [Ge(Me4cyclen)][GeCl3]2 is also described. The structures of the Me3tacn complexes show κ(3)-coordination of the macrocycle, with the anions interacting only weakly to produce very distorted five- or six-coordination at germanium. In contrast, the structure of [Ge(Me4cyclen)][O3SCF3]2 shows no anion interactions, and a distorted square planar geometry at germanium from coordination to the tetra-aza macrocycle. Crystal structures of the Si(iv) complexes, [SiCl3(Me3tacn)]Y (Y = O3SCF3, BAr(F); [B{3,5-(CF3)2C6H3}4]) and [SiHCl2(Me3tacn)][BAr(F)], obtained from reaction of SiCl4 or SiHCl3 with Me3tacn, followed by addition of either Me3SiO3SCF3 or Na[BAr(F)], contain distorted octahedral cations, with facialκ(3)-coordinated Me3tacn. The open-chain triamine, Me2NCH2CH2N(Me)CH2CH2NMe2 (pmdta), forms [SiCl3(pmdta)][BAr(F)] and [SiBr3(pmdta)][BAr(F)] under similar conditions, containing mer-octahedral cations.

  17. Open-ended formulation of self-consistent field response theory with the polarizable continuum model for solvation.

    PubMed

    Di Remigio, Roberto; Beerepoot, Maarten T P; Cornaton, Yann; Ringholm, Magnus; Steindal, Arnfinn Hykkerud; Ruud, Kenneth; Frediani, Luca

    2016-12-21

    The study of high-order absorption properties of molecules is a field of growing importance. Quantum-chemical studies can help design chromophores with desirable characteristics. Given that most experiments are performed in solution, it is important to devise a cost-effective strategy to include solvation effects in quantum-chemical studies of these properties. We here present an open-ended formulation of self-consistent field (SCF) response theory for a molecular solute coupled to a polarizable continuum model (PCM) description of the solvent. Our formulation relies on the open-ended, density matrix-based quasienergy formulation of SCF response theory of Thorvaldsen, et al., [J. Chem. Phys., 2008, 129, 214108] and the variational formulation of the PCM, as presented by Lipparini et al., [J. Chem. Phys., 2010, 133, 014106]. Within the PCM approach to solvation, the mutual solute-solvent polarization is represented by means of an apparent surface charge (ASC) spread over the molecular cavity defining the solute-solvent boundary. In the variational formulation, the ASC is an independent, variational degree of freedom. This allows us to formulate response theory for molecular solutes in the fixed-cavity approximation up to arbitrary order and with arbitrary perturbation operators. For electric dipole perturbations, pole and residue analyses of the response functions naturally lead to the identification of excitation energies and transition moments. We document the implementation of this approach in the Dalton program package using a recently developed open-ended response code and the PCMSolver libraries and present results for one-, two-, three-, four- and five-photon absorption processes of three small molecules in solution.

  18. Spillway sizing of large dams in Austria

    NASA Astrophysics Data System (ADS)

    Reszler, Ch.; Gutknecht, D.; Blöschl, G.

    2003-04-01

    This paper discusses the basic philosophy of defining and calculating design floods for large dams in Austria, both for the construction of new dams and for a re-assessment of the safety of existing dams. Currently the consensus is to choose flood peak values corresponding to a probability of exceedance of 2*10-4 for a given year. A two step procedure is proposed to estimate the design flood discharges - a rapid assessment and a detailed assessment. In the rapid assessment the design discharge is chosen as a constant multiple of flood values read from a map of regionalised floods. The safety factor or multiplier takes care of the uncertainties of the local estimation and the regionalisation procedure. If the current design level of a spillway exceeds the value so estimated, no further calculations are needed. Otherwise (and for new dams) a detailed assessment is required. The idea of the detailed assessment is to draw upon all existing sources of information to constrain the uncertainties. The three main sources are local flood frequency analysis, where flood data are available; regional flood estimation from hydrologically similar catchments; and rainfall-runoff modelling using design storms as inputs. The three values obtained by these methods are then assessed and weighted in terms of their reliability to facilitate selection of the design flood. The uncertainty assessment of the various methods is based on confidence intervals, estimates of regional heterogeneity, data availability and sensitivity analyses of the rainfall-runoff model. As the definition of the design floods discussed above is based on probability concepts it is also important to examine the excess risk, i.e. the possibility of the occurrence of a flood exceeding the design levels. The excess risk is evaluated based on a so called Safety Check Flood (SCF), similar to the existing practice in other countries in Europe. The SCF is a vehicle to analyse the damage potential of an event of this magnitude. This is to provide guidance for protective measures to dealing with very extreme floods. The SCF is used to check the vulnerability of the system with regard to structural stability, morphological effects, etc., and to develop alarm plans and disaster mitigation procedures. The basis for estimating the SCF are the uncertainty assessments of the design flood values estimated by the three methods including unlikely combinations of the controlling factors and attending uncertainties. Finally we discuss the impact on the downstream valley of floods exceeding the design values and of smaller floods and illustrate the basic concepts by examples from the recent flood in August 2002.

  19. Ab initio study of excited state electronic circular dichroism. Two prototype cases: methyl oxirane and R-(+)-1,1'-bi(2-naphthol).

    PubMed

    Rizzo, Antonio; Vahtras, Olav

    2011-06-28

    A computational approach to the calculation of excited state electronic circular dichroism (ESECD) spectra of chiral molecules is discussed. Frequency dependent quadratic response theory is employed to compute the rotatory strength for transitions between excited electronic states, by employing both a magnetic gauge dependent and a (velocity-based) magnetic gauge independent approach. Application is made to the lowest excited states of two prototypical chiral molecules, propylene oxide, also known as 1,2-epoxypropane or methyl oxirane, and R-(+)-1,1'-bi(2-naphthol), or BINOL. The dependence of the rotatory strength for transitions between the lowest three excited states of methyl oxirane upon the quality and extension of the basis set is analyzed, by employing a hierarchy of correlation consistent basis sets. Once established that basis sets of at least triple zeta quality, and at least doubly augmented, are sufficient to ensure sufficiently converged results, at least at the Hartree-Fock self-consistent field (HF-SCF) level, the rotatory strengths for all transitions between the lowest excited electronic states of methyl oxirane are computed and analyzed, employing HF-SCF, and density functional theory (DFT) electronic structure models. For DFT, both the popular B3LYP and its recently highly successful CAM-B3LYP extension are exploited. The strong dependence of the spectra upon electron correlation is highlighted. A HF-SCF and DFT study is carried out also for BINOL, a system where excited states show the typical pairing structure arising from the interaction of the two monomeric moieties, and whose conformational changes following photoexcitation were studied recently with via time-resolved CD.

  20. Removing seed coat fragments with a lint cleaner grid bar air knife

    USDA-ARS?s Scientific Manuscript database

    Seed coat fragments (SCF) in ginned lint cause spinning problems at the textile mill and undesirable defects in finished goods. Work continued on developing an air knife that may help remove SCF from ginned lint. The air knife is mounted on the 1st lint cleaner grid bar of a saw-type lint cleaner,...

  1. A Logical Approach to the Statement of Cash Flows

    ERIC Educational Resources Information Center

    Petro, Fred; Gean, Farrell

    2014-01-01

    Of the three financial statements in financial reporting, the Statement of Cash Flows (SCF) is perhaps the most challenging. The most difficult aspect of the SCF is in developing an understanding of how previous transactions are finalized in this document. The purpose of this paper is to logically explain the indirect approach of cash flow whereby…

  2. Preparation of ceramic filler from reusing sewage sludge and application in biological aerated filter for soy protein secondary wastewater treatment.

    PubMed

    Wu, Suqing; Qi, Yuanfeng; Yue, Qinyan; Gao, Baoyu; Gao, Yue; Fan, Chunzhen; He, Shengbing

    2015-01-01

    Dehydrated sewage sludge (DSS) and clay used as raw materials for preparation of novel media-sludge ceramic filler (SCF) and SCF employed in a lab-scale up-flow biological aerated filter (BAF) were investigated for soy protein secondary wastewater treatment. Single factor experiments were designed to investigate the preparation of SCF, and the characteristics (microstructure properties, toxic metal leaching property and other physical properties) of SCF prepared under the optimum conditions were examined. The influences of media height, hydraulic retention time (HRT) and air-liquid ratio (A/L) on chemical oxygen demand (CODcr) and ammonia nitrogen (NH4(+)-N) removal rate were studied. The results showed that the optimum addition of DSS was approximately 25.0 wt% according to the physical properties of SCF (expansion ratio of 53.0%, v/v, water absorption of 8.24 wt%, bulk density of 350.4 kg m(-3) and grain density of 931.5 kg m(-3)), and the optimum conditions of BAF system were media height of 75.0 cm, HRT of 10.0 h and A/L of 15:1 in terms of CODcr and NH4(+)-N removal rate (91.02% and 90.48%, respectively). Additionally, CODcr and NH4(+)-N (81.6 and 15.3 mg L(-1), respectively) in the final effluent of BAF system met the national standard (CODcr ≤ 100 mg L(-1), NH4(+)-N ≤ 25.0 mg L(-1), GB 18918-2002, secondary standard). Copyright © 2014 Elsevier B.V. All rights reserved.

  3. 40 CFR 98.253 - Calculating GHG emissions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... a flare. 0.001 = Unit conversion factor (metric tons per kilogram, mt/kg). n = Number of measurement... average. MVC = Molar volume conversion factor (849.5 scf/kg-mole at 68 °F and 14.7 pounds per square inch... (kg/kg-mole). MVC = Molar volume conversion factor (849.5 scf/kg-mole at 68 °F and 14.7 psia or 836.6...

  4. 40 CFR 98.253 - Calculating GHG emissions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... a flare. 0.001 = Unit conversion factor (metric tons per kilogram, mt/kg). n = Number of measurement... average. MVC = Molar volume conversion factor (849.5 scf/kg-mole at 68 °F and 14.7 pounds per square inch... (kg/kg-mole). MVC = Molar volume conversion factor (849.5 scf/kg-mole at 68 °F and 14.7 psia or 836.6...

  5. 40 CFR 98.253 - Calculating GHG emissions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... a flare. 0.001 = Unit conversion factor (metric tons per kilogram, mt/kg). n = Number of measurement... average. MVC = Molar volume conversion factor (849.5 scf/kg-mole at 68 °F and 14.7 pounds per square inch... (kg/kg-mole). MVC = Molar volume conversion factor (849.5 scf/kg-mole at 68 °F and 14.7 psia or 836.6...

  6. 40 CFR 98.253 - Calculating GHG emissions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... a flare. 0.001 = Unit conversion factor (metric tons per kilogram, mt/kg). n = Number of measurement... average. MVC = Molar volume conversion factor (849.5 scf/kg-mole at 68 °F and 14.7 pounds per square inch... (kg/kg-mole). MVC = Molar volume conversion factor (849.5 scf/kg-mole at 68 °F and 14.7 psia or 836.6...

  7. The torsional energy profile of 1,2-diphenylethane: an ab initio study

    NASA Astrophysics Data System (ADS)

    Ivanov, Petko M.

    1997-08-01

    Ab initio molecular orbital calculations were carried out for the antiperiplanar (ap), the synclinal (sc), phenyl/phenyl eclipsed (syn barrier), and phenyl/H eclipsed (ap/sc barrier) conformations of 1,2-diphenylethane, and the energy ordering of conformations thus obtained was compared with the torsional energy profile estimated with the MM2 and MM3 molecular mechanics force fields. The basis set effect on the results was studied at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory, and the electron correlation energies were corrected by the second-order (MP2) Møller-Plesset perturbation treatment using the 6-31G * basis set. The performance of a DFT model (Becke-style three-parameter hybrid method using the correlation functional of Lee, Yang and Parr, B3LYP) was also tested to assess relative energies of the conformations using two basis sets, 6-31G * and 6-311G **. The RHF and B3LYP results are qualitatively the same, while the MP2 calculations produced significant differences in the geometries and reversed the order of preference for the antiperiplanar and the synclinal conformations.

  8. Stem cell factor and interleukin-2/15 combine to enhance MAPK-mediated proliferation of human natural killer cells

    PubMed Central

    Benson, Don M.; Yu, Jianhua; Becknell, Brian; Wei, Min; Freud, Aharon G.; Ferketich, Amy K.; Trotta, Rossana; Perrotti, Danilo; Briesewitz, Roger

    2009-01-01

    Stem cell factor (SCF) promotes synergistic cellular proliferation in combination with several growth factors, and appears important for normal natural killer (NK)–cell development. CD34+ hematopoietic precursor cells (HPCs) require interleukin-15 (IL-15) for differentiation into human NK cells, and this effect can be mimicked by IL-2. Culture of CD34+ HPCs or some primary human NK cells in IL-2/15 and SCF results in enhanced growth compared with either cytokine alone. The molecular mechanisms responsible for this are unknown and were investigated in the present work. Activation of NK cells by IL-2/15 increases expression of c-kit whose kinase activity is required for synergy with IL-2/15 signaling. Mitogen-activated protein kinase (MAPK) signaling intermediaries that are activated both by SCF and IL-2/15 are enhanced in combination to facilitate earlier cell-cycle entry. The effect results at least in part via enhanced MAPK-mediated modulation of p27 and CDK4. Collectively the data reveal a novel mechanism by which SCF enhances cellular proliferation in combination with IL-2/15 in primary human NK cells. PMID:19060242

  9. Self-Determination in Health Research: An Alaska Native Example of Tribal Ownership and Research Regulation

    PubMed Central

    Hiratsuka, Vanessa Y.; Beans, Julie A.; Robinson, Renee F.; Shaw, Jennifer L.; Sylvester, Ileen; Dillard, Denise A.

    2017-01-01

    Alaska Native (AN) and American Indian (AI) people are underrepresented in health research, yet many decline to participate in studies due to past researcher misconduct. Southcentral Foundation (SCF), an Alaska Native-owned and operated health care organization, is transforming the relationship between researchers and the tribal community by making trust and accountability required features of health research in AN/AI communities. In 1998, SCF assumed ownership from the federal government of health services for AN/AI people in south central Alaska and transformed the health system into a relationship-based model of care. This change reimagines how researchers interact with tribal communities and established community oversight of all health research conducted with AN/AI people in the region. We describe the SCF research review process, which requires tribal approval of the research concept, full proposal, and dissemination products, as well as local institutional review board approval, and a researcher-signed contract. This review evaluates research through the lens of tribal principles, practices, and priorities. The SCF example provides a framework for other tribes and organizations seeking to reshape the future of health research in AN/AI communities. PMID:29088111

  10. Transitioning NWChem to the Next Generation of Manycore Machines

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bylaska, Eric J.; Apra, Edoardo; Kowalski, Karol

    The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM,more » AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.« less

  11. Molecular simulation of CO chemisorption on Co(0001) in presence of supercritical fluid solvent: A potential of mean force study

    NASA Astrophysics Data System (ADS)

    Asiaee, Alireza; Benjamin, Kenneth M.

    2016-08-01

    For several decades, heterogeneous catalytic processes have been improved through utilizing supercritical fluids (SCFs) as solvents. While numerous experimental studies have been established across a range of chemistries, such as oxidation, pyrolysis, amination, and Fischer-Tropsch synthesis, still there is little fundamental, molecular-level information regarding the role of the SCF on elementary heterogeneous catalytic steps. In this study, the influence of hexane solvent on the adsorption of carbon monoxide on Co(0001), as the first step in the reaction mechanism of many processes involving syngas conversion, is probed. Simulations are performed at various bulk hexane densities, ranging from ideal gas conditions (no SCF hexane) to various near- and super-critical hexane densities. For this purpose, both density functional theory and molecular dynamics simulations are employed to determine the adsorption energy and free energy change during CO chemisorption. Potential of mean force calculations, utilizing umbrella sampling and the weighted histogram analysis method, provide the first commentary on SCF solvent effects on the energetic aspects of the chemisorption process. Simulation results indicate an enhanced stability of CO adsorption on the catalyst surface in the presence of supercritical hexane within the reduced pressure range of 1.0-1.5 at a constant temperature of 523 K. Furthermore, it is shown that the maximum stability of CO in the adsorbed state as a function of supercritical hexane density at 523 K nearly coincides with the maximum isothermal compressibility of bulk hexane at this temperature.

  12. Evaluation of Non-Ozone-Depleting-Chemical Cleaning Methods for Space Mechanisms Using a Vacuum Spiral Orbit Rolling Contact Tribometer

    NASA Technical Reports Server (NTRS)

    Jansen, Mark J.; Jones, William R., Jr.; Wheeler, Donald R.; Keller, Dennis J.

    2000-01-01

    Because CFC 113, an ozone depleting chemical (ODC), can no longer be produced, alternative bearing cleaning methods must be studied. The objective of this work was to study the effect of the new cleaning methods on lubricant lifetime using a vacuum bearing simulator (spiral orbit rolling contact tribometer). Four alternative cleaning methods were studied: ultra-violet (UV) ozone, aqueous levigated alumina slurry (ALAS), super critical fluid (SCF) CO2 and aqueous Brulin 815GD. Baseline tests were done using CFC 113. Test conditions were the following: a vacuum of at least 1.3 x 10(exp -6) Pa, 440C steel components, a rotational speed of 10 RPM, a lubricant charge of between 60-75 micrograms, a perfluoropolyalkylether lubricant (Z-25), and a load of 200N (44.6 lbs., a mean Hertzian stress of 1.5 GPa). Normalized lubricant lifetime was determined by dividing the total number of ball orbits by the amount of lubricant. The failure condition was a friction coefficient of 0.38. Post-test XPS analysis was also performed, showing slight variations in post-cleaning surface chemistry. Statistical analysis of the resultant data was conducted and it was determined that the data sets were most directly comparable when subjected to a natural log transformation. The natural log life (NL-Life) data for each cleaning method were reasonably normally (statistically) distributed and yielded standard deviations that were not significantly different among the five cleaning methods investigated. This made comparison of their NL-Life means very straightforward using a Bonferroni multiple comparison of means procedure. This procedure showed that the ALAS, UV-ozone and CFC 113 methods were not statistically significantly different from one another with respect to mean NL-Life. It also found that the SCF CO2 method yielded a significantly higher mean NL-Life than the mean NL-Lives of the ALAS, UV-ozone and CFC 113 methods. It also determined that the aqueous Brulin 815GD method yielded a mean NL-Life that was statistically significantly higher than the mean NL-Lives of each of the other four methods. Baseline tests using CFC 113 cleaned parts yielded a mean NL-Life 3.62 orbits/micro-g. ALAS and UV-ozone yielded similar mean NL-Life (3.31 orbits/mg and 3.33 orbits/micro-g, respectively). SCF CO2, gave a mean NL-Life of 4.08 orbits/mg and aqueous Brulin 8l5GD data yielded the longest mean NL-Life (4.66 orbits/micro-g).

  13. The 3d Rydberg (3A2) electronic state observed by Herzberg and Shoosmith for methylene

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Yukio; Schaefer, Henry F., III

    1997-06-01

    In 1959 and 1961 Herzberg and Shoosmith reported the vacuum ultraviolet spectrum of the triplet state of CH2. The present study focuses on a characterization of the upper state, the 3d Rydberg (3A2) state, observed at 1415 Å. The theoretical interpretation of these experiments is greatly complicated by the presence of a lower-lying 3A2 valence state with a very small equilibrium bond angle. Ab initio electronic structure methods involving self-consistent-field (SCF), configuration interaction with single and double excitations (CISD), complete active space (CAS) SCF, state-averaged (SA) CASSCF, coupled cluster with single and double excitations (CCSD), CCSD with perturbative triple excitations [CCSD(T)], CASSCF second-order (SO) CI, and SACASSCF-SOCI have been employed with six distinct basis sets. With the largest basis set, triple zeta plus triple polarization with two sets of higher angular momentum functions and three sets of diffuse functions TZ3P(2 f,2d)+3diff, the CISD level of theory predicts the equilibrium geometry of the 3d Rydberg (3A2) state to be re=1.093 Å and θe=141.3 deg. With the same basis set the energy (Te value) of the 3d Rydberg state relative to the ground (X˜ 3B1) state has been determined to be 201.6 kcal mol-1 (70 500 cm-1) at the CCSD (T) level, 200.92kcal mol-1 (70 270 cm-1) at the CASSCF-SOCI level, and 200.89kcal mol-1 (70 260 cm-1) at the SACASSCF-SOCI level of theory. These predictions are in excellent agreement with the experimental T0 value of 201.95 kcalmol-1 (70 634 cm-1) reported by Herzberg.

  14. Characterization of a mast cell line that lacks the extracellular domain of membrane c-kit.

    PubMed

    Mekori, Y A; Oh, C K; Dastych, J; Goff, J P; Adachi, S; Bianchine, P J; Worobec, A; Semere, T; Pierce, J H; Metcalfe, D D

    1997-04-01

    Expression of the c-kit proto-oncogene receptor on mast cells is essential for their normal proliferation and maturation as well as for several biological responses such as chemotaxis and attachment. In the present study we report that the interleukin-3 (IL-3)-dependent mast cell line CFTL-15 lacks the extracellular domain of the c-kit receptor. This observation was made after noting that the c-kit ligand stem cell factor (SCF) could not prevent IL-3 deprivation-induced mast cell apoptosis and that CFTL-15 cells did not proliferate in response to SCF. Flow cytometric analysis employing monoclonal anti-c-kit antibodies, and immunogold labelling with analysis by electron microscopy, subsequently showed a diminished expression of c-kit on CFTL-15 cells. There was no identifiable message for the extracellular domain of c-kit in these cells, as determined by reverse transcriptase-polymerase chain reaction (RT-PCR). These previously unrecognized properties of the CFTL-15 mast cell line allowed the examination of other biological consequences of the lack of c-kit on mast cells. Analysing the ability of these cells to adhere to surface-bound fibronectin, it was found that addition of SCF did not increase their adhesion to this substrate, in opposition to what is reported with other mast cells. Similarly, CFTL-15 mast cells did not adhere to fibroblasts, which is known to require c-kit expression. Also, there was no protein tyrosine phosphorylation in these cells in response to SCF. CFTL-15 cells underwent apoptosis on removal of IL-3 coincident with a decrease in endogenous Bcl-2 mRNA. Overexpression of Bcl-2 cDNA prolonged survival of Bcl-2-transfected CFTL-15 cells upon withdrawal of IL-3. Thus, the CFTL-15 cell line that lacks surface c-kit is not able to proliferate in response to SCF, undergoes apoptosis in the presence of SCF, and does not adhere to fibroblasts. These results confirm earlier studies on the functional consequences of c-kit and provide a novel experimental model for further investigation.

  15. Characterization of a mast cell line that lacks the extracellular domain of membrane c-kit.

    PubMed Central

    Mekori, Y A; Oh, C K; Dastych, J; Goff, J P; Adachi, S; Bianchine, P J; Worobec, A; Semere, T; Pierce, J H; Metcalfe, D D

    1997-01-01

    Expression of the c-kit proto-oncogene receptor on mast cells is essential for their normal proliferation and maturation as well as for several biological responses such as chemotaxis and attachment. In the present study we report that the interleukin-3 (IL-3)-dependent mast cell line CFTL-15 lacks the extracellular domain of the c-kit receptor. This observation was made after noting that the c-kit ligand stem cell factor (SCF) could not prevent IL-3 deprivation-induced mast cell apoptosis and that CFTL-15 cells did not proliferate in response to SCF. Flow cytometric analysis employing monoclonal anti-c-kit antibodies, and immunogold labelling with analysis by electron microscopy, subsequently showed a diminished expression of c-kit on CFTL-15 cells. There was no identifiable message for the extracellular domain of c-kit in these cells, as determined by reverse transcriptase-polymerase chain reaction (RT-PCR). These previously unrecognized properties of the CFTL-15 mast cell line allowed the examination of other biological consequences of the lack of c-kit on mast cells. Analysing the ability of these cells to adhere to surface-bound fibronectin, it was found that addition of SCF did not increase their adhesion to this substrate, in opposition to what is reported with other mast cells. Similarly, CFTL-15 mast cells did not adhere to fibroblasts, which is known to require c-kit expression. Also, there was no protein tyrosine phosphorylation in these cells in response to SCF. CFTL-15 cells underwent apoptosis on removal of IL-3 coincident with a decrease in endogenous Bcl-2 mRNA. Overexpression of Bcl-2 cDNA prolonged survival of Bcl-2-transfected CFTL-15 cells upon withdrawal of IL-3. Thus, the CFTL-15 cell line that lacks surface c-kit is not able to proliferate in response to SCF, undergoes apoptosis in the presence of SCF, and does not adhere to fibroblasts. These results confirm earlier studies on the functional consequences of c-kit and provide a novel experimental model for further investigation. Images Figure 4 Figure 6 Figure 7 Figure 8 PMID:9176104

  16. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

    PubMed

    Sodt, Alexander J; Mei, Ye; König, Gerhard; Tao, Peng; Steele, Ryan P; Brooks, Bernard R; Shao, Yihan

    2015-03-05

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

  17. Ectromelia virus encodes a novel family of F-box proteins that interact with the SCF complex.

    PubMed

    van Buuren, Nick; Couturier, Brianne; Xiong, Yue; Barry, Michele

    2008-10-01

    Poxviruses are notorious for encoding multiple proteins that regulate cellular signaling pathways, including the ubiquitin-proteasome system. Bioinformatics indicated that ectromelia virus, the causative agent of lethal mousepox, encoded four proteins, EVM002, EVM005, EVM154, and EVM165, containing putative F-box domains. In contrast to cellular F-box proteins, the ectromelia virus proteins contain C-terminal F-box domains in conjunction with N-terminal ankyrin repeats, a combination that has not been previously reported for cellular proteins. These observations suggested that the ectromelia virus F-box proteins interact with SCF (Skp1, cullin-1, and F-box) ubiquitin ligases. We focused our studies on EVM005, since this protein had only one ortholog in cowpox virus. Using mass spectrometry, we identified cullin-1 as a binding partner for EVM005, and this interaction was confirmed by overexpression of hemagglutinin (HA)-cullin-1. During infection, Flag-EVM005 and HA-cullin-1 colocalized to distinct cellular bodies. Significantly, EVM005 coprecipitated with endogenous Skp1, cullin-1, and Roc1 and associated with conjugated ubiquitin, suggesting that EVM005 interacted with the components of a functional ubiquitin ligase. Interaction of EVM005 with cullin-1 and Skp1 was abolished upon deletion of the F-box, indicating that the F-box played a crucial role in interaction with the SCF complex. Additionally, EVM002 and EVM154 interacted with Skp1 and conjugated ubiquitin, suggesting that ectromelia virus encodes multiple F-box-containing proteins that regulate the SCF complex. Our results indicate that ectromelia virus has evolved multiple proteins that interact with the SCF complex.

  18. Double-stranded DNA breaks hidden in the neutral Comet assay suggest a role of the sperm nuclear matrix in DNA integrity maintenance

    PubMed Central

    Ribas-Maynou, J.; Gawecka, J.E.; Benet, J.; Ward, W.S.

    2014-01-01

    We used a mouse model in which sperm DNA damage was induced to understand the relationship of double-stranded DNA (dsDNA) breaks to sperm chromatin structure and to the Comet assay. Sperm chromatin fragmentation (SCF) produces dsDNA breaks located on the matrix attachment regions, between protamine toroids. In this model, epididymal sperm induced to undergo SCF can religate dsDNA breaks while vas deferens sperm cannot. Here, we demonstrated that the conventional neutral Comet assay underestimates the epididymal SCF breaks because the broken DNA ends remain attached to the nuclear matrix, causing the DNA to remain associated with the dispersion halo, and the Comet tails to be weak. Therefore, we term these hidden dsDNA breaks. When the Comet assay was modified to include an additional incubation with sodium dodecyl sulfate (SDS) and dithiothreitol (DTT) after the conventional lysis, thereby solubilizing the nuclear matrix, the broken DNA was released from the matrix, which resulted in a reduction of the sperm head halo and an increase in the Comet tail length, exposing the hidden dsDNA breaks. Conversely, SCF-induced vas deferens sperm had small halos and long tails with the conventional neutral Comet assay, suggesting that the broken DNA ends were not tethered to the nuclear matrix. These results suggest that the attachment to the nuclear matrix is crucial for the religation of SCF-induced DNA breaks in sperm. Our data suggest that the neutral Comet assay identifies only dsDNA breaks that are released from the nuclear matrix and that the addition of an SDS treatment can reveal these hidden dsDNA breaks. PMID:24282283

  19. Double-stranded DNA breaks hidden in the neutral Comet assay suggest a role of the sperm nuclear matrix in DNA integrity maintenance.

    PubMed

    Ribas-Maynou, J; Gawecka, J E; Benet, J; Ward, W S

    2014-04-01

    We used a mouse model in which sperm DNA damage was induced to understand the relationship of double-stranded DNA (dsDNA) breaks to sperm chromatin structure and to the Comet assay. Sperm chromatin fragmentation (SCF) produces dsDNA breaks located on the matrix attachment regions, between protamine toroids. In this model, epididymal sperm induced to undergo SCF can religate dsDNA breaks while vas deferens sperm cannot. Here, we demonstrated that the conventional neutral Comet assay underestimates the epididymal SCF breaks because the broken DNA ends remain attached to the nuclear matrix, causing the DNA to remain associated with the dispersion halo, and the Comet tails to be weak. Therefore, we term these hidden dsDNA breaks. When the Comet assay was modified to include an additional incubation with sodium dodecyl sulfate (SDS) and dithiothreitol (DTT) after the conventional lysis, thereby solubilizing the nuclear matrix, the broken DNA was released from the matrix, which resulted in a reduction of the sperm head halo and an increase in the Comet tail length, exposing the hidden dsDNA breaks. Conversely, SCF-induced vas deferens sperm had small halos and long tails with the conventional neutral Comet assay, suggesting that the broken DNA ends were not tethered to the nuclear matrix. These results suggest that the attachment to the nuclear matrix is crucial for the religation of SCF-induced DNA breaks in sperm. Our data suggest that the neutral Comet assay identifies only dsDNA breaks that are released from the nuclear matrix and that the addition of an SDS treatment can reveal these hidden dsDNA breaks.

  20. Prebiotic Potential of a Maize-Based Soluble Fibre and Impact of Dose on the Human Gut Microbiota.

    PubMed

    Costabile, Adele; Deaville, Eddie R; Morales, Agustin Martin; Gibson, Glenn R

    2016-01-01

    Dietary management of the human gut microbiota towards a more beneficial composition is one approach that may improve host health. To date, a large number of human intervention studies have demonstrated that dietary consumption of certain food products can result in significant changes in the composition of the gut microbiota i.e. the prebiotic concept. Thus the prebiotic effect is now established as a dietary approach to increase beneficial gut bacteria and it has been associated with modulation of health biomarkers and modulation of the immune system. Promitor™ Soluble Corn Fibre (SCF) is a well-known maize-derived source of dietary fibre with potential selective fermentation properties. Our aim was to determine the optimum prebiotic dose of tolerance, desired changes to microbiota and fermentation of SCF in healthy adult subjects. A double-blind, randomised, parallel study was completed where volunteers (n = 8/treatment group) consumed 8, 14 or 21 g from SCF (6, 12 and 18 g/fibre delivered respectively) over 14-d. Over the range of doses studied, SCF was well tolerated Numbers of bifidobacteria were significantly higher for the 6 g/fibre/day compared to 12 g and 18 g/fibre delivered/day (mean 9.25 and 9.73 Log10 cells/g fresh faeces in the pre-treatment and treatment periods respectively). Such a numerical change of 0.5 Log10 bifidobacteria/g fresh faeces is consistent with those changes observed for inulin-type fructans, which are recognised prebiotics. A possible prebiotic effect of SCF was therefore demonstrated by its stimulation of bifidobacteria numbers in the overall gut microbiota during a short-term intervention.

  1. Medium-chain triglycerides in infant formulas and their relation to plasma ketone body concentrations.

    PubMed

    Wu, P Y; Edmond, J; Auestad, N; Rambathla, S; Benson, J; Picone, T

    1986-04-01

    A mild ketosis is known to prevail in the mother, fetus, and newborn infant during the 3rd trimester and in the early neonatal period. It has been shown that during an equivalent period in the rat ketone bodies are readily oxidized and serve as key substrates for lipogenesis in brain. Since medium-chain triglycerides are known to be ketogenic, preterm infants may benefit from dietary medium-chain triglycerides beyond the point of enhanced fat absorption. Our objective was to determine the ketogenic response in preterm infants (gestational age: 33 +/- 0.8 wk) fed three different isocaloric formulas by measuring the concentrations of 3-hydroxybutyrate and acetoacetate in the plasma of these infants. At the time of entrance to the study the infants were receiving 110 kcal/kg/24 h. Study I (11 infants): the infants were fed sequentially in the order; PM 60/40 (PM), Special Care Formula (SCF), and Similac 20 (SIM). In SCF greater than 50% of the fat consists of medium-chain length fatty acids while PM and SIM contain about 25%. The concentration of 3-hydroxybutyrate in plasma was significantly higher when infants were fed SCF than PM and SIM [0.14 +/- 0.03, 0.06 +/- 0.01, and 0.05 +/- 0.01 mM, respectively (p less than 0.01)]. Study II (12 infants); the infants were fed SCF, then SIM, or the reverse. The concentration of acetoacetate in plasma was 0.05 +/- 0.01 and 0.03 +/- 0.01 mM when infants were fed SCF and SIM, respectively (0.1 greater than p greater than 0.05). The concentrations of 3-hydroxybutyrate in plasma were similar to those measured in study I for the respective formulas.(ABSTRACT TRUNCATED AT 250 WORDS)

  2. Rice black streaked dwarf virus P7-2 forms a SCF complex through binding to Oryza sativa SKP1-like proteins, and interacts with GID2 involved in the gibberellin pathway.

    PubMed

    Tao, Tao; Zhou, Cui-Ji; Wang, Qian; Chen, Xiang-Ru; Sun, Qian; Zhao, Tian-Yu; Ye, Jian-Chun; Wang, Ying; Zhang, Zong-Ying; Zhang, Yong-Liang; Guo, Ze-Jian; Wang, Xian-Bing; Li, Da-Wei; Yu, Jia-Lin; Han, Cheng-Gui

    2017-01-01

    As a core subunit of the SCF complex that promotes protein degradation through the 26S proteasome, S-phase kinase-associated protein 1 (SKP1) plays important roles in multiple cellular processes in eukaryotes, including gibberellin (GA), jasmonate, ethylene, auxin and light responses. P7-2 encoded by Rice black streaked dwarf virus (RBSDV), a devastating viral pathogen that causes severe symptoms in infected plants, interacts with SKP1 from different plants. However, whether RBSDV P7-2 forms a SCF complex and targets host proteins is poorly understood. In this study, we conducted yeast two-hybrid assays to further explore the interactions between P7-2 and 25 type I Oryza sativa SKP1-like (OSK) proteins, and found that P7-2 interacted with eight OSK members with different binding affinity. Co-immunoprecipitation assay further confirmed the interaction of P7-2 with OSK1, OSK5 and OSK20. It was also shown that P7-2, together with OSK1 and O. sativa Cullin-1, was able to form the SCF complex. Moreover, yeast two-hybrid assays revealed that P7-2 interacted with gibberellin insensitive dwarf2 (GID2) from rice and maize plants, which is essential for regulating the GA signaling pathway. It was further demonstrated that the N-terminal region of P7-2 was necessary for the interaction with GID2. Overall, these results indicated that P7-2 functioned as a component of the SCF complex in rice, and interaction of P7-2 with GID2 implied possible roles of the GA signaling pathway during RBSDV infection.

  3. Polyubiquitination of the B-cell translocation gene 1 and 2 proteins is promoted by the SCF ubiquitin ligase complex containing βTrCP.

    PubMed

    Sasajima, Hitoshi; Nakagawa, Koji; Kashiwayanagi, Makoto; Yokosawa, Hideyoshi

    2012-01-01

    B-cell translocation gene 1 and 2 (BTG1 and BTG2) are members of the BTG/Tob antiproliferative protein family, which is able to regulate the cell cycle and cell proliferation. We previously reported that BTG1, BTG2, Tob, and Tob2 are degraded via the ubiquitin-proteasome pathway. In this study, we investigated the mechanism of polyubiquitination of BTG1 and BTG2. Since the Skp1-Cdc53/Cullin 1-F-box protein (SCF) complex functions as one of the major ubiquitin ligases for cell cycle regulation, we first examined interactions between BTG proteins and components of the SCF complex, and found that BTG1 and BTG2 were capable of interacting with the SCF complex containing Cullin-1 (a scaffold protein) and Skp1 (a linker protein). As the SCF complex can ubiquitinate various target proteins by substituting different F-box proteins as subunits that recognize different target proteins, we next examined which F-box proteins could bind the two BTG proteins, and found that Skp2, β-transducin repeat-containing protein 1 (βTrCP1), and βTrCP2 were able to associate with both BTG1 and BTG2. Furthermore, we obtained evidence showing that βTrCP1 enhanced the polyubiquitination of both BTG1 and BTG2 more efficiently than Skp2 did, and that an F-box truncated mutant of βTrCP1 had a dominant negative effect on this polyubiquitination. Thus, we propose that BTG1 and BTG2 are subjected to polyubiquitination, more efficiently when it is mediated by SCFβTrCP than by SCFSkp2.

  4. Rice black streaked dwarf virus P7-2 forms a SCF complex through binding to Oryza sativa SKP1-like proteins, and interacts with GID2 involved in the gibberellin pathway

    PubMed Central

    Wang, Qian; Chen, Xiang-Ru; Sun, Qian; Zhao, Tian-Yu; Ye, Jian-Chun; Wang, Ying; Zhang, Zong-Ying; Zhang, Yong-Liang; Guo, Ze-Jian; Wang, Xian-Bing; Li, Da-Wei; Yu, Jia-Lin

    2017-01-01

    As a core subunit of the SCF complex that promotes protein degradation through the 26S proteasome, S-phase kinase-associated protein 1 (SKP1) plays important roles in multiple cellular processes in eukaryotes, including gibberellin (GA), jasmonate, ethylene, auxin and light responses. P7-2 encoded by Rice black streaked dwarf virus (RBSDV), a devastating viral pathogen that causes severe symptoms in infected plants, interacts with SKP1 from different plants. However, whether RBSDV P7-2 forms a SCF complex and targets host proteins is poorly understood. In this study, we conducted yeast two-hybrid assays to further explore the interactions between P7-2 and 25 type I Oryza sativa SKP1-like (OSK) proteins, and found that P7-2 interacted with eight OSK members with different binding affinity. Co-immunoprecipitation assay further confirmed the interaction of P7-2 with OSK1, OSK5 and OSK20. It was also shown that P7-2, together with OSK1 and O. sativa Cullin-1, was able to form the SCF complex. Moreover, yeast two-hybrid assays revealed that P7-2 interacted with gibberellin insensitive dwarf2 (GID2) from rice and maize plants, which is essential for regulating the GA signaling pathway. It was further demonstrated that the N-terminal region of P7-2 was necessary for the interaction with GID2. Overall, these results indicated that P7-2 functioned as a component of the SCF complex in rice, and interaction of P7-2 with GID2 implied possible roles of the GA signaling pathway during RBSDV infection. PMID:28494021

  5. Fast, accurate semiempirical molecular orbital calculations for macromolecules

    NASA Astrophysics Data System (ADS)

    Dixon, Steven L.; Merz, Kenneth M., Jr.

    1997-07-01

    A detailed review of the semiempirical divide-and-conquer (D&C) method is given, including a new approach to subsetting, which involves dual buffer regions. Comparisons are drawn between this method and other semiempirical macromolecular schemes. D&C calculations are carried out using a basic 32 Mbyte memory workstation on a variety of peptide systems, including proteins containing up to 1960 atoms. Aspects of storage and SCF convergence are addressed, and parallelization of the D&C algorithm is discussed.

  6. A Comparison of Aerosolization and Homogenization Techniques for Production of Alginate Microparticles for Delivery of Corticosteroids to the Colon.

    PubMed

    Samak, Yassmin O; El Massik, Magda; Coombes, Allan G A

    2017-01-01

    Alginate microparticles incorporating hydrocortisone hemisuccinate were produced by aerosolization and homogenization methods to investigate their potential for colonic drug delivery. Microparticle stabilization was achieved by CaCl 2 crosslinking solution (0.5 M and 1 M), and drug loading was accomplished by diffusion into blank microparticles or by direct encapsulation. Homogenization method produced smaller microparticles (45-50 μm), compared to aerosolization (65-90 μm). High drug loadings (40% wt/wt) were obtained for diffusion-loaded aerosolized microparticles. Aerosolized microparticles suppressed drug release in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF) prior to drug release in simulated colonic fluid (SCF) to a higher extent than homogenized microparticles. Microparticles prepared using aerosolization or homogenization (1 M CaCl 2 , diffusion loaded) released 5% and 17% of drug content after 2 h in SGF and 4 h in SIF, respectively, and 75% after 12 h in SCF. Thus, aerosolization and homogenization techniques show potential for producing alginate microparticles for colonic drug delivery in the treatment of inflammatory bowel disease. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  7. Investigation of the Semicoa SCF9550 and the International Rectifier IRHM57260SE for Single-Event Gate Rapture and Single-Event Burnout : NASA Electronic Parts and Packaging (NEPP) Program Office of Safety and Mission Assurance

    NASA Technical Reports Server (NTRS)

    Scheick, Leif

    2011-01-01

    Single-event-effect test results for hi-rel total-dose-hardened power MOSFETs are presented in this report. TheSCF9550 from Semicoa and the IRHM57260SE from International Rectifier were tested to NASA test condition/standards and requirements.The IRHM57260SE performed much better when compared to previous testing. These initial results confirm that parts from the Temecula line are marginally comparable to the El Segundo line. The SCF9550 from Semicoa was also tested and represents the initial parts offering from this vendor. Both parts experienced single-event gate rupture (SEGR) and single-event burnout (SEB). All of the SEGR was from gate to drain.

  8. Improved fireman's compressed air breathing system pressure vessel development program

    NASA Technical Reports Server (NTRS)

    King, H. A.; Morris, E. E.

    1973-01-01

    Prototype high pressure glass filament-wound, aluminum-lined pressurant vessels suitable for use in a fireman's compressed air breathing system were designed, fabricated, and acceptance tested in order to demonstrate the feasibility of producing such high performance, lightweight units. The 4000 psi tanks have a 60 standard cubic foot (SCF) air capacity, and have a 6.5 inch diamter, 19 inch length, 415 inch volume, weigh 13 pounds when empty, and contain 33 percent more air than the current 45 SCF (2250 psi) steel units. The current steel 60 SCF (3000 psi) tanks weigh approximately twice as much as the prototype when empty, and are 2 inches, or 10 percent shorter. The prototype units also have non-rusting aluminum interiors, which removes the hazard of corrosion, the need for internal coatings, and the possibility of rust particles clogging the breathing system.

  9. Micro-pulling-down furnace modification and single crystal fibers growth

    NASA Astrophysics Data System (ADS)

    Yuan, Dongsheng; Jia, Zhitai; Li, Yang; Wu, Baiyi; Tao, Xutang

    2016-03-01

    Single crystal fiber (SCF) combines the excellent instinct properties of conventional bulk laser crystals, and the special geometry advantage of active optical fibers. YAG and LuAG are proper host candidates for single crystal fiber laser with high thermal conductivity. Despite a lower thermal conductivity for pure crystal than YAG, LuAG crystal is easier to obtain homogeneous optical quality, and has a thermal conductivity nearly independent from the doping level. Micropulling- down (μ-PD) has relatively small thermal gradient, and here we use μ-PD to carry out high quality SCFs. Through the μ-PD furnace manufactured by ourselves, crystal fibers with different diameters have been grown successfully. We designed and fabricated a method to adjust the thermal distribution, and with the favor of pulling-down rate, the specific diameter can be controlled perfectly. The crystalline quality and homogeneity along the whole fiber were investigated, and LuAG SCF was confirmed to have a fine crystal quality for laser.

  10. Molecular structure and charge density analysis of p-methoxybenzoic acid (anisic acid)

    NASA Astrophysics Data System (ADS)

    Fausto, R.; Matos-Beja, A.; Paixão, J. A.

    1997-12-01

    A concerted X-ray and ab initio SCF-MO study of the structure and charge density of p-methoxybenzoic acid (anisic acid) is reported. An extensive X-ray data set (7401 reflections) was measured on a single crystal using Mo K α radiation and the structure refined with 2121 unique reflections, leading to a final R( F)-factor of 0.047 calculated for reflections with I>2 σ. The molecular geometry of crystalline anisic acid, where the molecules dimerize via a moderately strong CO-H⋯O hydrogen bond, is compared with that of the isolated molecule, resulting from SCF-MO ab initio calculations. A topological analysis of the molecular charge density was performed using Bader's method to gain insight into the dominant intra- and intermolecular interactions in this compound. In particular, the effects of the substituents on the observed distortions of the benzene ring were investigated as well as the internal rotation of the methyl group.

  11. Computer assisted generation of the matrix elements between contracted wavefunctions in a Complete Active Space scheme

    NASA Astrophysics Data System (ADS)

    Angeli, C.; Cimiraglia, R.

    2005-02-01

    Starting from a CAS-SCF calculation a sequence of contracted functions can be generated by applying strings of spin-traced replacement operators to the CAS-SCF solution. The laborious task of producing the Hamiltonian matrix elements between such functions can be substantially reduced making use of a computer algebra system. An implementation employing the MuPAD system is presented and illustrated.

  12. Comparative mapping of human alphoid centromeric sequences in great apes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Archidiacono, N.; Antonacci, R.; Marzella, R.

    1994-09-01

    Metaphase spreads from chimpanzees (Pan troglodytes and Pan paniscus) and gorilla (Gorilla gorilla) have been hybridized in situ with 27 alphoid DNA probes specific for the centromere of human chromosomes, to investigate the evolutionary relationship between centromeric regions of human and great apes. The results showed that most human probes do not recognize their corresponding homologs in great apes. Chromosome X is the only chromosome showing localization consistency in all the four species. Each suprachromosomal family (SCF) exhibits a distinct and peculiar evolutionary history. SCF1 (chromosomes 1, 3, 6, 7, 19, 12, 16) is very heterogeneous: some probes gave intensemore » signals, but always on non-homologous chromosomes; others did not produce any hybridization signal. All probes localized on SCF2 (chromosomes 2, 4, 8, 9, 13, 14, 15, 18, 20, 21, and 22) recognize a single chromosome: chromosome 11 (phylogenetic IX) in PTR and PPA; chromosome 4 (phylogenetic V) in GGO. SCF3 subsets (chromosomes 1, 11, 17, X) are substantially conserved in PTR and PPA, but not in GGO, with the exception restricted to chromosome X. No signals have been detected on PPA chromosomes I, III, IV, V, VI and in PTR chromosomes V, suggesting that the centromeric region of some chromsomes have probably lost homology with human alphoid sequences.« less

  13. Resveratrol Improves Cell Cycle Arrest in Chronic Prostatitis Rats, by C-kit/SCF Suppression.

    PubMed

    He, Yi; Zeng, Huizhi; Yu, Yang; Zhang, Jiashu; Zeng, Xiaona; Gong, Fengtao; Liu, Qi; Yang, Bo

    2017-08-01

    Chronic prostatitis (CP) with complex pathogenesis is difficult for treatment. c-kit has been associated with the control of cell proliferation of prostate cells. This study aims to evaluate the role of resveratrol, an activator of Sirt1, in regulating the expression of c-kit in CP and investigate the consequent effects on cell cycle. Rat model of CP was established through subcutaneous injections of diphtheria-pertussis-tetanus vaccine and subsequently treated with resveratrol. Hematoxylin and eosin staining was performed to identify the histopathological changes in prostates. Western blotting and immunohistochemical staining examined the expression level of c-kit, stem cell factor (SCF), Sirt1, and cell cycle-associated proteins. The model group exhibited severe diffuse chronic inflammation, characterized by leukocyte infiltration and papillary frond protrusion into the gland cavities, and a notable increase in prostatic epithelial height. Gland lumen diameter was also significantly smaller; the activity of c-kit/SCF in the CP rats was increased significantly compared to the control group. Meanwhile, the cell cycle proteins are dysregulated significantly in CP rats. Resveratrol treatment significantly improved these factors by Sirt1 activation. Dysregulation of cell cycle was involved in the pathological processes of CP, which was improved after resveratrol treatment by the downregulation of c-kit/SCF by activating Sirt1.

  14. The COP9 signalosome interacts with SCF UFO and participates in Arabidopsis flower development.

    PubMed

    Wang, Xiping; Feng, Suhua; Nakayama, Naomi; Crosby, W L; Irish, Vivian; Deng, Xing Wang; Wei, Ning

    2003-05-01

    The COP9 signalosome (CSN) is involved in multiple developmental processes. It interacts with SCF ubiquitin ligases and deconjugates Nedd8/Rub1 from cullins (deneddylation). CSN is highly expressed in Arabidopsis floral tissues. To investigate the role of CSN in flower development, we examined the expression pattern of CSN in developing flowers. We report here that two csn1 partially deficient Arabidopsis strains exhibit aberrant development of floral organs, decline of APETALA3 (AP3) expression, and low fertility in addition to defects in shoot and inflorescence meristems. We show that UNUSUAL FLORAL ORGANS (UFO) forms a SCF(UFO) complex, which is associated with CSN in vivo. Genetic interaction analysis indicates that CSN is necessary for the gain-of-function activity of the F-box protein UFO in AP3 activation and in floral organ transformation. Compared with the previously reported csn5 antisense and csn1 null mutants, partial deficiency of CSN1 causes a reduction in the level of CUL1 in the mutant flowers without an obvious defect in CUL1 deneddylation. We conclude that CSN is an essential regulator of Arabidopsis flower development and suggest that CSN regulates Arabidopsis flower development in part by modulating SCF(UFO)-mediated AP3 activation.

  15. Human embryonic stem cell-derived neural crest cells capable of expressing markers of osteochondral or meningeal-choroid plexus differentiation.

    PubMed

    Sternberg, Hal; Jiang, Jianjie; Sim, Pamela; Kidd, Jennifer; Janus, Jeffrey; Rinon, Ariel; Edgar, Ron; Shitrit, Alina; Larocca, David; Chapman, Karen B; Binette, Francois; West, Michael D

    2014-01-01

    The transcriptome and fate potential of three diverse human embryonic stem cell-derived clonal embryonic progenitor cell lines with markers of cephalic neural crest are compared when differentiated in the presence of combinations of TGFβ3, BMP4, SCF and HyStem-C matrices. The cell lines E69 and T42 were compared with MEL2, using gene expression microarrays, immunocytochemistry and ELISA. In the undifferentiated progenitor state, each line displayed unique markers of cranial neural crest including TFAP2A and CD24; however, none expressed distal HOX genes including HOXA2 or HOXB2, or the mesenchymal stem cell marker CD74. The lines also showed diverse responses when differentiated in the presence of exogenous BMP4, BMP4 and TGFβ3, SCF, and SCF and TGFβ3. The clones E69 and T42 showed a profound capacity for expression of endochondral ossification markers when differentiated in the presence of BMP4 and TGFβ3, choroid plexus markers in the presence of BMP4 alone, and leptomeningeal markers when differentiated in SCF without TGFβ3. The clones E69 and T42 may represent a scalable source of primitive cranial neural crest cells useful in the study of cranial embryology, and potentially cell-based therapy.

  16. Calculation of the vibrational spectra of betaine hydrochloride

    NASA Astrophysics Data System (ADS)

    Szafran, Miroslaw; Koput, Jacek

    1997-02-01

    The molecular geometries of betaine hydrochloride, BET·HCl, and free protonated betaine, BET·H +, were calculated with the 6-31G(d,p) basis set at the SCF, MP2 and DFT levels of theory. At the SCF level, the minimum energy corresponds to the ionic pair, B +Htctdot;A -, however, the equilibrium Otctdot;Cl distance is 0.14 Å shorter than the X-ray value. Inclusion of the correlation effects, both at the MP2 and DFT levels, predicts a minimum energy for the molecular complex, Btctdot;H-A, with the equilibrium Otctdot;Cl distance close to the experimental value. The frequencies and intensities of the vibrational bands of BET·HCl, BET·DCl and BET·H + were calculated at the SCF and DFT levels and compared with the solid IR spectra. All measured IR bands were interpreted in term of the calculated vibrational modes. The rms deviations between the experimental and calculated SCF frequencies were 21 and 29 cm -1 for BET·HCl and BET·DCl, respectively. The computed band intensities agree qualitatively with the experimental data. The coupling of the CO stretching and OH bending modes are discussed. The summation bands are probably enhanced in intensity by Fermi resonance with the fundamentals responsible for the main ν(OH) (ν(OD) absorption region.

  17. Beyond ubiquitination: the atypical functions of Fbxo7 and other F-box proteins.

    PubMed

    Nelson, David E; Randle, Suzanne J; Laman, Heike

    2013-10-09

    F-box proteins (FBPs) are substrate-recruiting subunits of Skp1-cullin1-FBP (SCF)-type E3 ubiquitin ligases. To date, 69 FBPs have been identified in humans, but ubiquitinated substrates have only been identified for a few, with the majority of FBPs remaining 'orphans'. In recent years, a growing body of work has identified non-canonical, SCF-independent roles for about 12% of the human FBPs. These atypical FBPs affect processes as diverse as transcription, cell cycle regulation, mitochondrial dynamics and intracellular trafficking. Here, we provide a general review of FBPs, with a particular emphasis on these expanded functions. We review Fbxo7 as an exemplar of this special group as it has well-defined roles in both SCF and non-SCF complexes. We review its function as a cell cycle regulator, via its ability to stabilize p27 protein and Cdk6 complexes, and as a proteasome regulator, owing to its high affinity binding to PI31. We also highlight recent advances in our understanding of Fbxo7 function in Parkinson's disease, where it functions in the regulation of mitophagy with PINK1 and Parkin. We postulate that a few extraordinary FBPs act as platforms that seamlessly segue their canonical and non-canonical functions to integrate different cellular pathways and link their regulation.

  18. Performance characteristics of two multiaxis thrust-vectoring nozzles at Mach numbers up to 1.28

    NASA Technical Reports Server (NTRS)

    Wing, David J.; Capone, Francis J.

    1993-01-01

    The thrust-vectoring axisymmetric (VA) nozzle and a spherical convergent flap (SCF) thrust-vectoring nozzle were tested along with a baseline nonvectoring axisymmetric (NVA) nozzle in the Langley 16-Foot Transonic Tunnel at Mach numbers from 0 to 1.28 and nozzle pressure ratios from 1 to 8. Test parameters included geometric yaw vector angle and unvectored divergent flap length. No pitch vectoring was studied. Nozzle drag, thrust minus drag, yaw thrust vector angle, discharge coefficient, and static thrust performance were measured and analyzed, as well as external static pressure distributions. The NVA nozzle and the VA nozzle displayed higher static thrust performance than the SCF nozzle throughout the nozzle pressure ratio (NPR) range tested. The NVA nozzle had higher overall thrust minus drag than the other nozzles throughout the NPR and Mach number ranges tested. The SCF nozzle had the lowest jet-on nozzle drag of the three nozzles throughout the test conditions. The SCF nozzle provided yaw thrust angles that were equal to the geometric angle and constant with NPR. The VA nozzle achieved yaw thrust vector angles that were significantly higher than the geometric angle but not constant with NPR. Nozzle drag generally increased with increases in thrust vectoring for all the nozzles tested.

  19. On the Bonding in Fe2(CO)9

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.

    1986-01-01

    The bonding in Fe2(CO)9 is analyzed using an self consistend field (SCF) wave function for a large basis set. There is no direct Fe-Fe metal-metal bond. The bridging CO's hold the two Fe(CO)3 fragments together by a sigma donation into the empty Fe-Fe d pi orbital and metal donation from the d pi* orbital into the CO 2pi* orbital. The bonding of the terminal CO is similar to that in Ni(CO)4 and the equatorial groups in Fe(CO)5.

  20. Molecular simulation of CO chemisorption on Co(0001) in presence of supercritical fluid solvent: A potential of mean force study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Asiaee, Alireza; Benjamin, Kenneth M., E-mail: kenneth.benjamin@sdsmt.edu

    2016-08-28

    For several decades, heterogeneous catalytic processes have been improved through utilizing supercritical fluids (SCFs) as solvents. While numerous experimental studies have been established across a range of chemistries, such as oxidation, pyrolysis, amination, and Fischer-Tropsch synthesis, still there is little fundamental, molecular-level information regarding the role of the SCF on elementary heterogeneous catalytic steps. In this study, the influence of hexane solvent on the adsorption of carbon monoxide on Co(0001), as the first step in the reaction mechanism of many processes involving syngas conversion, is probed. Simulations are performed at various bulk hexane densities, ranging from ideal gas conditions (nomore » SCF hexane) to various near- and super-critical hexane densities. For this purpose, both density functional theory and molecular dynamics simulations are employed to determine the adsorption energy and free energy change during CO chemisorption. Potential of mean force calculations, utilizing umbrella sampling and the weighted histogram analysis method, provide the first commentary on SCF solvent effects on the energetic aspects of the chemisorption process. Simulation results indicate an enhanced stability of CO adsorption on the catalyst surface in the presence of supercritical hexane within the reduced pressure range of 1.0–1.5 at a constant temperature of 523 K. Furthermore, it is shown that the maximum stability of CO in the adsorbed state as a function of supercritical hexane density at 523 K nearly coincides with the maximum isothermal compressibility of bulk hexane at this temperature.« less

  1. Revision of the experimental electron affinity of BO

    NASA Astrophysics Data System (ADS)

    Rienstra, Jonathan C.; Schaefer, Henry F., III

    1997-05-01

    The experimental electron affinity of BO has proven questionable. We obtained the electron affinity of BO using the large aug-cc-pVQZ basis with SCF, CISD, CISD+Q, CCSD, and CCSD(T) methods and predict a value of 2.57 eV, or 0.55 eV smaller than the latest experimental value. The 2∑+ to 2Π excitation energy of BO has also been obtained with the CCSD(T) method and found to be 2.82 eV.

  2. Large-amplitude, circularly polarized, compressive, obliquely propagating electromagnetic proton cyclotron waves throughout the Earth's magnetosheath: low plasma β conditions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Remya, B.; Reddy, R. V.; Lakhina, G. S.

    2014-09-20

    During 1999 August 18, both Cassini and WIND were in the Earth's magnetosheath and detected transverse electromagnetic waves instead of the more typical mirror-mode emissions. The Cassini wave amplitudes were as large as ∼14 nT (peak to peak) in a ∼55 nT ambient magnetic field B {sub 0}. A new method of analysis is applied to study these waves. The general wave characteristics found were as follows. They were left-hand polarized and had frequencies in the spacecraft frame (f {sub scf}) below the proton cyclotron frequency (f{sub p} ). Waves that were either right-hand polarized or had f {sub scf}more » > f{sub p} are shown to be consistent with Doppler-shifted left-hand waves with frequencies in the plasma frame f{sub pf} < f{sub p} . Thus, almost all waves studied are consistent with their being electromagnetic proton cyclotron waves. Most of the waves (∼55%) were found to be propagating along B {sub 0} (θ{sub kB{sub 0}}<30{sup ∘}), as expected from theory. However, a significant fraction of the waves were found to be propagating oblique to B {sub 0}. These waves were also circularly polarized. This feature and the compressive ([B {sub max} – B {sub min}]/B {sub max}, where B {sub max} and B {sub min} are the maximum and minimum field magnitudes) nature (ranging from 0.27 to 1.0) of the waves are noted but not well understood at this time. The proton cyclotron waves were shown to be quasi-coherent, theoretically allowing for rapid pitch-angle transport of resonant protons. Because Cassini traversed the entire subsolar magnetosheath and WIND was in the dusk-side flank of the magnetosheath, it is surmised that the entire region was filled with these waves. In agreement with past theory, it was the exceptionally low plasma β (0.35) that led to the dominance of the proton cyclotron wave generation during this interval. A high-speed solar wind stream ((V{sub sw} ) = 598 km s{sup –1}) was the source of this low-β plasma.« less

  3. Water is a poor solvent for densely grafted poly(ethylene oxide) chains: a conclusion drawn from a self-consistent field theory-based analysis of neutron reflectivity and surface pressure-area isotherm data.

    PubMed

    Lee, Hoyoung; Kim, Dae Hwan; Witte, Kevin N; Ohn, Kimberly; Choi, Je; Akgun, Bulent; Satija, Sushil; Won, You-Yeon

    2012-06-21

    By use of a combined experimental and theoretical approach, a model poly(ethylene oxide) (PEO) brush system, prepared by spreading a poly(ethylene oxide)-poly(n-butyl acrylate) (PEO-PnBA) amphiphilic diblock copolymer onto an air-water interface, was investigated. The polymer segment density profiles of the PEO brush in the direction normal to the air-water interface under various grafting density conditions were determined by using the neutron reflectivity (NR) measurement technique. To achieve a theoretically sound analysis of the reflectivity data, we used a data analysis method that utilizes the self-consistent field (SCF) theoretical modeling as a tool for predicting expected reflectivity results for comparison with the experimental data. Using this data analysis technique, we discovered that the effective Flory-Huggins interaction parameter of the PEO brush chains is significantly greater than that corresponding to the θ condition in Flory-Huggins solutions (i.e., χ(PEO-water)(brush chains)/χ(PEO-water)(θ condition) ≈ 1.2), suggesting that contrary to what is more commonly observed for PEO in normal situations (χ(PEO-water)(free chains)/χ(PEO-water)(θ condition) ≈ 0.92), the PEO chains are actually not "hydrophilic" when they exist as polymer brush chains, because of the many body interactions that are forced to be effective in the brush situation. This result is further supported by the fact that the surface pressures of the PEO brush calculated on the basis of the measured χ(PEO-water) value are in close agreement with the experimental surface pressure-area isotherm data. The SCF theoretical analysis of the surface pressure behavior of the PEO brush also suggests that even though the grafted PEO chains experience a poor solvent environment, the PEO brush layer exhibits positive surface pressures, because the hydrophobicity of the PEO brush chains (which favors compression) is insufficient to overcome the opposing effect of the chain conformational entropy (which resists compression).

  4. The ubiquitin conjugating enzyme UbcH10 competes with UbcH3 for binding to the SCF complex, a ubiquitin ligase involved in cell cycle progression

    USDA-ARS?s Scientific Manuscript database

    Ubiquitylation, which regulates most biological pathways, occurs through an enzymatic cascade involving a ubiquitin (ub) activating enzyme (E1), a ub conjugating enzyme (E2) and a ub ligase (E3). UbcH3 is the E2 that interacts with SCF (Skp1/Cul1/F-box protein) complex and ubiquitylates many protein...

  5. NASA Astrophysics Data System (ADS)

    Knosp, B.; Neely, S.; Zimdars, P.; Mills, B.; Vance, N.

    2007-12-01

    The Microwave Limb Sounder (MLS) Science Computing Facility (SCF) stores over 50 terabytes of data, has over 240 computer processing hosts, and 64 users from around the world. These resources are spread over three primary geographical locations - the Jet Propulsion Laboratory (JPL), Raytheon RIS, and New Mexico Institute of Mining and Technology (NMT). A need for a grid network system was identified and defined to solve the problem of users competing for finite, and increasingly scarce, MLS SCF computing resources. Using Sun's Grid Engine software, a grid network was successfully created in a development environment that connected the JPL and Raytheon sites, established master and slave hosts, and demonstrated that transfer queues for jobs can work among multiple clusters in the same grid network. This poster will first describe MLS SCF resources and the lessons that were learned in the design and development phase of this project. It will then go on to discuss the test environment and plans for deployment by highlighting benchmarks and user experiences.

  6. Two-dimensional nanoscale correlations in the strong negative thermal expansion material ScF 3

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Handunkanda, Sahan U.; Occhialini, Connor A.; Said, Ayman H.

    We present diffuse x-ray scattering data on the strong negative thermal expansion (NTE) material ScF3 and find that two-dimensional nanoscale correlations exist at momentum-space regions associated with possibly rigid rotations of the perovskite octahedra. We address the extent to which rigid octahedral motion describes the dynamical fluctuations behind NTE by generalizing a simple model supporting a single floppy mode that is often used to heuristically describe instances of NTE. We find this model has tendencies toward dynamic inhomogeneities and its application to recent and existing experimental data suggest an intricate link between the nanometer correlation length scale, the energy scalemore » for octahedral tilt fluctuations, and the coefficient of thermal expansion in ScF3. We then investigate the breakdown of the rigid limit and propose a resolution to an outstanding debate concerning the role of molecular rigidity in strong NTE materials.« less

  7. MEK1-independent activation of MAPK and MEK1-dependent activation of p70 S6 kinase by stem cell factor (SCF) in ovarian cancer cells

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Lian, E-mail: tounao@126.com; Institute of Immunology, School of Medicine, Shandong University, Jinan 250012; Zhang, Xin

    We discovered a stem cell factor (SCF)-triggered, MEK1-independent, and PI3K-dependent MAPK activation pathway in the Kit-expressing ovarian cancer cell line HEY. When we knocked down MEK1 with RNA interference (RNAi) to study the function of MEK1 on the proliferation and survival of ovarian cancer cells, we found that impaired cell growth still occurred after MEK1 expression had been suppressed, although MAPK activation remained intact. This suggests that there is MEK1-independent activation of MAPK in the SCF-induced ovarian cancer cell growth process, and that MEK1 still plays a crucial role in maintaining the malignant properties of ovarian cancer cells even whenmore » it fails to activate MAPK as expected.« less

  8. Carica papaya induces in vitro thrombopoietic cytokines secretion by mesenchymal stem cells and haematopoietic cells.

    PubMed

    Aziz, Jazli; Abu Kassim, Noor Lide; Abu Kasim, Noor Hayaty; Haque, Nazmul; Rahman, Mohammad Tariqur

    2015-07-08

    Use of Carica papaya leaf extracts, reported to improve thrombocyte counts in dengue patients, demands further analysis on the underlying mechanism of its thrombopoietic cytokines induction In vitro cultures of peripheral blood leukocytes (PBL) and stem cells from human exfoliated deciduous teeth (SHED) were treated with unripe papaya pulp juice (UPJ) to evaluate its potential to induce thrombopoietic cytokines (IL-6 and SCF) RESULTS: In vitro scratch gap closure was significantly faster (p < .05) in SHED culture treated with UPJ. IL-6 concentration was significantly increased (p < .05) in SHED and PBL culture supernatant when treated with UPJ. SCF synthesis in SHED culture was also significantly increased (p < .05) when treated with UPJ CONCLUSION: In vitro upregulated synthesis of IL -6 and SCF both in PBL and SHED reveals the potential mechanism of unripe papaya to induce thrombopoietic cytokines synthesis in cells of hematopoietic and mesenchymal origin.

  9. Computational Modeling of a Mechanized Benchtop Apparatus for Leading-Edge Slat Noise Treatment Device Prototypes

    NASA Technical Reports Server (NTRS)

    Turner, Travis L.; Moore, James B.; Long, David L.

    2017-01-01

    Airframe noise is a growing concern in the vicinity of airports because of population growth and gains in engine noise reduction that have rendered the airframe an equal contributor during the approach and landing phases of flight for many transport aircraft. The leading-edge-slat device of a typical high-lift system for transport aircraft is a prominent source of airframe noise. Two technologies have significant potential for slat noise reduction; the slat-cove filler (SCF) and the slat-gap filler (SGF). Previous work was done on a 2D section of a transport-aircraft wing to demonstrate the implementation feasibility of these concepts. Benchtop hardware was developed in that work for qualitative parametric study. The benchtop models were mechanized for quantitative measurements of performance. Computational models of the mechanized benchtop apparatus for the SCF were developed and the performance of the system for five different SCF assemblies is demonstrated.

  10. Complete genome sequence of “Enterobacter lignolyticus” SCF1

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    DeAngelis, Kristen M.; D'Haeseleer, Patrik; Chivian, Dylan

    2011-09-23

    In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated 'Ente-robacter lignolyticus' SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anae-robically, we sequenced the genome. The genome of 'E. lignolyticus' SCF1 is 4.81 Mbpmore » with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohy-drate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degra-dation pathway encoded in a single gene cluster.« less

  11. Methane production by anaerobic digestion of Bermuda grass

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Klass, D.L.; Ghosh, S.

    1979-01-01

    Bermuda grass (Cynodon dactylon) is one of the high-yield warm-season grasses that has been suggested as a promising raw material for conversion to methane. Experimental work performed with laboratory digesters to study the anaerobic digestion of Coastal Bermuda grass harvested in Louisiana and having a C/N ratio of 24 is described. Methane yields of about 1.9 SCF/lb of volatile solids( VS) added were observed under conventional mesophilic high-rate conditions. When supplemental nitrogen additions were made, the yields increased up to 3.5 SCF/lb of VS added indicating that the nitrogen content of the grass examined was insufficient to sustain high-rate digestionmore » at the higher yield level. Thermophilic digestion with supplemental nitrogen additions afforded methane yields of about 2.7 SCF/lb VS added. Carbon and energy balances were calculated and the relative biodegradabilities of the organics were estimated.« less

  12. [Characterization and determination of antibiotic resistance profiles of a single clone Acinetobacter baumannii strains isolated from blood cultures].

    PubMed

    Karagöz, Alper; Baran, Irmak; Aksu, Neriman; Acar, Sümeyra; Durmaz, Rıza

    2014-10-01

    Acinetobacter baumannii which is a significant cause of nosocomial infections, increases the rate of morbidity and mortality in health care settings especially in intensive care units (ICUs). The aim of this study was to determine the antibiotic resistance profiles of A.baumannii strains isolated from blood cultures of inpatients from different ICUs, wards and hospital environment and evaluate their clonal relationships and epidemiologic features. A total of 54 A.baumannii strains (47 from the blood cultures and 7 from the hospital environment), identified between 01 January 2012-28 December 2012 at the Clinical Microbiology Laboratory of Ankara Numune Training and Research Hospital, Turkey, were included in the study. Identification of A.baumannii isolates and their antimicrobial [sulbactam-ampicillin (SAM), piperacillin (PIP), piperacillin-tazobactam (TZP), ceftazidime (CFZ), cefoperazone-sulbactam (SCF), cefepime (CEF), imipenem (IMP), meropenem (MER), amikacin (AMK), gentamicin (GEN), netilmicin (NT), ciprofloxacin (CIP), levofloxacin (LVF), tetracycline (TET), tigecycline (TG), colistin (COL), trimethoprim-sulfamethoxazole (SXT)] susceptibility testing were performed by Vitek 2 (bioMérieux, France) system. The clonal relationship between the A.baumannii isolates was analysed by pulsed-field gel electrophoresis (PFGE). In our study colistin, tigecycline and netilmicin were found to be the most effective agents against A.baumannii isolates. All of the clinical isolates (n= 47) were found susceptible to COL, however all were resistant to SAM, PIP, TZP, CEF, IPM, CFZ, MER and CIP. While 1.85%, 14.8%, 14.8%, 16.6%, 59.2% and 22.2% of the isolates were susceptible to SCF, AMK, NT, GEN, TG and SXT, respectively; 1.85%, 1.85%, 9.2%, 16.6%, 38.8% and 27.7% of the isolates were intermediate to SCF, TET, AMK, NT, LVF and TG, respectively. Similarly, all of the environmental A.baumannii isolates (n= 7) were resistant to SAM, PIP, TZP, CFZ, CEF, IPM, MER and CIP, and all were susceptible to TG and COL. The resistance rates of the environmental isolates to SCF, AMK, GEN, NT, LVF, TET and SXT were determined as 57.1%, 85.7%, 85.7%, 28.8%, 28.6%, 85.7% and 57.1%, respectively. PFGE analysis done by the use of ApaI enzyme revealed the presence of one major clone. Dendogram analysis indicated that environmental and clinical isolates were in the same clone indicating that the outbreak was possibly originated from the same internal ICUs. Our data emphasized that multidrug resistant A.baumannii isolates were quite common in our hospital, and enviromental cross-contamination throughout the year was confirmed by molecular methods. Despite the precautions such as continous education on effective hand washing, use of gloves and hospital cleaning, established in our hospital, this single clonal spread was attributed to staff shortage and poor adherence to infection control rules. In conclusion, for the prevention of dissemination of multidrug resistant A.baumannii strains and control of nosocomial infections, infection control strategies should be established and strict compliance to these rules should be provided.

  13. On the chain length dependence of local correlations in polymer melts and a perturbation theory of symmetric polymer blends.

    PubMed

    Morse, David C; Chung, Jun Kyung

    2009-06-14

    The self-consistent field (SCF) approach to the thermodynamics of dense polymer liquids is based on the idea that short-range correlations in a polymer liquid are almost independent of how monomers are connected into polymers over larger scales. Some limits of this idea are explored in the context of a perturbation theory for symmetric polymer blends. We consider mixtures of two structurally identical polymers, A and B, in which the AB monomer pair interaction differs slightly from the AA and BB interactions by an amount proportional to a parameter alpha. An expansion of the free energy to first order in alpha yields an excess free energy of mixing per monomer of the form alphaz(N)phi(A)phi(B) in both lattice and continuum models, where z(N) is a measure of the number of intermolecular near neighbors per monomer in a one-component (alpha=0) reference liquid with chains of length N. The quantity z(N) decreases slightly with increasing N because the concentration of intramolecular near neighbors is slightly higher for longer chains, creating a slightly deeper intermolecular correlation hole. We predict that z(N)=z(infinity)[1+betaN(-1/2)], where N is an invariant degree of polymerization and beta=(6/pi)(3/2) is a universal coefficient. This and related predictions about the slight N dependence of local correlations are confirmed by comparison to simulations of a continuum bead-spring model and to published lattice Monte Carlo simulations. We show that a renormalized one-loop theory for blends correctly describes this N dependence of local liquid structure. We also propose a way to estimate the effective interaction parameter appropriate for comparisons of simulation data to SCF theory and to coarse-grained theories of corrections to SCF theory, which is based on an extrapolation of perturbation theory to the limit N-->infinity.

  14. Next-generation Lunar Laser Retroreflectors for Precision Tests of General Relativity

    NASA Astrophysics Data System (ADS)

    Ciocci, Emanuele; dell'Agnello, Simone; Delle Monache, Giovanni; Martini, Manuele; Contessa, Stefania; Porcelli, Luca; Tibuzzi, Mattia; Salvatori, Lorenzo; Patrizi, Giordano; Maiello, Mauro; Intaglietta, Nicola; Mondaini, Chiara; Currie, Douglas; Chandler, John; Bianco, Giuseppe; Murphy, Tom

    2016-04-01

    Since 1969, Lunar Laser Ranging (LLR) to the Apollo Cube Corner Retroreflectors (CCRs) has supplied almost all significant tests of General Relativity (GR). When first installed in the 1970s, the Apollo CCRs geometry contributed only a negligible fraction of the ranging error budget. Today, because of lunar librations, this contribution dominates the error budget, limiting the precision of the experimental tests of gravitational theories. The new MoonLIGHT-2 (Moon Laser Instrumentation for General relativity High-accuracy Tests) apparatus is a new-generation LLR payload developed by the SCF_Lab (http://www.lnf.infn.it/esperimenti/etrusco/) at INFN-LNF in collaboration with the Maryland University. With the unique design of a single large CCR unaffected by librations, MoonLIGHT-2 can increase up to a factor 100 the precision of the measurement of the lunar geodetic precession and other General Relativity (GR) tests respect to Apollo CCRs. MoonLIGHT-2 is approved to be launched with the Moon Express mission MEX-1 and will be deployed on the Moon surface in 2018. MoonLIGHT-2 is also proposed for the Roscosmos mission Luna-27. To validate/optimize MoonLIGHT-2 for MEX-1, the SCF_Lab is carrying out a unique experimental test called SCF-Test: the concurrent measurement of the optical Far Field Diffraction Pattern (FFDP) and the temperature distribution of the CCR under thermal conditions produced with a close-match solar simulator and simulated space environment. We perform test of GR with current LLR data and also different GR simulation of the expected improvement in GR test provided by MoonLIGHT-2, using the Planetary Ephemeris Program in collaboration with CfA. Our ultimate goal is to improve GR tests by a factor up to 100, and provide constraints on the new gravitational theories like non-miminally coupled gravity and spacetime torision.

  15. Rotational spectrum of 14N 2 · H 35Cl and 14N 2 · H 37Cl: electric field gradients at the nitrogen nuclei

    NASA Astrophysics Data System (ADS)

    Kisiel, Z.; Pszczólkowski, L.; Fowler, P. W.; Legon, A. C.

    1997-09-01

    Rotational spectra of the most abundant isotopic species of the weakly bound dimer formed between dinitrogen and hydrogen chloride were investigated. Spectroscopic constants for 14N 2 · H 37Cl were determined for the first time and those for 14N 2 · H 35Cl improved. Analysis of observed nuclear quadrupole spliting patterns within the framework of coupling of three nonequivalent nuclear spins allowed determination of splitting constants for both nuclei in the complexed dinitrogen molecule. Electric field gradient calculations at the SCF supermolecule level for the dimer are presented and account for the observed values of the nitrogen splitting constants.

  16. A novel dissolution method for evaluation of polysaccharide based colon specific delivery systems: A suitable alternative to animal sacrifice.

    PubMed

    Singh, Sachin Kumar; Yadav, Ankit Kumar; Prudhviraj, G; Gulati, Monica; Kaur, Puneet; Vaidya, Yogyata

    2015-06-20

    The most extensively used test for predicting in-vivo release kinetics of a drug from its orally administered dosage forms is dissolution testing. For polysaccharide based, colon targeted oral delivery systems, the entire path of the gut traversed by the dosage form needs to be simulated for assessing its in-vivo dissolution pattern. This includes the dissolution testing sequentially in simulated gastric fluid (SGF), simulated intestinal fluid (SIF) and simulated colonic fluid (SCF). For SGF and SIF, simple and standardized composition is well-known. However, preparation of SCF requires addition of either the colonic contents of rodents or human faecal slurry. A method is proposed, wherein a mixture of five probiotics cultured in the presence of a prebiotic under anaerobic conditions is able to surrogate the colonic fluid. Release profiles of drug from colon targeted delivery systems in this medium were studied and compared to those generated in the conventionally used media containing rodent caecal contents and human faecal slurry. The results from the three studies were found to be quite similar. These findings suggest that the proposed medium may prove to be useful not only as a biorelevant and discriminatory method but may also help in achieving the 3Rs objective regarding the ethical use of animals. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Modeling the Thermodynamic and Transport Properties of Decahydronaphthalene/Propane Mixtures: Phase Equilibria, Density, and Viscosity

    DTIC Science & Technology

    2011-01-01

    expanded with supercritical fluids (ScF) have been investigated as alternative chemical process media for more than two decades. ScF expanded liquids can...internal surfaces of porous catalysts. As examples, solvents expanded by supercritical and subcritical ScFs have been used in homogeneous catalytic...decahydronaphthalene (DHN) expanded by supercritical carbon dioxide (scCO2) [4, 5, 7]. Although the addition of scCO2 improved the hydrogenation rate under many

  18. Direct dehydroxytrifluoromethylthiolation of alcohols using silver(I) trifluoromethanethiolate and tetra-n-butylammonium iodide.

    PubMed

    Liu, Jian-Bo; Xu, Xiu-Hua; Chen, Zeng-Hao; Qing, Feng-Ling

    2015-01-12

    An unprecedented reaction for the direct trifluoromethylthiolation and fluorination of alkyl alcohols using AgSCF3 and nBu4NI has been developed. The trifluoromethylthiolated compounds and alkyl fluorides were selectively formed by changing the ratio of AgSCF3/nBu4NI. This protocol is tolerant of different functional groups and might be applicable to late-stage trifluoromethylthiolation of alcohols. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. [Effect of guishen zhiyang recipe for treatment of patients with senile pruritus of blood-deficiency and Gan-hyperactive syndrome type and its impact on stem cell factor and dynorphin].

    PubMed

    Lan, Dong; Zhang, Hai-Yan; Pang, Bao-Sen

    2009-07-01

    To explore the mechanism of Chinese medicinal therapy for nourishing blood and softening Gan in treating senile pruritus through observing the impact of Guishen Zhiyang Recipe (GZR) on serum levels of stem cell factor (SCF) and dynorphin (DYN) in patients suffered from the disease of blood-deficiency and Gan-hyperactive syndrome type (BDGH). Sixty patients with senile pruritus were equally randomized into two groups, the patients in the treated group (33 cases) were treated by GZR, and those in the control group (28 cases) were treated by Fuyang Granule, all for 8 weeks. Changes of symptoms and skin lesions as well as blood levels of SCF and DYN were observed before and after treatment. Three patients were rejected from the treated group. Twenty patients in the treated group were cured after treatment, the cure rate being 66.7%, which was significantly higher than that in the control group (10 patients, 35.7%, P < 0.05). Levels of SCF and DYN in the treated group significantly lowered after treatment (all P < 0.01), and were lower than those in the control group (P < 0.05 and P < 0.01, respectively). GZR shows favorite effect in treating senile pruritus of BDGH type and it may be achieved by regulating SCF and DYN levels to improve the pruritus associated inflammatory media.

  20. In vitro long-term culture of human primitive hematopoietic cells supported by murine stromal cell line MS-5.

    PubMed

    Nishi, N; Ishikawa, R; Inoue, H; Nishikawa, M; Yoneya, T; Kakeda, M; Tsumura, H; Ohashi, H; Mori, K J

    1997-04-01

    When Lin-CD34+CD38- cells from normal human cord blood were cocultured with MS-5, colony forming cells were maintained for over 8 weeks. Prevention of contact between MS-5 and Lin-CD34+CD38- cells by using a membrane filter was negligible for this activity, indicating that the activity of MS-5 on human primitive hematopoietic cells may be due to soluble factor(s) secreted from MS-5. We tried to purify this activity by a [3H]TdR incorporation assay. The activity was found in 150 kD fraction and was neutralized with anti-mSCF (stem cell factor) antibody. Another 20-30 kD fraction synergized with mSCF to stimulate the growth of Lin-CD34+CD38- cells but failed alone. This fraction supported the growth of the G-CSF (granulocyte-colony stimulating factor)-dependent cell line FD/GR3, FDC-P2 transfected with mG-CSF receptor cDNA. This synergy was canceled in the presence of soluble mG-CSF receptor. Addition of anti-mSCF antibody and soluble mG-CSF receptor to the culture completely abrogated the activity of MS-5-culture supernatant. These results indicate the activity of MS-5 on Lin-CD34+CD38- cells is due to synergistic effect of mSCF and mG-CSF.

  1. Stable sugar-based protein formulations by supercritical fluid drying.

    PubMed

    Jovanović, Natasa; Bouchard, Andréanne; Sutter, Marc; Van Speybroeck, Michiel; Hofland, Gerard W; Witkamp, Geert-Jan; Crommelin, Daan J A; Jiskoot, Wim

    2008-01-04

    The aim of this work was to produce stable, sugar-containing protein formulations by supercritical fluid (SCF) drying. Lysozyme solutions with and without added sucrose or trehalose were dried by spraying them in an SCF composed of CO(2) and ethanol or CO(2) only. The protein-to-sugar ratio was varied between 1:0 and 1:10 (w/w). Dried formulations were stored at 4 degrees C for three months and analyzed by Karl Fischer titration, scanning electron microscopy, X-ray powder diffraction, differential scanning calorimetry and Fourier transform infrared spectroscopy. Lysozyme stability after reconstitution was determined by an enzymatic activity assay, UV/Vis spectroscopy, and SDS-PAGE. Smooth, spherical particles of 1-25 microm size were obtained. All formulations were initially amorphous. Crystallization during storage only occurred with a protein-to-sugar ratio of 1:10 and could be avoided by performing SCF drying without ethanol. Absence of residual ethanol in dried trehalose formulations increased the glass transition temperature up to 120 degrees C. Lysozyme in dried formulations was structurally stable, with exception of the 1:0 and 1:1 protein-to-sugar ratios, where reversible protein aggregation occurred. The results show that by avoiding ethanol, which up to now has been considered mandatory for efficient drying of aqueous solutions, and by choosing the proper protein-to-sugar ratio, it is possible to obtain stable, sugar-based protein formulations through SCF drying.

  2. Risk assessment of dioxins and dioxin-like PCBs in food--comments by the German Federal Environmental Agency.

    PubMed

    Gies, Andreas; Neumeier, Günther; Rappolder, Marianne; Konietzka, Rainer

    2007-04-01

    Human health risk assessments for dioxins and dioxin-like PCBs (with the exception of the one by US-EPA) recommend health based exposure limits within the range of 1-4 pg WHO-TEQ/kg bw per day. As all humans are exposed to measurable levels of dioxins and related substances, the determination of the tolerated daily intake is a very significant decision and may influence limit values guiding risk reduction measures and target levels. The proposed TDI has to protect all human subpopulations. In the case of dioxin this is particularly important as the exposure of infants through breast-feeding may exceed the exposure of adults by one or two orders of magnitude. An overview of recently recommended limit values (WHO, SCF, JECFA) for PCDDs, PCDFs and dioxin-like PCBs using WHO-TEFs shows the common feature that the values were derived only from non carcinogenic endpoints. In November 2000 the Scientific Committee on Food of the European Commission published an 'Opinion of the SCF on the Risk Assessment of Dioxins and Dioxin-like PCBs in Food' [SCF, Scientific Committee on Food 2000. Opinion of the SCF on the risk assessment of dioxins and dioxin-like PCBs in food. European Commission, Brussels, Adopted on November 2000 http://europa.eu.int/comm/food/fs/sc/scf/out78_en.pdf]. On the basis of this extensive review of data and experimental results the Committee recommended a temporary tolerable weekly intake (t-TWI) of 7 pg WHO-TEQ/kg bw. Only six months later the SCF carried out a re-evaluation of its t-TWI from November 2000. The reconsideration of 'pivotal studies' led to the situation that the re-assessment is now based only on rat studies which investigated only reproductive effects only on male offspring and, in addition, three of these studies are single dose studies at gestational day 15. Applying an overall uncertainty factor of 10 to the LOAEL derived estimated human daily intakes (EHDI) the SCF concluded that 14 pg/kg bw per week should be considered as a tolerable intake for 2,3,7,8-TCDD. The SCF stated that on a body weight basis, the dioxin intake of breast-fed infants has been estimated to be one to two orders of magnitude higher than the average adult intake. Recent German data suggest that the body burden of formerly breast-fed children aged 9-11 is still about 30% higher than those of their formula-fed age-mates. As breast-feeding has measurable benefits for neurological and immunological development, formula feeding cannot be recommended as an alternative to lower dioxin intake. So the only remaining way to lower the dioxin uptake is to drastically reduce the background exposure of the general population. It is acknowledged that any recommendation of a precise number for a TDI is flawed by uncertainties and the possibility of different weight being given to the studies of relevance. The determination of the TDI has influence on all regulatory limit values that are based on the TDI value. A higher TDI lowers the level of protection for humans. It is proposed by the German Federal Environmental Agency that the TDI should be reassessed in a process transparent to the public and on the basis of all relevant endpoints from animal experiments and human epidemiology, including the assessment of cancer risks.

  3. Geopressured-geothermal test of the EDNA Delcambre No. 1 well, Tigre Lagoon Field, Vermilion Parish, Louisiana: analysis of water an dissolved natural gas. Final report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hankins, B.E.; Karkalits, O.C.

    1978-09-01

    The Edna Delcambre et al. No. 1 gas well, shut-in since June 1975, was made available for the project. Two geopressured sand-bed aquifers were tested: sand No. 3 at a depth of 12,900 feet and sand No. 1 at a depth of 12,600 feet. Each aquifer was subjected to flow tests which lasted approximately three weeks in each case. Water samples were obtained during flow testing of the two geopressured aquifers. The water contained 11.3 to 13.3% dissolved solids. Several radioactive species were measured. Radium-226 was found to be approximately 10 times more concentrated than the average amount observed inmore » surface waters. No appreciable amount of heavy metals was detected. Recombination studies at bottom-hole conditions indicate the solubility of natural gas per barrel of water to be about 24 SCF. The methane content was 93 to 95%, and the gas had a heating value in the range of 1020 to 1070 Btu/cu.ft. During the flow tests, the gas/water ratio at the well-head was observed to be 45 to 88 SCF/Bbl water produced. (MHR)« less

  4. Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

    PubMed Central

    2015-01-01

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy. PMID:25321186

  5. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

    DOE PAGES

    Sodt, Alexander J.; Mei, Ye; Konig, Gerhard; ...

    2014-10-16

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completelymore » avoided at each configuration. Here, they produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.« less

  6. Interrupted E2F1-miR-34c-SCF negative feedback loop by hyper-methylation promotes colorectal cancer cell proliferation

    PubMed Central

    Yang, Shu; Wu, Bo; Sun, Haimei; Ji, Fengqing; Sun, Tingyi; Zhao, Yan; Zhou, Deshan

    2015-01-01

    Tumour suppressor miR-34c deficiency resulted from hyper-methylation in its promoter is believed to be one of the main causes of colorectal cancer (CRC). Till date, miR-34c has been validated as a direct target of p53; but previous evidence suggested other transcription factor(s) must be involved in miR-34c transcription. In the present study, we in the first place identified a core promoter region (−1118 to −883 bp) of pre-miR-34c which was embedded within a hyper-methylated CpG island. Secondly, E2F1 promoted miR-34c transcription by physical interaction with the miR-34c promoter at site −897 to −889 bp. The transcriptional activating effect of E2F1 on miR-34c was in a p53 independent manner but profoundly promoted in the presence of p53 with exposure to 5-aza-2′-deoxycytidine (DAC). Thirdly, stem cell factor (SCF), a miR-34c target, was specifically reduced upon an introduction of E2F1 which lead to suppression of CRC cell proliferation. The E2F1-suppressed cell proliferation was partially abrogated by additional miR-34c inhibitor, indicating that the anti-proliferation effect of E2F1 was probably through activating miR-34c-SCF axis. Finally, SCF/KIT signalling increased E2F1 production by reducing its proteosomal degradation dependent on PI3K/Akt-GSK3β pathway. In conclusion, our results suggested the existence of E2F1-miR-34c-SCF negative feedback loop which was interrupted by the hyper-methylation of miR-34c promoter in CRC cells and increased cell proliferation. PMID:26704889

  7. Body Mass Index Is Associated with Increased Creatinine Clearance by a Mechanism Independent of Body Fat Distribution

    PubMed Central

    Gerchman, Fernando; Tong, Jenny; Utzschneider, Kristina M.; Zraika, Sakeneh; Udayasankar, Jayalakshmi; McNeely, Marguerite J.; Carr, Darcy B.; Leonetti, Donna L.; Young, Bessie A.; de Boer, Ian H.; Boyko, Edward J.; Fujimoto, Wilfred Y.; Kahn, Steven E.

    2009-01-01

    Context: Although obesity has been, in general, associated with glomerular hyperfiltration, visceral adiposity has been suggested to be associated with reduced glomerular filtration. Objective: The aim of the study was to evaluate the differential effects of obesity and body fat distribution on glomerular filtration. Design and Setting: We conducted a cross-sectional study of the Japanese-American community in Seattle, Washington. Participants: We studied a representative sample of second-generation Japanese-American men and women with normal glucose tolerance (n = 124) and impaired glucose metabolism (impaired fasting glucose and/or impaired glucose tolerance) (n = 144) residing in King County, Washington. Main Outcome Measures: Glomerular filtration rate was estimated by 24-h urinary creatinine clearance, body size by body mass index (BMI), and intra-abdominal fat (IAF), sc fat (SCF), and lean thigh areas by CT scan. Results: Creatinine clearance was positively correlated with BMI (r = 0.429; P < 0.001), fasting glucose (r = 0.198; P = 0.001), and insulin levels (r = 0.125; P = 0.042), as well as IAF (r = 0.239; P < 0.001), SCF (r = 0.281; P < 0.001), and lean thigh (r = 0.353; P < 0.001) areas. The association between creatinine clearance and BMI remained significant after adjustments for IAF, SCF areas, and fasting insulin levels (r = 0.337; P < 0.001); whereas IAF and SCF areas were not independently associated with creatinine clearance after adjusting for BMI. Creatinine clearance increased with increasing BMI after adjusting for fasting insulin, fasting glucose, IAF and SCF areas in subjects with normal glucose tolerance (r = 0.432; P < 0.001) and impaired glucose metabolism (r = 0.471; P < 0.001). Conclusions: BMI rather than body fat distribution is an independent determinant of creatinine clearance in nondiabetic subjects. Lean body mass, rather than adiposity, may explain this association. PMID:19584179

  8. A Peek into a Cul-De-Sac and a Mews of Martian Dust Storm Activity: Western Hellas and Syria-Claritas Fossae During Mars Year 29

    NASA Astrophysics Data System (ADS)

    Heavens, N. G.

    2016-12-01

    Western Hellas Planitia (WHP) and the region encompassed by Syria Planum and Claritas Fossae are the main centers of textured dust storm activity in Mars's southern low to mid-latitudes. (Texture in this context refers to distinct fine structure at the cloud tops indicative of active lifting.) WHP is a well-known initiation zone for regional and global dust storm activity and often the end point of the Utopia "flushing storm" track. Syria-Claritas Fossae (SCF), too, can be a lifting center in global dust storm activity. Indeed, SCF and the area to its west was the region most denuded of dust by the Mars Year (MY) 25 global dust storm, perhaps suggesting that SCF contained the principal lifting center of the storm. Thus, if the Acidalia and Utopia storm tracks are Mars's dust storm alleys, through which dust storms pass quickly again and again; WHP might be a cul-de-sac and SCF something like a mews, where dust storm activity can enter more or less easily but may not as easily leave. In this presentation, I will focus on dust storm activity in these areas in a typical non-global dust storm year, MY 29. Synthesizing visible imagery by the Mars Color Imager (MARCI) on board Mars Reconnaissance Orbiter (MRO) and Mars Climate Sounder (MCS) also on board MRO, I will consider the climatology, morphology, texture, and vertical structure of dust storm activity in these areas in order to infer their governing dynamics. This investigation has two aims: (1) to understand why these areas are centers of textured dust storm activity; and (2) to connect the characteristics of smaller-scale dust storm activity in these regions to the underlying dynamics in order to understand the role of WHP and SCF in the dynamics of global dust storms. This work is supported by NASA's Mars Data Analysis Program (NNX14AM32G).

  9. [4-t-butylphenyl]-N-(4-imidazol-1-yl phenyl)sulfonamide (ISCK03) inhibits SCF/c-kit signaling in 501mel human melanoma cells and abolishes melanin production in mice and brownish guinea pigs.

    PubMed

    Na, Yong Joo; Baek, Heung Su; Ahn, Soo Mi; Shin, Hyun Jung; Chang, Ih-Seop; Hwang, Jae Sung

    2007-09-01

    It is well known that c-kit is related to pigmentation as well as to the oncology target protein. The objective of this study was to discover a skin-whitening agent that regulates c-kit activity. We have developed a high-throughput screening system using recombinant human c-kit protein. Approximately 10,000 synthetic compounds were screened for their effect on c-kit activity. Phenyl-imidazole sulfonamide derivatives showed inhibitory activity on c-kit phosphorylation in vitro. The effects of one derivative, [4-t-butylphenyl]-N-(4-imidazol-1-yl phenyl)sulfonamide (ISCK03), on stem-cell factor (SCF)/c-kit cellular signaling in 501mel human melanoma cells were examined further. Pretreatment of 501mel cells with ISCK03 inhibited SCF-induced c-kit phosphorylation dose dependently. ISCK03 also inhibited p44/42 ERK mitogen-activated protein kinase (MAPK) phosphorylation, which is known to be involved in SCF/c-kit downstream signaling. However ISCK03 did not inhibit hepatocyte growth factor (HGF)-induced phosphorylation of p44/42 ERK proteins. To determine the in vivo potency of ISCK03, it was orally administered to depilated C57BL/6 mice. Interestingly, oral administration of ISCK03 induced the dose-dependent depigmentation of newly regrown hair, and this was reversed with cessation of ISCK03 treatment. Finally, to investigate whether the inhibitory effect of ISCK03 on SCF/c-kit signaling abolished UV-induced pigmentation, ISCK03 was applied to UV-induced pigmented spots on brownish guinea pig skin. The topical application of ISCK03 promoted the depigmentation of UV-induced hyperpigmented spots. Fontana-Masson staining analysis showed epidermal melanin was diminished in spots treated with ISCK03. These results indicate that phenyl-imidazole sulfonamide derivatives are potent c-kit inhibitors and might be used as skin-whitening agents.

  10. Improving ethanol productivity through self-cycling fermentation of yeast: a proof of concept.

    PubMed

    Wang, Jie; Chae, Michael; Sauvageau, Dominic; Bressler, David C

    2017-01-01

    The cellulosic ethanol industry has developed efficient strategies for converting sugars obtained from various cellulosic feedstocks to bioethanol. However, any further major improvements in ethanol productivity will require development of novel and innovative fermentation strategies that enhance incumbent technologies in a cost-effective manner. The present study investigates the feasibility of applying self-cycling fermentation (SCF) to cellulosic ethanol production to elevate productivity. SCF is a semi-continuous cycling process that employs the following strategy: once the onset of stationary phase is detected, half of the broth volume is automatically harvested and replaced with fresh medium to initiate the next cycle. SCF has been shown to increase product yield and/or productivity in many types of microbial cultivation. To test whether this cycling process could increase productivity during ethanol fermentations, we mimicked the process by manually cycling the fermentation for five cycles in shake flasks, and then compared the results to batch operation. Mimicking SCF for five cycles resulted in regular patterns with regards to glucose consumption, ethanol titer, pH, and biomass production. Compared to batch fermentation, our cycling strategy displayed improved ethanol volumetric productivity (the titer of ethanol produced in a given cycle per corresponding cycle time) and specific productivity (the amount of ethanol produced per cellular biomass) by 43.1 ± 11.6 and 42.7 ± 9.8%, respectively. Five successive cycles contributed to an improvement of overall productivity (the aggregate amount of ethanol produced at the end of a given cycle per total processing time) and the estimated annual ethanol productivity (the amount of ethanol produced per year) by 64.4 ± 3.3 and 33.1 ± 7.2%, respectively. This study provides proof of concept that applying SCF to ethanol production could significantly increase productivities, which will help strengthen the cellulosic ethanol industry.

  11. Tranilast prevents renal interstitial fibrosis by blocking mast cell infiltration in a rat model of diabetic kidney disease.

    PubMed

    Yin, Dan-Dan; Luo, Jun-Hui; Zhao, Zhu-Ye; Liao, Ying-Jun; Li, Ying

    2018-05-01

    Renal interstitial fibrosis is a final pathway that is observed in various types of kidney diseases, including diabetic kidney disease (DKD). The present study investigated the effect of tranilast on renal interstitial fibrosis and the association between its role and mast cell infiltration in a rat model of DKD. A total of 30 healthy 6‑week‑old male Sprague‑Dawley rats were randomly divided into the following four groups: Normal control group; DKD model group; low‑dose tranilast group (200 mg/kg/day); and high‑dose tranilast group (400 mg/kg/day). The morphological alterations of tubulointerstitial fibrosis were evaluated by Masson's trichrome staining, while mast cell infiltration into the renal tubular interstitium was measured by toluidine blue staining and complement C3a receptor 1 (C3aR) immunohistochemical staining (IHC). The expression of fibronectin (FN), collagen I (Col‑I), stem cell factor (SCF) and proto‑oncogene c‑kit (c‑kit) was detected by IHC, western blotting and reverse transcription‑quantitative‑polymerase chain reaction. The results demonstrated that tubulointerstitial fibrosis and mast cell infiltration were observed in DKD model rats, and this was improved dose‑dependently in the tranilast treatment groups. The expression of FN, Col‑I, SCF and c‑kit mRNA and protein was upregulated in the tubulointerstitium of DKD model rats compared with the normal control rats, and tranilast inhibited the upregulated expression of these markers. Furthermore, the degree of SCF and c‑kit expression demonstrated a significant positive correlation with C3aR‑positive mast cells and the markers of renal interstitial fibrosis. The results of the present study indicate that mast cell infiltration may promote renal interstitial fibrosis via the SCF/c‑kit signaling pathway. Tranilast may prevent renal interstitial fibrosis through inhibition of mast cell infiltration mediated through the SCF/c-kit signaling pathway.

  12. Comparison of two different in vivo models and an in vitro model for caloric determination of four novel fiber ingredients.

    PubMed

    Cervantes-Pahm, Sarah; Knapp, Brenda K; Kim, Beob G; Liu, Yanhong; Parsons, Carl M; Fahey, George C; Stein, Hans H

    2013-12-18

    The objective of this study was to compare two in vivo methods using pigs and roosters and an in vitro method for determining the caloric value of four fiber sources [i.e., two resistant starches (RS 60 and RS 75), soluble corn fiber (SCF 70), and pullulan]. Metabolizable energy (ME) in pigs and true metabolizable energy (TMEn) in roosters were determined by using 72 barrows and 24 roosters, respectively. A two-step in vitro procedure was used to quantify monosaccharides released. Results of the two in vivo experiments corresponded well with RS 75 having the least caloric value (7.55 MJ/kg in pigs; 6.19 MJ/kg in roosters) and pullulan having the greatest caloric value (12.21 MJ/kg in pigs; 13.94 MJ/kg in roosters). The caloric values for all the fiber ingredients were less (P < 0.05) than in MD both in pigs and in roosters. Despite some limitations, results of the in vitro procedure corresponded well with the in vivo experiments where the concentration of glucose hydrolyzed from RS 60, RS 75, and SCF 70, but not pullulan, was less (P < 0.05) than the concentration of glucose hydrolyzed from MD. However, the greatest accuracy was obtained in the in vivo experiments.

  13. Performance analysis of next-generation lunar laser retroreflectors

    NASA Astrophysics Data System (ADS)

    Ciocci, Emanuele; Martini, Manuele; Contessa, Stefania; Porcelli, Luca; Mastrofini, Marco; Currie, Douglas; Delle Monache, Giovanni; Dell'Agnello, Simone

    2017-09-01

    Starting from 1969, Lunar Laser Ranging (LLR) to the Apollo and Lunokhod Cube Corner Retroreflectors (CCRs) provided several tests of General Relativity (GR). When deployed, the Apollo/Lunokhod CCRs design contributed only a negligible fraction of the ranging error budget. Today the improvement over the years in the laser ground stations makes the lunar libration contribution relevant. So the libration now dominates the error budget limiting the precision of the experimental tests of gravitational theories. The MoonLIGHT-2 project (Moon Laser Instrumentation for General relativity High-accuracy Tests - Phase 2) is a next-generation LLR payload developed by the Satellite/lunar/GNSS laser ranging/altimetry and Cube/microsat Characterization Facilities Laboratory (SCF _ Lab) at the INFN-LNF in collaboration with the University of Maryland. With its unique design consisting of a single large CCR unaffected by librations, MoonLIGHT-2 can significantly reduce error contribution of the reflectors to the measurement of the lunar geodetic precession and other GR tests compared to Apollo/Lunokhod CCRs. This paper treats only this specific next-generation lunar laser retroreflector (MoonLIGHT-2) and it is by no means intended to address other contributions to the global LLR error budget. MoonLIGHT-2 is approved to be launched with the Moon Express 1(MEX-1) mission and will be deployed on the Moon surface in 2018. To validate/optimize MoonLIGHT-2, the SCF _ Lab is carrying out a unique experimental test called SCF-Test: the concurrent measurement of the optical Far Field Diffraction Pattern (FFDP) and the temperature distribution of the CCR under thermal conditions produced with a close-match solar simulator and simulated space environment. The focus of this paper is to describe the SCF _ Lab specialized characterization of the performance of our next-generation LLR payload. While this payload will improve the contribution of the error budget of the space segment (MoonLIGHT-2) to GR tests and to constraints on new gravitational theories (like non-minimally coupled gravity and spacetime torsion), the description of the associated physics analysis and global LLR error budget is outside of the chosen scope of present paper. We note that, according to Reasenberg et al. (2016), software models used for LLR physics and lunar science cannot process residuals with an accuracy better than few centimeters and that, in order to process millimeter ranging data (or better) coming from (not only) future reflectors, it is necessary to update and improve the respective models inside the software package. The work presented here on results of the SCF-test thermal and optical analysis shows that a good performance is expected by MoonLIGHT-2 after its deployment on the Moon. This in turn will stimulate improvements in LLR ground segment hardware and help refine the LLR software code and models. Without a significant improvement of the LLR space segment, the acquisition of improved ground LLR hardware and challenging LLR software refinements may languish for lack of motivation, since the librations of the old generation LLR payloads largely dominate the global LLR error budget.

  14. Ab initio SCF calculations on the potential energy surface of potassium cyanide (KCN)

    NASA Astrophysics Data System (ADS)

    Wormer, Paul E. S.; Tennyson, Jonathan

    1981-08-01

    The potential energy surface of KCN has been generated by ab initio SCF calculations in the region of equilibrium bond distances. An analytic representation of the surface is presented. The calculations show that the bonding between K and CN is ionic, and that the structure of KCN is triangular, which confirms recent experimental findings. The computed geometry is &KCN = 62.4°, rCK = 5.492a0, and rCN = 2.186a0.

  15. Excited-state potential-energy surfaces of metal-adsorbed organic molecules from linear expansion Δ-self-consistent field density-functional theory (ΔSCF-DFT).

    PubMed

    Maurer, Reinhard J; Reuter, Karsten

    2013-07-07

    Accurate and efficient simulation of excited state properties is an important and much aspired cornerstone in the study of adsorbate dynamics on metal surfaces. To this end, the recently proposed linear expansion Δ-self-consistent field method by Gavnholt et al. [Phys. Rev. B 78, 075441 (2008)] presents an efficient alternative to time consuming quasi-particle calculations. In this method, the standard Kohn-Sham equations of density-functional theory are solved with the constraint of a non-equilibrium occupation in a region of Hilbert-space resembling gas-phase orbitals of the adsorbate. In this work, we discuss the applicability of this method for the excited-state dynamics of metal-surface mounted organic adsorbates, specifically in the context of molecular switching. We present necessary advancements to allow for a consistent quality description of excited-state potential-energy surfaces (PESs), and illustrate the concept with the application to Azobenzene adsorbed on Ag(111) and Au(111) surfaces. We find that the explicit inclusion of substrate electronic states modifies the topologies of intra-molecular excited-state PESs of the molecule due to image charge and hybridization effects. While the molecule in gas phase shows a clear energetic separation of resonances that induce isomerization and backreaction, the surface-adsorbed molecule does not. The concomitant possibly simultaneous induction of both processes would lead to a significantly reduced switching efficiency of such a mechanism.

  16. A New Global Potential Energy Surface for the Hydroperoxyl Radical, HO2: Reaction Coefficients for H + O2 and Vibrational Splittings for H Atom Transfer

    NASA Technical Reports Server (NTRS)

    Dateo, Christopher E.; Arnold, James O. (Technical Monitor)

    1994-01-01

    A new analytic global potential energy surface describing the hydroperoxyl radical system H((sup 2)S) + O2(X (sup 3)Sigma((sup -)(sub g))) (reversible reaction) HO2 ((X-tilde) (sup 2)A'') (reversible reaction) O((sup 3)P) + O H (X (sup 2)Pi) has been fitted using the ab initio complete active space SCF (self-consistent-field)/externally contracted configuration interaction (CASSCF/CCI) energy calculations of Walch and Duchovic. Results of quasiclassical trajectory studies to determine the rate coefficients of the forward and reverse reactions at combustion temperatures will be presented. In addition, vibrational energy levels were calculated using the quantum DVR-DGB (discrete variable representation-distributed Gaussian basis) method and the splitting due to H atom migration is investigated. The material of the proposed presentation was reviewed and the technical content will not reveal any information not already in the public domain and will not give any foreign industry or government a competitive advantage.

  17. The Climate-Agriculture-Modeling and Decision Tool (CAMDT) for Climate Risk Management in Agriculture

    NASA Astrophysics Data System (ADS)

    Ines, A. V. M.; Han, E.; Baethgen, W.

    2017-12-01

    Advances in seasonal climate forecasts (SCFs) during the past decades have brought great potential to improve agricultural climate risk managements associated with inter-annual climate variability. In spite of popular uses of crop simulation models in addressing climate risk problems, the models cannot readily take seasonal climate predictions issued in the format of tercile probabilities of most likely rainfall categories (i.e, below-, near- and above-normal). When a skillful SCF is linked with the crop simulation models, the informative climate information can be further translated into actionable agronomic terms and thus better support strategic and tactical decisions. In other words, crop modeling connected with a given SCF allows to simulate "what-if" scenarios with different crop choices or management practices and better inform the decision makers. In this paper, we present a decision support tool, called CAMDT (Climate Agriculture Modeling and Decision Tool), which seamlessly integrates probabilistic SCFs to DSSAT-CSM-Rice model to guide decision-makers in adopting appropriate crop and agricultural water management practices for given climatic conditions. The CAMDT has a functionality to disaggregate a probabilistic SCF into daily weather realizations (either a parametric or non-parametric disaggregation method) and to run DSSAT-CSM-Rice with the disaggregated weather realizations. The convenient graphical user-interface allows easy implementation of several "what-if" scenarios for non-technical users and visualize the results of the scenario runs. In addition, the CAMDT also translates crop model outputs to economic terms once the user provides expected crop price and cost. The CAMDT is a practical tool for real-world applications, specifically for agricultural climate risk management in the Bicol region, Philippines, having a great flexibility for being adapted to other crops or regions in the world. CAMDT GitHub: https://github.com/Agro-Climate/CAMDT

  18. The electron affinities of C{sub 3}O and C{sub 4}O

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rienstra-Kiracofe, J.C.; Ellison, G.B.; Hoffman, B.C.

    The authors predict the adiabatic electron affinities of C{sub 3}O and C{sub 4}O based on electronic structure calculations, using a large triple-{zeta} basis set with polarization and diffuse functions (TZ2Pf+diff) with the SCF, CCSD, and CCSD(T) methods as well as with the aug-cc-pVDZ and aug-cc-pVTZ basis sets. The results imply electron affinities for C{sub 3}O and C{sub 4}O; EA(C{sub 3}O) = 0.93 eV {+-} 0.10 and EA(C{sub 4}O) = 2.99 {+-} 0.10. The EA(C{sub 3}O) is 0.41 eV lower than the experimental value of 1.34 {+-} 0.15 eV, while the EA(C{sub 4}O) is 0.94 eV higher than the experimental valuemore » of 2.05 {+-} 0.15 eV. Optimized geometries for all species at each level of theory are given, and harmonic vibrational frequencies are reported at the SCF/TZ2Pf+diff and CCSD/aug-cc-pVDZ levels.« less

  19. Parallel SCF Adaptor Capture Proteomics Reveals a Role for SCFFBXL17 in NRF2 Activation via BACH1 Repressor Turnover

    PubMed Central

    Tan, Meng-Kwang Marcus; Lim, Hui-Jun; Bennett, Eric J.; Shi, Yang; Harper, J. Wade

    2014-01-01

    Modular Cullin-RING E3 ubiquitin ligases (CRLs) use substrate binding adaptor proteins to specify target ubiquitylation. Many of the ~200 human CRL adaptor proteins remain poorly studied due to a shortage of efficient methods to identify biologically relevant substrates. Here, we report the development of Parallel Adaptor Capture (PAC) proteomics, and its use to systematically identify candidate targets for the leucine-rich repeat family of F-box proteins (FBXLs) that function with SKP1-CUL1-F-box protein (SCF) E3s. In validation experiments, we identify the unstudied F-box protein FBXL17 as a regulator of the NFR2 oxidative stress pathway. We demonstrate that FBXL17 controls the transcription of the NRF2 target HMOX1 via turnover of the transcriptional repressor BACH1 in the absence or presence of extrinsic oxidative stress. This work identifies a role for SCFFBXL17 in controlling the threshold for NRF2-dependent gene activation and provides a framework for elucidating the functions of CRL adaptor proteins. PMID:24035498

  20. Computer-based attention training in the schools for children with attention deficit/hyperactivity disorder: a preliminary trial.

    PubMed

    Steiner, Naomi J; Sheldrick, Radley Christopher; Gotthelf, David; Perrin, Ellen C

    2011-07-01

    Objective. This study examined the efficacy of 2 computer-based training systems to teach children with attention deficit/hyperactivity disorder (ADHD) to attend more effectively. Design/methods. A total of 41 children with ADHD from 2 middle schools were randomly assigned to receive 2 sessions a week at school of either neurofeedback (NF) or attention training through a standard computer format (SCF), either immediately or after a 6-month wait (waitlist control group). Parents, children, and teachers completed questionnaires pre- and postintervention. Results. Primary parents in the NF condition reported significant (P < .05) change on Conners's Rating Scales-Revised (CRS-R) and Behavior Assessment Scales for Children (BASC) subscales; and in the SCF condition, they reported significant (P < .05) change on the CRS-R Inattention scale and ADHD index, the BASC Attention Problems Scale, and on the Behavioral Rating Inventory of Executive Functioning (BRIEF). Conclusion. This randomized control trial provides preliminary evidence of the effectiveness of computer-based interventions for ADHD and supports the feasibility of offering them in a school setting.

  1. Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.

    PubMed

    Khudyakov, Jane I; D'haeseleer, Patrik; Borglin, Sharon E; Deangelis, Kristen M; Woo, Hannah; Lindquist, Erika A; Hazen, Terry C; Simmons, Blake A; Thelen, Michael P

    2012-08-07

    To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. We previously isolated Enterobacter lignolyticus strain SCF1, a lignocellulolytic bacterium from tropical rain forest soil, and report here that it can grow in the presence of 0.5 M 1-ethyl-3-methylimidazolium chloride, a commonly used ionic liquid. We investigated molecular mechanisms of SCF1 ionic liquid tolerance using a combination of phenotypic growth assays, phospholipid fatty acid analysis, and RNA sequencing technologies. Potential modes of resistance to 1-ethyl-3-methylimidazolium chloride include an increase in cyclopropane fatty acids in the cell membrane, scavenging of compatible solutes, up-regulation of osmoprotectant transporters and drug efflux pumps, and down-regulation of membrane porins. These findings represent an important first step in understanding mechanisms of ionic liquid resistance in bacteria and provide a basis for engineering microbial tolerance.

  2. The high-pressure electronic structure of magnesiowustite (Mg, Fe)O: applications to the physics and chemistry of the lower mantle

    USGS Publications Warehouse

    Sherman, David M.

    1991-01-01

    The electronic structure of magnesiowustite is investigated using self-consistent field X?? scattered wave (SCF-X??-SW) molecular orbital calculations on (FeO6)10- and (FeMg12O14)2- clusters. Calculated one-electron transition energies are used to interpret the optical spectrum of (Mg, Fe)O. The results are applied to the electrical and thermal conductivity of the lower mantle. This is especially true if Fe2+ adopts the low-spin configuration. The geophysically significant properties of (Fe, Mg)O probably result from defect Fe3+. -from Author

  3. Polymers at interfaces and in colloidal dispersions.

    PubMed

    Fleer, Gerard J

    2010-09-15

    This review is an extended version of the Overbeek lecture 2009, given at the occasion of the 23rd Conference of ECIS (European Colloid and Interface Society) in Antalya, where I received the fifth Overbeek Gold Medal awarded by ECIS. I first summarize the basics of numerical SF-SCF: the Scheutjens-Fleer version of Self-Consistent-Field theory for inhomogeneous systems, including polymer adsorption and depletion. The conformational statistics are taken from the (non-SCF) DiMarzio-Rubin lattice model for homopolymer adsorption, which enumerates the conformational details exactly by a discrete propagator for the endpoint distribution but does not account for polymer-solvent interaction and for the volume-filling constraint. SF-SCF corrects for this by adjusting the field such that it becomes self-consistent. The model can be generalized to more complex systems: polydispersity, brushes, random and block copolymers, polyelectrolytes, branching, surfactants, micelles, membranes, vesicles, wetting, etc. On a mean-field level the results are exact; the disadvantage is that only numerical data are obtained. Extensions to excluded-volume polymers are in progress. Analytical approximations for simple systems are based upon solving the Edwards diffusion equation. This equation is the continuum variant of the lattice propagator, but ignores the finite segment size (analogous to the Poisson-Boltzmann equation without a Stern layer). By using the discrete propagator for segments next to the surface as the boundary condition in the continuum model, the finite segment size can be introduced into the continuum description, like the ion size in the Stern-Poisson-Boltzmann model. In most cases a ground-state approximation is needed to find analytical solutions. In this way realistic analytical approximations for simple cases can be found, including depletion effects that occur in mixtures of colloids plus non-adsorbing polymers. In the final part of this review I discuss a generalization of the free-volume theory (FVT) for the phase behavior of colloids and non-adsorbing polymer. In FVT the polymer is considered to be ideal: the osmotic pressure Pi follows the Van 't Hoff law, the depletion thickness delta equals the radius of gyration. This restricts the validity of FVT to the so-called colloid limit (polymer much smaller than the colloids). We have been able to find simple analytical approximations for Pi and delta which account for non-ideality and include established results for the semidilute limit. So we could generalize FVT to GFVT, and can now also describe the so-called protein limit (polymer larger than the 'protein-like' colloids), where the binodal polymer concentrations scale in a simple way with the polymer/colloid size ratio. For an intermediate case (polymer size approximately colloid size) we could give a quantitative description of careful experimental data. Copyright 2010 Elsevier B.V. All rights reserved.

  4. Scalability Analysis and Use of Compression at the Goddard DAAC and End-to-End MODIS Transfers

    NASA Technical Reports Server (NTRS)

    Menasce, Daniel A.

    1998-01-01

    The goal of this task is to analyze the performance of single and multiple FTP transfer between SCF's and the Goddard DAAC. We developed an analytic model to compute the performance of FTP sessions as a function of various key parameters, implemented the model as a program called FTP Analyzer, and carried out validations with real data obtained by running single and multiple FTP transfer between GSFC and the Miami SCF. The input parameters to the model include the mix to FTP sessions (scenario), and for each FTP session, the file size. The network parameters include the round trip time, packet loss rate, the limiting bandwidth of the network connecting the SCF to a DAAC, TCP's basic timeout, TCP's Maximum Segment Size, and TCP's Maximum Receiver's Window Size. The modeling approach used consisted of modeling TCP's overall throughput, computing TCP's delay per FTP transfer, and then solving a queuing network model that includes the FTP clients and servers.

  5. On the uniqueness of the constrained space orbital variation (CSOV) technique

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.

    1986-01-01

    Several CSOV analyses are performed for the 1Sigma(+) state of NiCO, and it is shown that the importance of the CO sigma donation, Ni pi back donation, and interunit polarizations are virtually independent of the order of the CSOV steps, provided that the open-shell 3d sigma and 4s Ni orbitals are orthogonalized to the CO. This order of orthogonalization is consistent with the polarization of the Ni observed in the unconstrained SCF wavefunction. If instead the CO is orthogonalized to the open-shell Ni orbitals, the frozen orbital repulsion and entire CSOV analysis becomes unphysical. A comparison of the SCF and CAS SCF descriptions for the NiCO 1Sigma(+) state shows the importance of the s to d promotion and sd hybridization in reducing the repulsion and increasing the Ni to CO pi bonding. For LiF, CSOV analyses starting from both the neutral and ionic asymptotes show the bonding to be predominantly Li(+) - F(-). These examples show the uniqueness of the CSOV decomposition.

  6. SCF(KMD) controls cytokinin signaling by regulating the degradation of type-B response regulators.

    PubMed

    Kim, Hyo Jung; Chiang, Yi-Hsuan; Kieber, Joseph J; Schaller, G Eric

    2013-06-11

    Cytokinins are plant hormones that play critical roles in growth and development. In Arabidopsis, the transcriptional response to cytokinin is regulated by action of type-B Arabidopsis response regulators (ARRs). Although central elements in the cytokinin signal transduction pathway have been identified, mechanisms controlling output remain to be elucidated. Here we demonstrate that a family of F-box proteins, called the kiss me deadly (KMD) family, targets type-B ARR proteins for degradation. KMD proteins form an S-phase kinase-associated PROTEIN1 (SKP1)/Cullin/F-box protein (SCF) E3 ubiquitin ligase complex and directly interact with type-B ARR proteins. Loss-of-function KMD mutants stabilize type-B ARRs and exhibit an enhanced cytokinin response. In contrast, plants with elevated KMD expression destabilize type-B ARR proteins leading to cytokinin insensitivity. Our results support a model in which an SCF(KMD) complex negatively regulates cytokinin responses by controlling levels of a key family of transcription factors.

  7. Gyre-scale deep convection in the subpolar North Atlantic Ocean during winter 2014-2015

    NASA Astrophysics Data System (ADS)

    Piron, A.; Thierry, V.; Mercier, H.; Caniaux, G.

    2017-02-01

    Using Argo floats, we show that a major deep convective activity occurred simultaneously in the Labrador Sea (LAB), south of Cape Farewell (SCF), and the Irminger Sea (IRM) during winter 2014-2015. Convection was driven by exceptional heat loss to the atmosphere (up to 50% higher than the climatological mean). This is the first observation of deep convection over such a widespread area. Mixed layer depths exceptionally reached 1700 m in SCF and 1400 m in IRM. The deep thermocline density gradient limited the mixed layer deepening in the Labrador Sea to 1800 m. Potential densities of deep waters were similar in the three basins (27.73-27.74 kg m-3) but warmer by 0.3°C and saltier by 0.04 in IRM than in LAB and SCF, meaning that each basin formed locally its own deep water. The cold anomaly that developed recently in the North Atlantic Ocean favored and was enhanced by this exceptional convection.

  8. Resveratrol improves prostate fibrosis during progression of urinary dysfunction in chronic prostatitis.

    PubMed

    He, Yi; Zeng, Hui-Zhi; Yu, Yang; Zhang, Jia-Shu; Duan, Xingping; Zeng, Xiao-Na; Gong, Feng-Tao; Liu, Qi; Yang, Bo

    2017-09-01

    We investigated whether prostate fibrosis was associated with urinary dysfunction in chronic prostatitis (CP) and whether resveratrol improved urinary dysfunction and the underlying molecular mechanism. Rat model of CP was established via subcutaneous injections of DPT vaccine and subsequently treated with resveratrol. Bladder pressure and volume tests investigated the effect of resveratrol on urinary dysfunction in CP rats. Western blotting and immunohistochemical staining examined the expression level of C-kit/SCF and TGF-β/Wnt/β-catenin. Compared to the control group, the maximum capacity of the bladder, residual urine volume and maximum voiding pressure, the activity of C-kit/SCF and TGF-β/Wnt/β-catenin pathways were increased significantly in the CP group. Resveratrol treatment significantly improved these factors. CP induced significantly prostate fibrosis, which exhibits a close relationship with urinary dysfunction. Resveratrol improved fibrosis, which may be associated with the suppression of C-kit/SCF and TGF-β/Wnt/β-catenin pathway. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Structural Basis for Activation of the Receptor Tyrosine Kinase KIT by Stem Cell Factor

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yuzawa,S.; Opatowsky, Y.; Zhang, Z.

    2007-01-01

    Stem Cell Factor (SCF) initiates its multiple cellular responses by binding to the ectodomain of KIT, resulting in tyrosine kinase activation. We describe the crystal structure of the entire ectodomain of KIT before and after SCF stimulation. The structures show that KIT dimerization is driven by SCF binding whose sole role is to bring two KIT molecules together. Receptor dimerization is followed by conformational changes that enable lateral interactions between membrane proximal Ig-like domains D4 and D5 of two KIT molecules. Experiments with cultured cells show that KIT activation is compromised by point mutations in amino acids critical for D4-D4more » interaction. Moreover, a variety of oncogenic mutations are mapped to the D5-D5 interface. Since key hallmarks of KIT structures, ligand-induced receptor dimerization, and the critical residues in the D4-D4 interface, are conserved in other receptors, the mechanism of KIT stimulation unveiled in this report may apply for other receptor activation.« less

  10. Caspase-activated ROCK-1 allows erythroblast terminal maturation independently of cytokine-induced Rho signaling

    PubMed Central

    Gabet, A-S; Coulon, S; Fricot, A; Vandekerckhove, J; Chang, Y; Ribeil, J-A; Lordier, L; Zermati, Y; Asnafi, V; Belaid, Z; Debili, N; Vainchenker, W; Varet, B; Hermine, O; Courtois, G

    2011-01-01

    Stem cell factor (SCF) and erythropoietin are strictly required for preventing apoptosis and stimulating proliferation, allowing the differentiation of erythroid precursors from colony-forming unit-E to the polychromatophilic stage. In contrast, terminal maturation to generate reticulocytes occurs independently of cytokine signaling by a mechanism not fully understood. Terminal differentiation is characterized by a sequence of morphological changes including a progressive decrease in cell size, chromatin condensation in the nucleus and disappearance of organelles, which requires transient caspase activation. These events are followed by nucleus extrusion as a consequence of plasma membrane and cytoskeleton reorganization. Here, we show that in early step, SCF stimulates the Rho/ROCK pathway until the basophilic stage. Thereafter, ROCK-1 is activated independently of Rho signaling by caspase-3-mediated cleavage, allowing terminal maturation at least in part through phosphorylation of the light chain of myosin II. Therefore, in this differentiation system, final maturation occurs independently of SCF signaling through caspase-induced ROCK-1 kinase activation. PMID:21072057

  11. Preparation of carbon fiber unsaturated sizing agent for enhancing interfacial strength of carbon fiber/vinyl ester resin composite

    NASA Astrophysics Data System (ADS)

    Jiao, Weiwei; Cai, Yemeng; Liu, Wenbo; Yang, Fan; Jiang, Long; Jiao, Weicheng; Wang, Rongguo

    2018-05-01

    The practical application of carbon fiber (CF) reinforced vinyl ester resin (VE) composite was hampered seriously by the poor interfacial adhesion property. In this work, a novel unsaturated sizing agent was designed and prepared to improve the interfacial strength by covalently bonding CF with VE matrix. The main component of the sizing agent, N-(4‧4-diaminodiphenyl methane)-2-hydroxypropyl methacrylate (DMHM), was synthesized and confirmed by FTIR and NMR. XPS results of sized carbon fiber (SCF) showed that DMHM has adhered to desized fiber surface and reacted with some active functional groups on the surface. The SCF was characterized by high surface roughness and surface energy (especially the polar component), which means better wettability by VE. As a result, the interface shear strength and interlaminar shear strength of SCF/VE composite were enhanced by 96.56% and 66.07% respectively compared with CF/VE composite, benefited mainly from the strong and tough interphase.

  12. In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery

    PubMed Central

    Bahal, Raman; Ali McNeer, Nicole; Quijano, Elias; Liu, Yanfeng; Sulkowski, Parker; Turchick, Audrey; Lu, Yi-Chien; Bhunia, Dinesh C.; Manna, Arunava; Greiner, Dale L.; Brehm, Michael A.; Cheng, Christopher J.; López-Giráldez, Francesc; Ricciardi, Adele; Beloor, Jagadish; Krause, Diane S.; Kumar, Priti; Gallagher, Patrick G.; Braddock, Demetrios T.; Mark Saltzman, W.; Ly, Danith H.; Glazer, Peter M.

    2016-01-01

    The blood disorder, β-thalassaemia, is considered an attractive target for gene correction. Site-specific triplex formation has been shown to induce DNA repair and thereby catalyse genome editing. Here we report that triplex-forming peptide nucleic acids (PNAs) substituted at the γ position plus stimulation of the stem cell factor (SCF)/c-Kit pathway yielded high levels of gene editing in haematopoietic stem cells (HSCs) in a mouse model of human β-thalassaemia. Injection of thalassemic mice with SCF plus nanoparticles containing γPNAs and donor DNAs ameliorated the disease phenotype, with sustained elevation of blood haemoglobin levels into the normal range, reduced reticulocytosis, reversal of splenomegaly and up to 7% β-globin gene correction in HSCs, with extremely low off-target effects. The combination of nanoparticle delivery, next generation γPNAs and SCF treatment may offer a minimally invasive treatment for genetic disorders of the blood that can be achieved safely and simply by intravenous administration. PMID:27782131

  13. Evaluation of advanced combustion concepts for dry NO sub x suppression with coal-derived, gaseous fuels

    NASA Technical Reports Server (NTRS)

    Beebe, K. W.; Symonds, R. A.; Notardonato, J. J.

    1982-01-01

    The emissions performance of a rich lean combustor (developed for liquid fuels) was determined for combustion of simulated coal gases ranging in heating value from 167 to 244 Btu/scf (7.0 to 10.3 MJ/NCM). The 244 Btu/scf gas is typical of the product gas from an oxygen blown gasifier, while the 167 Btu/scf gas is similar to that from an air blown gasifier. NOx performance of the rich lean combustor did not meet program goals with the 244 Btu/scf gas because of high thermal NOx, similar to levels expected from conventional lean burning combustors. The NOx emissions are attributed to inadequate fuel air mixing in the rich stage resulting from the design of the large central fuel nozzle delivering 71% of the total gas flow. NOx yield from ammonia injected into the fuel gas decreased rapidly with increasing ammonia level, and is projected to be less than 10% at NH3 levels of 0.5% or higher. NOx generation from NH3 is significant at ammonia concentrations significantly less than 0.5%. These levels may occur depending on fuel gas cleanup system design. CO emissions, combustion efficiency, smoke and other operational performance parameters were satisfactory. A test was completed with a catalytic combustor concept with petroleum distillate fuel. Reactor stage NOx emissions were low (1.4g NOx/kg fuel). CO emissions and combustion efficiency were satisfactory. Airflow split instabilities occurred which eventually led to test termination.

  14. High temperature fiber sensor using the interference effect within a suspended core microstructured optical fiber

    NASA Astrophysics Data System (ADS)

    Nguyen, Linh V.; Warren-Smith, Stephen C.; Ebendorff-Heidepriem, Heike; Monro, Tanya M.

    2016-04-01

    We report a high temperature fiber sensor based on the multimode interference effect within a suspended core microstructured optical fiber (SCF). By splicing a short section of SCF with a lead-in single-mode fiber (SMF), the sensor head was formed. A complex interference pattern was obtained in the reflection spectrum as the result of the multiple excited modes in the SCF. The complexity of the interference indicates that there are more than two dominantly excited modes in the SCF, as resolved by Fast Fourier Transform (FFT) analysis of the interference. The proposed sensor was subjected to temperature variation from 20°C to 1100°C. The fringe of the filtered spectrum red-shifted linearly with respect to temperature varying between 20°C and 1100°C, with similar temperature sensitivity for increasing and decreasing temperature. Phase monitoring was used for an extended temperature experiment (80 hours) in which the sensor was subjected to several different temperature variation conditions namely (i) step-wise increase/decrease with 100°C steps between 20°C and 1100°C, (ii) dwelling overnight at 400°C, (iii) free fall from 1100°C to 132°C, and (iv) continuous increase of temperature from 132°C to 1100°C. Our approach serves as a simple and cost-effective alternative to the better-known high temperature fiber sensors such as the fiber Bragg grating (FBG) in sapphire fibers or regenerated FBG in photosensitive optical fibers.

  15. SCF/C-Kit/JNK/AP-1 Signaling Pathway Promotes Claudin-3 Expression in Colonic Epithelium and Colorectal Carcinoma.

    PubMed

    Wang, Yaxi; Sun, Tingyi; Sun, Haimei; Yang, Shu; Li, Dandan; Zhou, Deshan

    2017-04-06

    Claudin-3 is a major protein of tight junctions (TJs) in the intestinal epithelium and is critical for maintaining cell-cell adhesion, barrier function, and epithelium polarity. Recent studies have shown high claudin-3 levels in several solid tumors, but the regulation mechanism of claudin-3 expression remains poorly understood. In the present study, colorectal cancer (CRC) tissues, HT-29 and DLD-1 CRC cell lines, CRC murine model (C57BL/6 mice) and c-kit loss-of-function mutant mice were used. We demonstrated that elevated claudin-3 levels were positively correlated with highly expressed c-kit in CRC tissues based upon analysis of protein expression. In vitro, claudin-3 expression was clearly increased in CRC cells by overexpressed c-kit or stimulated by exogenous recombinant human stem cell factor (rhSCF), while significantly decreased by the treatment with c-kit or c-Jun N-terminal kinase (JNK) inhibitors. Chromatin immunoprecipitation (ChIP) and luciferase reporter assay showed that SCF/c-kit signaling significantly promoted activator protein-1 (AP-1) binding with CLDN-3 promoter and enhanced its transcription activity. Furthermore, decreased expression of claudin-3 was obtained in the colonic epithelium from the c-Kit loss-of-function mutant mice. In conclusion, SCF/c-kit-JNK/AP-1 signaling pathway significantly promoted claudin-3 expression in colonic epithelium and CRC, which could contribute to epithelial barrier function maintenance and to CRC development.

  16. Joint DEnKF-albedo assimilation scheme that considers the common land model subgrid heterogeneity and a snow density-based observation operator for improving snow depth simulations

    NASA Astrophysics Data System (ADS)

    Xu, Jianhui; Zhang, Feifei; Zhao, Yi; Shu, Hong; Zhong, Kaiwen

    2016-07-01

    For the large-area snow depth (SD) data sets with high spatial resolution in the Altay region of Northern Xinjiang, China, we present a deterministic ensemble Kalman filter (DEnKF)-albedo assimilation scheme that considers the common land model (CoLM) subgrid heterogeneity. In the albedo assimilation of DEnKF-albedo, the assimilated albedos over each subgrid tile are estimated with the MCD43C1 bidirectional reflectance distribution function (BRDF) parameters product and CoLM calculated solar zenith angle. The BRDF parameters are hypothesized to be consistent over all subgrid tiles within a specified grid. In the SCF assimilation of DEnKF-albedo, a DEnKF combining a snow density-based observation operator considers the effects of the CoLM subgrid heterogeneity and is employed to assimilate MODIS SCF to update SD states over all subgrid tiles. The MODIS SCF over a grid is compared with the area-weighted sum of model predicted SCF over all the subgrid tiles within the grid. The results are validated with in situ SD measurements and AMSR-E product. Compared with the simulations, the DEnKF-albedo scheme can reduce errors of SD simulations and accurately simulate the seasonal variability of SD. Furthermore, it can improve simulations of SD spatiotemporal distribution in the Altay region, which is more accurate and shows more detail than the AMSR-E product.

  17. Studies of an Isolated 15N- 15N Spin Pair. Off-Angle Fast-Sample-Spinning NMR and Self-Consistent-Field Calculations for Diazo Systems

    NASA Astrophysics Data System (ADS)

    Challoner, Robin; Harris, Robin K.; Tossell, John A.

    1997-05-01

    An off-magic-angle spinning study of the nonassociated molecular solid, doubly15N-labeled 5-methyl-2-diazobenzenesulphonic acid hydrochloride (I) is reported. The validity of the off-magic-angle spinning approach under fast-spinning conditions is verified by average Hamiltonian theory. Ab initio SCF calculations were performed on the simpler molecule, C6H5N2+, to provide the shielding parameters, the dipolar coupling between the two nitrogen nuclei, and the electric field gradient existing at both the α-nitrogen and β-nitrogen sites. The calculated values are in good agreement with the shielding and effective dipolar coupling data elucidated in the present investigation, and with a previous study of the two singly15N-labeled isotopomers in which information concerning the electric field gradient at the α and β sites was deduced.

  18. Significant Effect of Acupressure in Elevating Blood Stem Cell Factor During Chemotherapy in Patients With Gynecologic Cancer.

    PubMed

    Shih, Ya-Wen; Yang, Shun-Fa; Chien, Ming-Hsien; Chang, Ching-Wen; Chang, Vincent H S; Tsai, Hsiu-Ting

    2017-12-09

    Chemotherapy is used mainly to treat and control the progression of gynecological cancer. Bone marrow suppression, one of the adverse side effects of chemotherapy, may decrease immune function, increasing the risk of serious, fatal infections. The aims of this study were to evaluate the effectiveness of noninvasive acupressure in preventing and diminishing chemotherapy-induced myelosuppression in patients with gynecologic cancer and to determine whether this effect is associated with the regulation of the expressions of granulocyte-macrophage colony-stimulating factor and stem cell factor (SCF). In total, 28 women with gynecological cancer were randomly assigned either to the experimental group (n = 10) or to the control group (n = 18). The experimental group received acupressure of 5-minute duration to the Hegu (LI4), Quchi (LI11), Xuehai (SP10), Sanyinjiao (SP6), Taixi (K3), Zusanli (ST36), Taichong (LR3), and Baihui (GV20) points, respectively, three times per day for 6 weeks. The control group did not receive the acupressure intervention. The blood count, including white blood cells, platelets, and hemoglobin, and serum levels for SCF and granulocyte-macrophage colony-stimulating factor were assessed before (pretest) and 6 weeks after (posttest) the participants' first course of chemotherapy. At posttest, blood hemoglobin had significantly decreased from (mean ± SD) 11.6 ± 2.2 to 10.8 ±1.6 mg/dl (p = .03) in the control group. However, no significant pretest-posttest difference in hemoglobin concentration (11.4 ± 1.0 vs. 10.9 ± 1.1 mg/dl) was detected in the experimental group. Levels of SCF increased significantly between pretest and posttest in both the control group (from 1196.10 ± 293.17 to 1325.05 ± 253.77 ng/ml; p = .01) and the acupressure group (from 1046.78 ± 469.52 to 1387.06 ± 310.00 ng/ml; p = .007). In addition, a borderline difference (p = .05) in mean pretest-posttest SCF increase was found between the acupressure group (340.28 ± 255.46 ng/ml) and the control group (128.94 ± 250.64 ng/ml). Finally, a significant time-dependent interactive effect was found between acupressure and the increased blood level of SCF at posttest (β = 211.34, p = .02). The findings support that acupressure on specific acupoints increases blood SCF levels significantly, which may help protect chemotherapy patients from experiencing reduced hemoglobin levels and may relieve chemotherapy-induced myelosuppression in patients with gynecologic cancer. This noninvasive approach is suggested for practical implementation in patients undergoing a course of chemotherapy.

  19. NSs Virulence Factor of Rift Valley Fever Virus Engages the F-Box Proteins FBXW11 and β-TRCP1 To Degrade the Antiviral Protein Kinase PKR

    PubMed Central

    Kainulainen, Markus; Lau, Simone; Samuel, Charles E.; Hornung, Veit

    2016-01-01

    ABSTRACT Rift Valley fever virus (RVFV, family Bunyaviridae, genus Phlebovirus) is a relevant pathogen of both humans and livestock in Africa. The nonstructural protein NSs is a major virulence factor known to suppress the type I interferon (IFN) response by inhibiting host cell transcription and by proteasomal degradation of a major antiviral IFN effector, the translation-inhibiting protein kinase PKR. Here, we identified components of the modular SCF (Skp1, Cul1, F-box protein)-type E3 ubiquitin ligases as mediators of PKR destruction by NSs. Small interfering RNAs (siRNAs) against the conserved SCF subunit Skp1 protected PKR from NSs-mediated degradation. Consequently, RVFV replication was severely reduced in Skp1-depleted cells when PKR was present. SCF complexes have a variable F-box protein subunit that determines substrate specificity for ubiquitination. We performed an siRNA screen for all (about 70) human F-box proteins and found FBXW11 to be involved in PKR degradation. The partial stabilization of PKR by FBXW11 depletion upregulated PKR autophosphorylation and phosphorylation of the PKR substrate eIF2α and caused a shutoff of host cell protein synthesis in RVFV-infected cells. To maximally protect PKR from the action of NSs, knockdown of structurally and functionally related FBXW1 (also known as β-TRCP1), in addition to FBXW11 deletion, was necessary. Consequently, NSs was found to interact with both FBXW11 and β-TRCP1. Thus, NSs eliminates the antiviral kinase PKR by recruitment of SCF-type E3 ubiquitin ligases containing FBXW11 and β-TRCP1 as substrate recognition subunits. This antagonism of PKR by NSs is essential for efficient RVFV replication in mammalian cells. IMPORTANCE Rift Valley fever virus is a pathogen of humans and animals that has the potential to spread from Africa and the Arabian Peninsula to other regions. A major virulence mechanism is the proteasomal degradation of the antiviral kinase PKR by the viral protein NSs. Here, we demonstrate that NSs requires E3 ubiquitin ligase complexes of the SCF (Skp1, Cul1, F-box protein) type to destroy PKR. SCF-type complexes can engage variant ubiquitination substrate recognition subunits, and we found the F-box proteins FBXW11 and β-TRCP1 to be relevant for the action of NSs against PKR. Thus, we identified the host cell factors that are critically needed by Rift Valley fever virus to uphold its replication against the potent antiviral kinase PKR. PMID:27122577

  20. Evaluation of soluble corn fiber on chemical composition and nitrogen-corrected true metabolizable energy and its effects on in vitro fermentation and in vivo responses in dogs.

    PubMed

    Panasevich, M R; Kerr, K R; Serao, M C Rossoni; de Godoy, M R C; Guérin-Deremaux, L; Lynch, G L; Wils, D; Dowd, S E; Fahey, G C; Swanson, K S; Dilger, R N

    2015-05-01

    Dietary fermentable fiber is known to benefit intestinal health of companion animals. Soluble corn fiber (SCF) was evaluated for its chemical composition, nitrogen-corrected true ME (TMEn) content, in vitro digestion and fermentation characteristics, and in vivo effects on nutrient digestibility, fecal fermentation end products, and modulation of the fecal microbiome of dogs. Soluble corn fiber contained 78% total dietary fiber, all present as soluble dietary fiber; 56% was low molecular weight soluble fiber (did not precipitate in 95% ethanol). The SCF also contained 26% starch and 8% resistant starch and had a TMEn value of 2.6 kcal/g. Soluble corn fiber was first subjected to in vitro hydrolytic-enzymatic digestion to determine extent of digestibility and then fermented using dog fecal inoculum, with fermentative outcomes measured at 0, 3, 6, 9, and 12 h. Hydrolytic-enzymatic digestion of SCF was only 7%. In vitro fermentation showed increased (P < 0.05) concentrations of short-chain fatty acids through 12 h, with acetate, propionate, and butyrate reaching peak concentrations of 1,803, 926, and 112 μmol/g DM, respectively. Fermentability of SCF was higher (P < 0.05) than for cellulose but lower (P < 0.05) than for pectin. In the in vivo experiment, 10 female dogs (6.4 ± 0.2 yr and 22 ± 2.1 kg) received 5 diets with graded concentrations of SCF (0, 0.5, 0.75, 1.0, or 1.25% [as-is basis]) replacing cellulose in a replicated 5 × 5 Latin square design. Dogs were first acclimated to the experimental diets for 10 d followed by 4 d of total fecal collection. Fresh fecal samples were collected to measure fecal pH and fermentation end products and permit a microbiome analysis. For microbiome analysis, extraction of DNA was followed by amplification of the V4 to V6 variable region of the 16S rRNA gene using barcoded primers. Sequences were classified into taxonomic levels using a nucleotide basic local alignment search tool (BLASTn) against a curated GreenGenes database. Few changes in nutrient digestibility or fecal fermentation end products or stool consistency were observed, and no appreciable modulation of the fecal microbiome occurred. In conclusion, SCF was fermentable in vitro, but higher dietary concentrations may be necessary to elicit potential in vivo responses.

  1. Granulocyte-colony stimulating factor and stem cell factor are the crucial factors in long-term culture of human primitive hematopoietic cells supported by a murine stromal cell line.

    PubMed

    Nishi, N; Ishikawa, R; Inoue, H; Nishikawa, M; Kakeda, M; Yoneya, T; Tsumura, H; Ohashi, H; Yamaguchi, Y; Motoki, K; Sudo, T; Mori, K J

    1996-09-01

    The findings that murine marrow stromal cell line MS-5 supported the proliferation of human lineage-negative (Lin-) CD34+CD38- bone marrow cells in long-term culture have been reported. In this study, we analyzed this proliferating activity of MS-5-conditioned medium (CM) on human primitive hematopoietic cells. When Lin-CD34+CD38- cells of normal human cord blood cells were co-cultured with MS-5, colony forming cells (CFCs) were maintained over 7 weeks in vitro. Prevention of contact between MS-5 and Lin-CD34+CD38- cells by using membrane filter (0.45 micron) was negligible for this activity. This indicated that the activity of MS-5 on human primitive hematopoietic cells is a soluble factor(s) secreted from MS-5, which is not induced by the contact between MS-5 and Lin-CD34+CD38- cells. We tried to purify this soluble activity. An active material with a molecular weight of about 150 kDa, determined by gel filtration chromatography, solely supported the growth of Lin-CD34+CD38- cells and Mo7e, a human megakaryocytic cell line. This activity not only reacted with anti-mouse stem cell factor (mSCF) antibody on Western blots, but it was also neutralized in the presence of anti-mSCF antibody. Another active material with a molecular weight of about 20-30 kDa synergized with mSCF to stimulate the growth of Lin-CD34+CD38- cells but failed to do so alone, although this synergy was inhibited in the presence of soluble mouse granulocyte-colony stimulating factor (mG-CSF) receptor, which is a chimeric protein consisting of the extracellular domain of mG-CSF receptor and the Fe region of human IgG1. In addition, the latter molecule supported the growth of the G-CSF dependent cell line FD/GR3, which is a murine myeloid leukemia cell line, FDC-P2, transfected with mG-CSF receptor cDNA. Adding of anti-mSCF antibody and soluble mG-CSF receptor to the culture completely abrogated the activity of MS-5-CM. Recombinant (r) mSCF and rmG-CSF had synergistic activity on the growth of Lin-CD34+CD38- cells. These results indicated that the activity on Lin-CD34+CD38- cells included in MS-5-CM is based upon the synergistic effects of mSCF and mG-CSF.

  2. Vertical Electron Detachment Energies for Octahedral Closed-Shell Multiply Charged Anions

    DTIC Science & Technology

    1994-04-22

    however, at low theoretical levels, motivating us to extend the investigations to: a) higher levels of theory, b) analogous closed-shell singly- and...hundredths of an eV. This further supports our choice of SBKJ+diff as the basis set for the production runs. The SCF relaxation energies for F- and Cl...intensities for the product molecules ML 5(’)" (D3h) and ML 4 (n-2 )" 15 (Td) were determined at the SCF/SBKJ level and are reported in Table V

  3. Effect of molecular environment on the vibrational dynamics of pyrimidine bases as analysed by NIS, optical spectroscopy and quantum mechanical force fields

    NASA Astrophysics Data System (ADS)

    Ghomi, M.; Aamouche, A.; Cadioli, B.; Berthier, G.; Grajcar, L.; Baron, M. H.

    1997-06-01

    A complete set of vibrational spectra, obtained from several spectroscopic techniques, i.e. neutron inelastic scattering (NIS), Raman scattering and infrared absorption (IR), has been used in order to assign the vibrational modes of pyrimidine bases (uracil, thymine, cytosine) and their N-deuterated species. The spectra of solid and aqueous samples allowed us to analyse the effects of hydrogen bonding in crystal and in solution. In a first step, to assign the observed vibrational modes, we have resorted to harmonic quantum mechanical force field, calculated at SCF + MP2 level using double-zeta 6-31G and D95V basis sets with non-standard exponents for d-orbital polarisation functions. In order to improve the agreement between the experimental results obtained in condensed phases and the calculated ones based on isolated molecules, the molecular force field has been scaled. In a second step, to estimate the effect of intermolecular interactions on the vibrational dynamics of pyrimidine bases, we have undertaken additional calculations with the density functional theory (DFT) method using B3LYP functionals and polarised 6-31G basis sets. Two theoretical models have been considered: 1. a uracil embedded in a dielectric continuum ( ɛ = 78), and 2. a uracil H-bonded to two water molecules (through N1 and N3 atoms).

  4. Nanoparticles in the pharmaceutical industry and the use of supercritical fluid technologies for nanoparticle production.

    PubMed

    Sheth, Pratik; Sandhu, Harpreet; Singhal, Dharmendra; Malick, Waseem; Shah, Navnit; Kislalioglu, M Serpil

    2012-05-01

    Poor aqueous solubility of drug candidates is a major challenge for the pharmaceutical scientists involved in drug development. Particle size reduction appears as an effective and versatile option for solubility improvement. Nanonization is an attractive solution to improve the bioavailability of the poorly soluble drugs, improved therapies, in vivo imaging, in vitro diagnostics and for the production of biomaterials and active implants. In drug delivery, application of nanotechnology is commonly referred to as Nano Drug Delivery Systems (NDDS). In this article, commercially available nanosized drugs, their dosage forms and proprietors, as well as the methods used for preparation like milling, high pressure homogenization, vacuum deposition, and high temperature evaporation were listed. Unlike the traditional methods used for the particle size reduction, supercritical fluid-processing techniques offer advantages ranging from superior particle size control to clean processing. The primary focus of this review article is the use of supercritical CO2 based technologies for small particle generation. Particles that have the smooth surfaces, small particle size and distribution and free flowing can be obtained with particular SCF techniques. In almost all techniques, the dominating process variables may be thermodynamic and aerodynamic in nature, and the design of the particle collection environment. Rapid Expansion of Supercritical Solutions (RESS), Supercritical Anti Solvent (SAS) and Particles from Gas Saturated Solutions (PGSS) are three groups of processes which lead to the production of fine and monodisperse powders. Few of them may also control crystal polymorphism. Among the aforementioned processes, RESS involves dissolving a drug in a supercritical fluid (SCF) and passing it through an appropriate nozzle. Rapid depressurization of this solution causes an extremely rapid nucleation of the product. This process has been known for a long time but its application is limited. Carbon dioxide, which is the only supercritical fluid that is preferentially used in pharmaceutical processes, is not a good solvent for many Active Pharmaceutical Ingredients (API). Various researchers have modified the RESS process to overcome its solubilizing limitations, by introducing RESOLV, RESAS, and RESS-SC. Overall, all RESS based processes are difficult to scale up. The SAS processes are based on decreasing the solvent power of a polar organic solvent in which the substrate (API & polymer of interest) is dissolved, by saturating it with carbon dioxide (CO2) at supercritical conditions. CO2 causes precipitation and recrystalization of the drug. SAS is scalable and can be applied to a wide variety of APIs and polymers. Minor modifications of basic SAS process include GAS, ASES, SAS-DEM and SAS-EM. Processes where SCF is used as an anti solvent and dispersing agent include SEDS, SAA, and A-SAIS. The mechanisms and applications of these processes were briefly discussed. In PGSS, CO2 is dissolved in organic solutions or melted compounds and it is successfully used for manufacturing drug products as well as for drying purposes. The two widely used methods, PGSSdrying and CAN-BD SCF, were also included in discussions. Among the limitations of the techniques involved, the poor solvent power of CO2, the cost and necessity of voluminous usage of the CO2 can be mentioned. There is still confusion in contribution of each variable on the particle morphology and properties regardless of the number of mechanistic studies available. The advantages of especially SAS and PGSS based techniques are the production of the nano or micro sized spherical particles with smooth surfaces and narrow particle size distribution. Regardless of its advantages, the reasons why 25 years of active research, and more than 10 years of process development could not promote the use of (SCF) technology, and produced only few commercial drug products, necessitate further evaluation of this technique.

  5. Melanocyte development: with a message of encouragement to young women scientists.

    PubMed

    Mizoguchi, Masako

    2004-10-01

    This is a semi-biographical review describing my research on melanocyte development and related personal experiences. Having been educated and trained as a dermatologist, I have been involved in many clinically-oriented studies, however, what has always interested me the most is pigment cell biology. Since I started working at St Marianna University in 1991, I have been undertaking research on melanocyte development and relevant growth factors using mice as models. My research in this field was inspired by my collaborations with various scientists, mostly from the field of biology. Many of these specialists I have met at meetings of the Societies of Pigment Cell Research (PCR). Stem cell factor (SCF, Kitl) and endothelin 3 (EDN3) have been identified as indispensable factors regulating the development of melanocytes. Mice mutant at loci encoding those factors (or their receptors) such as Sl/Sl (receptors W/W) and ls/ls (receptors s/s) have white coat colors and white patches, respectively. Our murine neural crest cell (NCC) primary cultures derived from Sl/Sl embryos showed that EDN3 cannot develop melanocyte precursors without SCF and that EDN3 can elicit proliferation and differentiation in the presence of SCF. These results suggest that without EDN3 and the endothelin type B receptor (EDNRB), melanocytes can not fully increase in number, which could well be the cause of the partial white coat color of ls/ls and s/s mice. Contamination with factors derived from the serum in medium or in feeder cells sometimes causes experimental errors, and therefore we established three immortal cell lines derived from NCC in different developmental stages and designated them as NCCmelb4, NCCmelb4M5 and NCCmelan5, all of which can survive without feeder cells. Using these cell lines and NCC primary cultures, we studied the effect of many factors related to melanocyte development. From the results, it has become evident that Vitamin D3 induces EDNRB expression by NCCmelb4 cells. In addition to the International Pigment Cell Conference (IPCC), I have also taken part in many annual meetings of the Japanese Society for Pigment Cell Research (JSPCR), Pan American Society for Pigment Cell Research (PASPCR) and European Society for Pigment Cell Research (ESPCR). Not only have I learned a great deal, I have enjoyed myself immensely at those meetings. Moreover, I have made many good friends there, some of whom I have collaborated with in my research. To conclude, I would like to give my message 'be ambitious' to young scientists, especially young women.

  6. Molecular Characterization of PDGFR-α/PDGF-A and c-KIT/SCF in Gliosarcomas

    PubMed Central

    Reis, Rui M.; Martins, Albino; Ribeiro, Susana A.; Basto, Diana; Longatto-Filho, Adhemar; Schmitt, Fernando C.; Lopes, José M.

    2005-01-01

    Gliosarcomas are rare and poorly characterized malignant brain tumors that exhibit a biphasic tissue pattern with areas of gliomatous and sarcomatous differentiation. These tumors are histological variants of glioblastoma, displaying a similar genetic profile and dismal prognosis. Up-regulation of PDGFR subfamily of tyrosine kinase members, PDGFR-α and c-Kit, and their intracellular effectors RAS/RAF/MAPK has a crucial role in the cancer development. In addition, signal transduction mediated by activating mutations of c-Kit and PDGFR can be effectively blocked by specific tyrosine kinase inhibitors, such as Imatinib mesylate. The aim of this study was to characterize the molecular alterations of PDGFR signaling in gliosarcomas. Six cases were analyzed by immunohistochemistry for the expression of PDGFR-α, c-Kit and their ligands PDGF-A and SCF, respectively. The cases were further evaluated for the presence of activating mutations of PDGFR-α (exons 12 and 18) and c-kit (exons 9, 11, 13, and 17), as well as B-RAF (exons 11 and 15). Expression of PDGF-A was found in all cases and co-expression of PDGFR-α was observed in three cases. Four cases showed expression of SCF, and c-Kit was observed only in one case that also expressed SCF. Generally, immunoreaction predominates in the glial component. The mutational analysis of PDGFR-α showed the presence of an IVS17-50insT intronic insertion in two cases, one of them also with a 2472C > T silent mutation; this silent mutation was also found in another case. Glioma cell line analysis of IVS17-50insT insertion showed no influence on PDGFR-α gene splicing. No mutations were detected in c-kit and B-RAF oncogenes. Our Results indicate that activating mutations of PDGFR-α, c-kit and B-RAF are absent in gliosarcomas. Nevertheless, the presence of a PDGFR-a/PDGFA and c-Kit/SCF autocrine/paracrine stimulation loop in a proportion of cases, supports the potential role of specific tyrosine kinase inhibitors in the treatment of gliosarcomas. PMID:16373964

  7. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Orellana, Roberto; Chaput, Gina; Markillie, Lye Meng

    The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growthmore » conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.« less

  8. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Orellana, Roberto; Chaput, Gina; Markillie, Lye Meng

    The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growthmore » conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, midexponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.« less

  9. Different auditory feedback control for echolocation and communication in horseshoe bats.

    PubMed

    Liu, Ying; Feng, Jiang; Metzner, Walter

    2013-01-01

    Auditory feedback from the animal's own voice is essential during bat echolocation: to optimize signal detection, bats continuously adjust various call parameters in response to changing echo signals. Auditory feedback seems also necessary for controlling many bat communication calls, although it remains unclear how auditory feedback control differs in echolocation and communication. We tackled this question by analyzing echolocation and communication in greater horseshoe bats, whose echolocation pulses are dominated by a constant frequency component that matches the frequency range they hear best. To maintain echoes within this "auditory fovea", horseshoe bats constantly adjust their echolocation call frequency depending on the frequency of the returning echo signal. This Doppler-shift compensation (DSC) behavior represents one of the most precise forms of sensory-motor feedback known. We examined the variability of echolocation pulses emitted at rest (resting frequencies, RFs) and one type of communication signal which resembles an echolocation pulse but is much shorter (short constant frequency communication calls, SCFs) and produced only during social interactions. We found that while RFs varied from day to day, corroborating earlier studies in other constant frequency bats, SCF-frequencies remained unchanged. In addition, RFs overlapped for some bats whereas SCF-frequencies were always distinctly different. This indicates that auditory feedback during echolocation changed with varying RFs but remained constant or may have been absent during emission of SCF calls for communication. This fundamentally different feedback mechanism for echolocation and communication may have enabled these bats to use SCF calls for individual recognition whereas they adjusted RF calls to accommodate the daily shifts of their auditory fovea.

  10. Different Auditory Feedback Control for Echolocation and Communication in Horseshoe Bats

    PubMed Central

    Liu, Ying; Feng, Jiang; Metzner, Walter

    2013-01-01

    Auditory feedback from the animal's own voice is essential during bat echolocation: to optimize signal detection, bats continuously adjust various call parameters in response to changing echo signals. Auditory feedback seems also necessary for controlling many bat communication calls, although it remains unclear how auditory feedback control differs in echolocation and communication. We tackled this question by analyzing echolocation and communication in greater horseshoe bats, whose echolocation pulses are dominated by a constant frequency component that matches the frequency range they hear best. To maintain echoes within this “auditory fovea”, horseshoe bats constantly adjust their echolocation call frequency depending on the frequency of the returning echo signal. This Doppler-shift compensation (DSC) behavior represents one of the most precise forms of sensory-motor feedback known. We examined the variability of echolocation pulses emitted at rest (resting frequencies, RFs) and one type of communication signal which resembles an echolocation pulse but is much shorter (short constant frequency communication calls, SCFs) and produced only during social interactions. We found that while RFs varied from day to day, corroborating earlier studies in other constant frequency bats, SCF-frequencies remained unchanged. In addition, RFs overlapped for some bats whereas SCF-frequencies were always distinctly different. This indicates that auditory feedback during echolocation changed with varying RFs but remained constant or may have been absent during emission of SCF calls for communication. This fundamentally different feedback mechanism for echolocation and communication may have enabled these bats to use SCF calls for individual recognition whereas they adjusted RF calls to accommodate the daily shifts of their auditory fovea. PMID:23638137

  11. Structural modifications of the salivary conditioning film upon exposure to sodium bicarbonate: implications for oral lubrication and mouthfeel.

    PubMed

    Ash, A; Wilde, P J; Bradshaw, D J; King, S P; Pratten, J R

    2016-03-14

    The salivary conditioning film (SCF) that forms on all surfaces in the mouth plays a key role in lubricating the oral cavity. As this film acts as an interface between tongue, enamel and oral mucosa, it is likely that any perturbations to its structure could potentially lead to a change in mouthfeel perception. This is often experienced after exposure to oral hygiene products. For example, consumers that use dentifrice that contain a high concentration of sodium bicarbonate (SB) often report a clean mouth feel after use; an attribute that is clearly desirable for oral hygiene products. However, the mechanisms by which SB interacts with the SCF to alter lubrication in the mouth is unknown. Therefore, saliva and the SCF was exposed to high ionic strength and alkaline solutions to elucidate whether the interactions observed were a direct result of SB, its high alkalinity or its ionic strength. Characteristics including bulk viscosity of saliva and the viscoelasticity of the interfacial salivary films that form at both the air/saliva and hydroxyapatite/saliva interfaces were tested. It was hypothesised that SB interacts with the SCF in two ways. Firstly, the ionic strength of SB shields electrostatic charges of salivary proteins, thus preventing protein crosslinking within the film and secondly; the alkaline pH (≈8.3) of SB reduces the gel-like structure of mucins present in the pellicle by disrupting disulphide bridging of the mucins via the ionization of their cysteine's thiol group, which has an isoelectric point of ≈8.3.

  12. Ectromelia virus encodes a family of Ankyrin/F-box proteins that regulate NFκB

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Burles, Kristin, E-mail: burles@ualberta.ca; Buuren, Nicholas van; Barry, Michele

    2014-11-15

    A notable feature of poxviruses is their ability to inhibit the antiviral response, including the nuclear factor kappa B (NFκB) pathway. NFκB is a transcription factor that is sequestered in the cytoplasm until cell stimulation, and relies on the SCF (Skp1, culllin-1, F-box) ubiquitin ligase to target its inhibitor, IκBα, for degradation. IκBα is recruited to the SCF by the F-box domain-containing protein βTrCP. Here, we show that ectromelia virus, the causative agent of mousepox, encodes four F-box-containing proteins, EVM002, EVM005, EVM154, and EVM165, all of which contain Ankyrin (Ank) domains. The Ank/F-box proteins inhibit NFκB nuclear translocation, and thismore » inhibition is dependent on the F-box domain. We also demonstrate that EVM002, EVM005, EVM154, and EVM165 prevent IκBα degradation, suggesting that they target the SCF. This study identifies a new mechanism by which ectromelia virus inhibits NFκB. - Highlights: • Ectromelia virus encodes four Ank/F-box proteins, EVM002, EVM005, EVM154 and EVM165. • The Ank/F-box proteins inhibit NFκB nuclear translocation, dependent on the F-box. • The Ank/F-box proteins prevent IκBα degradation, suggesting they target the SCF. • Deletion of a single Ank/F-box gene from ECTV does not prevent viral NFκB inhibition. • This study identifies a new mechanism by which ectromelia virus inhibits NFκB.« less

  13. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium.

    PubMed

    Orellana, Roberto; Chaput, Gina; Markillie, Lye Meng; Mitchell, Hugh; Gaffrey, Matt; Orr, Galya; DeAngelis, Kristen M

    2017-01-01

    The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.

  14. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium

    PubMed Central

    Chaput, Gina; Markillie, Lye Meng; Mitchell, Hugh; Gaffrey, Matt; Orr, Galya; DeAngelis, Kristen M.

    2017-01-01

    The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future. PMID:29049419

  15. Stress concentration factors at saddle and crown positions on the central brace of two-planar welded CHS DKT-connections

    NASA Astrophysics Data System (ADS)

    Ahmadi, Hamid; Lotfollahi-Yaghin, Mohammad Ali; Aminfar, Mohammad H.

    2012-03-01

    A set of parametric stress analyses was carried out for two-planar tubular DKT-joints under different axial loading conditions. The analysis results were used to present general remarks on the effects of the geometrical parameters on stress concentration factors (SCFs) at the inner saddle, outer saddle, and crown positions on the central brace. Based on results of finite element (FE) analysis and through nonlinear regression analysis, a new set of SCF parametric equations was established for fatigue design purposes. An assessment study of equations was conducted against the experimental data and original SCF database. The satisfaction of acceptance criteria proposed by the UK Department of Energy (UK DoE) was also checked. Results of parametric study showed that highly remarkable differences exist between the SCF values in a multi-planar DKT-joint and the corresponding SCFs in an equivalent uni-planar KT-joint having the same geometrical properties. It can be clearly concluded from this observation that using the equations proposed for uni-planar KT-connections to compute the SCFs in multi-planar DKT-joints will lead to either considerably under-predicting or over-predicting results. Hence, it is necessary to develop SCF formulae specially designed for multi-planar DKT-joints. Good results of equation assessment according to UK DoE acceptance criteria, high values of correlation coefficients, and the satisfactory agreement between the predictions of the proposed equations and the experimental data guarantee the accuracy of the equations. Therefore, the developed equations can be reliably used for fatigue design of offshore structures.

  16. Spatially Resolved Temperature and Water Vapor Concentration Distributions in Supersonic Combustion Facilities by TDLAT

    NASA Technical Reports Server (NTRS)

    Busa, K. M.; McDaniel J. C.; Diskin, G. S.; DePiro, M. J.; Capriotti, D. P.; Gaffney, R. L.

    2012-01-01

    Detailed knowledge of the internal structure of high-enthalpy flows can provide valuable insight to the performance of scramjet combustors. Tunable Diode Laser Absorption Spectroscopy (TDLAS) is often employed to measure temperature and species concentration. However, TDLAS is a path-integrated line-of-sight (LOS) measurement, and thus does not produce spatially resolved distributions. Tunable Diode Laser Absorption Tomography (TDLAT) is a non-intrusive measurement technique for determining two-dimensional spatially resolved distributions of temperature and species concentration in high enthalpy flows. TDLAT combines TDLAS with tomographic image reconstruction. More than 2500 separate line-of-sight TDLAS measurements are analyzed in order to produce highly resolved temperature and species concentration distributions. Measurements have been collected at the University of Virginia's Supersonic Combustion Facility (UVaSCF) as well as at the NASA Langley Direct-Connect Supersonic Combustion Test Facility (DCSCTF). Due to the UVaSCF s unique electrical heating and ability for vitiate addition, measurements collected at the UVaSCF are presented as a calibration of the technique. Measurements collected at the DCSCTF required significant modifications to system hardware and software designs due to its larger measurement area and shorter test duration. Tomographic temperature and water vapor concentration distributions are presented from experimentation on the UVaSCF operating at a high temperature non-reacting case for water vitiation level of 12%. Initial LOS measurements from the NASA Langley DCSCTF operating at an equivalence ratio of 0.5 are also presented. Results show the capability of TDLAT to adapt to several experimental setups and test parameters.

  17. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium

    DOE PAGES

    Orellana, Roberto; Chaput, Gina; Markillie, Lye Meng; ...

    2017-10-19

    The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growthmore » conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.« less

  18. Spontaneous cholecystocutaneous fistula as a primary manifestation of gallbladder adenocarcinoma associated with gallbladder lithiasis - case report.

    PubMed

    Micu, Bogdan Vasile; Andercou, Octavian Aurel; Micu, Carmen Maria; Militaru, Valentin; Jeican, IonuŢ Isaia; Bungărdean, Cătălina Ileana; Mogoantă, Stelian ŞtefăniŢă; Miclăuş, Dan Radu; Pop, Tudor Radu

    2017-01-01

    Spontaneous cholecystocutaneous fistula (SCF) is a rare complication of neglected calculous biliary disease and also an extremely rare complication of gallbladder neoplasm. This pathology has become even rarer because of prompt diagnosis and expedient surgical intervention for gallstones. So far, there is one published report of a SCF due to gallbladder adenocarcinoma. We present the case of a woman aged 87 years, admitted to the Vth Department of Surgery, Clinical Municipal Hospital of Cluj-Napoca (Romania) for a tumoral mass located in the epigastrium. In the epigastrium, the patient had three skin orifices of about 1-2 mm each, through which purulent secretion occurred. The abdominal ultrasound highlighted a cholecystocutaneous fistula with the presence of a subcutaneous gallstone. Intraoperatively, we found a cholecystocutaneous fistula, a 1 cm subcutaneous gallstone, gallbladder with thickened walls containing a cylinder-shaped gallstone of 5÷3 cm. Fistulectomy, gallstones extraction and cholecystectomy were performed. The histopathological examination highlighted gallbladder adenocarcinoma. In conclusion, SCF can be the first significant manifestation of gallbladder cancer associated with neglected calculous biliary disease.

  19. Ectromelia virus encodes a family of Ankyrin/F-box proteins that regulate NFκB.

    PubMed

    Burles, Kristin; van Buuren, Nicholas; Barry, Michele

    2014-11-01

    A notable feature of poxviruses is their ability to inhibit the antiviral response, including the nuclear factor kappa B (NFκB) pathway. NFκB is a transcription factor that is sequestered in the cytoplasm until cell stimulation, and relies on the SCF (Skp1, culllin-1, F-box) ubiquitin ligase to target its inhibitor, IκBα, for degradation. IκBα is recruited to the SCF by the F-box domain-containing protein βTrCP. Here, we show that ectromelia virus, the causative agent of mousepox, encodes four F-box-containing proteins, EVM002, EVM005, EVM154, and EVM165, all of which contain Ankyrin (Ank) domains. The Ank/F-box proteins inhibit NFκB nuclear translocation, and this inhibition is dependent on the F-box domain. We also demonstrate that EVM002, EVM005, EVM154, and EVM165 prevent IκBα degradation, suggesting that they target the SCF. This study identifies a new mechanism by which ectromelia virus inhibits NFκB. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. MLL-ENL cooperates with SCF to transform primary avian multipotent cells.

    PubMed

    Schulte, Cathleen E; von Lindern, Marieke; Steinlein, Peter; Beug, Hartmut; Wiedemann, Leanne M

    2002-08-15

    The MLL gene is targeted by chromosomal translocations, which give rise to heterologous MLL fusion proteins and are associated with distinct types of acute lymphoid and myeloid leukaemia. To determine how MLL fusion proteins alter the proliferation and/or differentiation of primary haematopoietic progenitors, we introduced the MLL-AF9 and MLL-ENL fusion proteins into primary chicken bone marrow cells. Both fusion proteins caused the sustained outgrowth of immature haematopoietic cells, which was strictly dependent on stem cell factor (SCF). The renewing cells have a long in vitro lifespan exceeding the Hayflick limit of avian cells. Analysis of clonal cultures identified the renewing cells as immature, multipotent progenitors, expressing erythroid, myeloid, lymphoid and stem cell surface markers. Employing a two-step commitment/differentiation protocol involving the controlled withdrawal of SCF, the MLL-ENL-transformed progenitors could be induced to terminal erythroid or myeloid differentiation. Finally, in cooperation with the weakly leukaemogenic receptor tyrosine kinase v-Sea, the MLL-ENL fusion protein gave rise to multilineage leukaemia in chicks, suggesting that other activated, receptor tyrosine kinases can substitute for ligand-activated c-Kit in vivo.

  1. Computational and Experimental Fluid-Structure Interaction Analysis of a High-Lift Wing with a Slat-Cove Filler for Noise Reduction

    NASA Technical Reports Server (NTRS)

    Scholten, William D.; Patterson, Ryan D.; Hartl, Darren J.; Strganac, Thomas W.; Chapelon, Quentin H. C.; Turner, Travis

    2017-01-01

    Airframe noise is a significant component of overall noise produced by transport aircraft during landing and approach (low speed maneuvers). A significant source for this noise is the cove of the leading-edge slat. The slat-cove filler (SCF) has been shown to be effective at mitigating slat noise. The objective of this work is to understand the fluid-structure interaction (FSI) behavior of a superelastic shape memory alloy (SMA) SCF in flow using both computational and physical models of a high-lift wing. Initial understanding of flow around the SCF and wing is obtained using computational fluid dynamics (CFD) analysis at various angles of attack. A framework compatible with an SMA constitutive model (implemented as a user material subroutine) is used to perform FSI analysis for multiple flow and configuration cases. A scaled physical model of the high-lift wing is constructed and tested in the Texas A&M 3 ft-by-4-foot wind tunnel. Initial validation of both CFD and FSI analysis is conducted by comparing lift, drag and pressure distributions with experimental results.

  2. [Evaluation of the treatment effectiveness of domestic G-SCF preparations in experiments on irradiated dogs].

    PubMed

    Rozhdestvenskiĭ, L M; Shliakova, T G; Shchegoleva, R A; Lisina, N I; Zorin, V V

    2013-01-01

    We have evaluated the treatment effectiveness of Leucostim and Neupomax in dogs exposed to radiation at lethal doses of 3 and 3.5 Gy, correspondingly, by testing the dynamics of the blood cell number, first of all, leucocytes and neutrophiles, and the 45-day survival. Supportive therapy for all the dogs, including the control ones, consisted in antibiotic treatment during the acute period of 7-24 days. It was shown that both pre-parations administered consecutively for about 17-21 days after irradiation positively influenced the dynamics of all blood cells but predominantly impacted the neutrophile number dynamics. The latter ones manifested a higher nadir level and an earlier onset of restoration in the G-SCF treated dogs in comparison with the control ones. The tendency to a positive influence on the survival has been shown in Neupomax-treated dogs exposed to 3.5 Gy of radiation (plus about 40%). The results of the experiments were in good accordance with the data by foreign authors who used Neupogen. This allows a conclusion that home-produced G-SCF preparations can replace their foreign analogues.

  3. Preoptimised VB: a fast method for the ground and excited states of ionic clusters II. Delocalised preoptimisation for He 2+, Ar 2+, He 3+ and Ar 3+

    NASA Astrophysics Data System (ADS)

    Archirel, Pierre

    1997-09-01

    We generalise the preoptimisation of orbitals within VB (Part I of this series) through letting the orbitals delocalise on the neighbouring fragments. The method is more accurate than the local preoptimisation. The method is tested on the rare gas clusters He 2+, Ar 2+, He 3+ and Ar 3+. The results are in good agreement with previously published data on these systems. We complete these data with higher excited states. The binding energies of (ArCO) +, (ArN 2) + and N 4+ are revisited. The simulation of the SCF method is extended to Cu +H 2O.

  4. Theoretical investigation of polarization effects in solution: Importance of solvent collective motions

    NASA Astrophysics Data System (ADS)

    Ishida, Tateki

    2015-01-01

    Recent theoretical studies on interesting topics related to polarization effects in solutions are presented. As one of interesting topics, ionic liquids (ILs) solvents are focused on. The collective dynamics of electronic polarizability through interionic dynamics and the effect of polarization in ILs, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), are studied with molecular dynamics simulation. Also, the time-dependent polarization effect on the probe betaine dye molecule, pyridinium N-phenoxide, in water is investigated by a time-dependent reference interaction site model self-consistent field (time-dependent RISM-SCF) approach. The importance of considering polarization effects on solution systems related to solvent collective motions is shown.

  5. An SCF and MCSCF description of the low-lying states of MgO. [Configuration State Functions Multiconfiguration Self Consistent Field

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.; Silver, D. M.; Yarkony, D. R.

    1980-01-01

    The paper presents the multiconfiguration-self-consistent (MCSCF) and configuration state functions (CSF) for the low-lying electronic states of MgO. It was shown that simple description of these states was possible provided the 1 Sigma(+) states are individually optimized at the MCSCF level, noting that the 1(3 Sigma)(+) and 2(1 Sigma)(+) states which nominally result from the same electron occupation are separated energetically. The molecular orbitals obtained at this level of approximation should provide a useful starting point for extended configuration interaction calculations since they have been optimized for the particular states of interest.

  6. Bend-resistant large mode area fiber with novel segmented cladding

    NASA Astrophysics Data System (ADS)

    Ma, Shaoshuo; Ning, Tigang; Pei, Li; Li, Jing; Zheng, Jingjing

    2018-01-01

    A novel structure of segment cladding fiber (SCF) with characteristics of bend-resistance and large-mode-area (LMA) is proposed. In this new structure, the high refractive index (RI) core is periodically surrounded by high RI fan-segmented claddings. Numerical investigations show that effective single-mode operation of the proposed fiber with mode field area of 700 μm2 can be achieved when the bending radius is 15 cm. Besides, this fiber is insensitive to the bending orientation at the ranging of [-180°, 180°]. The proposed design shows great potential in high power fiber lasers and amplifiers with compact structure.

  7. HeI photoelectron spectroscopic studies on the electronic structure of alkyl nitrosamines

    NASA Astrophysics Data System (ADS)

    Jiang, Peng; Qian, Ximei; Li, Chunhui; Qiao, Chunhua; Wang, Dianxun

    1997-10-01

    HeI photoelectron spectroscopic (PES) studies on the electronic structure of alkyl nitrosamines R 2N 2O (R = CH 3-, CH 3CH 2-, and CH 3CH 2CH 2-) are reported. The assignment of the PES bands for this series of compounds has been made with the aid of the band shapes, the band intensity and ab initio SCF MO calculations based on the 631 ∗ G basis sets. Both PES experiment and the ab initio SCF MO calculations show that the detoxification ability of nitrosamine with longer alkyl chain is stronger.

  8. NSs Virulence Factor of Rift Valley Fever Virus Engages the F-Box Proteins FBXW11 and β-TRCP1 To Degrade the Antiviral Protein Kinase PKR.

    PubMed

    Kainulainen, Markus; Lau, Simone; Samuel, Charles E; Hornung, Veit; Weber, Friedemann

    2016-07-01

    Rift Valley fever virus (RVFV, family Bunyaviridae, genus Phlebovirus) is a relevant pathogen of both humans and livestock in Africa. The nonstructural protein NSs is a major virulence factor known to suppress the type I interferon (IFN) response by inhibiting host cell transcription and by proteasomal degradation of a major antiviral IFN effector, the translation-inhibiting protein kinase PKR. Here, we identified components of the modular SCF (Skp1, Cul1, F-box protein)-type E3 ubiquitin ligases as mediators of PKR destruction by NSs. Small interfering RNAs (siRNAs) against the conserved SCF subunit Skp1 protected PKR from NSs-mediated degradation. Consequently, RVFV replication was severely reduced in Skp1-depleted cells when PKR was present. SCF complexes have a variable F-box protein subunit that determines substrate specificity for ubiquitination. We performed an siRNA screen for all (about 70) human F-box proteins and found FBXW11 to be involved in PKR degradation. The partial stabilization of PKR by FBXW11 depletion upregulated PKR autophosphorylation and phosphorylation of the PKR substrate eIF2α and caused a shutoff of host cell protein synthesis in RVFV-infected cells. To maximally protect PKR from the action of NSs, knockdown of structurally and functionally related FBXW1 (also known as β-TRCP1), in addition to FBXW11 deletion, was necessary. Consequently, NSs was found to interact with both FBXW11 and β-TRCP1. Thus, NSs eliminates the antiviral kinase PKR by recruitment of SCF-type E3 ubiquitin ligases containing FBXW11 and β-TRCP1 as substrate recognition subunits. This antagonism of PKR by NSs is essential for efficient RVFV replication in mammalian cells. Rift Valley fever virus is a pathogen of humans and animals that has the potential to spread from Africa and the Arabian Peninsula to other regions. A major virulence mechanism is the proteasomal degradation of the antiviral kinase PKR by the viral protein NSs. Here, we demonstrate that NSs requires E3 ubiquitin ligase complexes of the SCF (Skp1, Cul1, F-box protein) type to destroy PKR. SCF-type complexes can engage variant ubiquitination substrate recognition subunits, and we found the F-box proteins FBXW11 and β-TRCP1 to be relevant for the action of NSs against PKR. Thus, we identified the host cell factors that are critically needed by Rift Valley fever virus to uphold its replication against the potent antiviral kinase PKR. Copyright © 2016 Kainulainen et al.

  9. [Effects of naloxone on the expression of stem cell factor and C-kit receptor in combined oxygen-glucose deprivation of primary cultured human embryonic neuron in vitro].

    PubMed

    Zhu, Bo; Li, Lan-ying; Lü, Guo-yi; Xue, Yu-liang; Ye, Tie-hu

    2010-04-01

    To explore the effects of naloxone on the expression of c-kit receptor (c-kit R) and its ligand stem cell factor (SCF) in human embryo neuronal hypoxic injury. Serum-free cerebral cortical cultures prepared from embryonic human brains were deprived of both oxygen and glucose which would set up an environment more likely with that of in vivo ischemic injury. Neurons in 24-well culture plates were randomly divided into four groups: control group, hypoxia group, naloxone 0.5 microg/ml group and naloxone 10 microg/ml group. MTT assay and biological analysis were performed to study the cell death and the changes of extracellular concentrations of lactate dehydrogenase (LDH) after combined oxygen-glucose deprivation. Neurons in 25 ml culture flasks were also randomly allocated into four groups as previously described. Intracellular total RNA were extracted at different time points: pre-hypoxia, immediately after hypoxia, and 3, 6, 12, and 24 hours after reoxygenation. The changes of SCF/c-kit R mRNA expression in hypoxic neurons treated with different concentrations of naloxone pre and post oxygen-glucose deprivation were determined with RT-PCR. The cell vitality detected by MTT assay decreased significantly in hypoxia group and naloxone 0.5 microg/ml group when compared with control group (P<0.01), while no significant difference was found between naloxone 0.5 microg/ml group and hypoxia group or between naloxone 10 microg/ml group and control group. Extracellular concentration of LDH significantly increased in hypoxia group (P<0.05), while no difference was found between naloxone 0.5 microg/ml group and control group, between naloxone 0.5 microg/ml and hypoxia group, or between naloxone 10 microg/ml and control group (all P>0.05). Immediately after oxygen-glucose deprivation, the expression of SCF/c-kit R mRNA increased significantly (P<0.01). Among those the expression of SCF presented a distribution of double-peak value within 24 hours. After treated with different concentrations of naloxone, the peak value of each group were delayed to appear and went down with the increasing of naloxone concentration. The peak values in all treated groups were significantly different from that in control group (P<0.01). The expression of SCF/c-kit R mRNA increases at the early stage after combined oxygen-glucose deprivation. Naloxone 0.5 microg/ml can attenuate cell injuries and regulate the expression of SCF/c-kit R. Naloxone may protect neurons by modulating the expressions of some cytokines.

  10. Combined Approach for the Structural Characterization of Alkali Fluoroscandates: Solid-State NMR, Powder X-ray Diffraction, and Density Functional Theory Calculations.

    PubMed

    Rakhmatullin, Aydar; Polovov, Ilya B; Maltsev, Dmitry; Allix, Mathieu; Volkovich, Vladimir; Chukin, Andrey V; Boča, Miroslav; Bessada, Catherine

    2018-02-05

    The structures of several fluoroscandate compounds are presented here using a characterization approach combining powder X-ray diffraction and solid-state NMR. The structure of K 5 Sc 3 F 14 was fully determined from Rietveld refinement performed on powder X-ray diffraction data. Moreover, the local structures of NaScF 4 , Li 3 ScF 6 , KSc 2 F 7 , and Na 3 ScF 6 compounds were studied in detail from solid-state 19 F and 45 Sc NMR experiments. The 45 Sc chemical shift ranges for six- and seven-coordinated scandium environments were defined. The 19 F chemical shift ranges for bridging and terminal fluorine atoms were also determined. First-principles calculations of the 19 F and 45 Sc NMR parameters were carried out using plane-wave basis sets and periodic boundary conditions (CASTEP), and the results were compared with the experimental data. A good agreement between the calculated shielding constants and experimental chemical shifts was obtained. This demonstrates the good potential of computational methods in spectroscopic assignments of solid-state 45 Sc NMR spectroscopy.

  11. Immunohistochemical evidence for an endocrine/paracrine role for ghrelin in the reproductive tissues of sheep

    PubMed Central

    Miller, David W; Harrison, Joanne L; Brown, Yvonne A; Doyle, Una; Lindsay, Alanna; Adam, Clare L; Lea, Richard G

    2005-01-01

    Background The gut hormone, ghrelin, is involved in the neuroendocrine and metabolic responses to hunger. In monogastric species, circulating ghrelin levels show clear meal-related and body weight-related changes. The pattern of secretion and its role in ruminant species is less clear. Ghrelin acts via growth hormone secretagogue receptors (GHSR-1a) to alter food intake, fat utilization, and cellular proliferation. There is also evidence that ghrelin is involved in reproductive function. In the present study we used immunohistochemistry to investigate the presence of ghrelin and GHSR-1a in sheep reproductive tissues. In addition, we examined whether ghrelin and GHSR-1a protein expression is developmentally regulated in the adult and fetal ovine testis, and whether there is an association with markers of cellular proliferation, i.e. stem cell factor (SCF) and proliferating cell nuclear antigen (PCNA). Methods Antibodies raised against ghrelin and its functional receptor, GHSR-type 1a, were used in standard immunohistochemical protocols on various reproductive tissues collected from adult and fetal sheep. GHSR-1a mRNA presence was also confirmed by in situ hybridisation. SCF and PCNA immunoexpression was investigated in fetal testicular samples. Adult and fetal testicular immunostaining for ghrelin, GHSR-1a, SCF and PCNA was analysed using computer-aided image analysis. Image analysis data were subjected to one-way ANOVA, with differences in immunostaining between time-points determined by Fisher's least significant difference. Results In adult sheep tissue, ghrelin and GHSR-1a immunostaining was detected in the stomach (abomasum), anterior pituitary gland, testis, ovary, and hypothalamic and hindbrain regions of the brain. In the adult testis, there was a significant effect of season (photoperiod) on the level of immunostaining for ghrelin (p < 0.01) and GHSR-1a (p < 0.05). In the fetal sheep testis, there was a significant effect of gestational age on the level of immunostaining for ghrelin (p < 0.001), GHSR-1a (p < 0.05), SCF (p < 0.05) and PCNA (p < 0.01). Conclusion Evidence is presented for the presence of ghrelin and its receptor in various reproductive tissues of the adult and fetal sheep. In addition, the data indicate that testicular expression of ghrelin and its receptor is physiologically regulated in the adult and developmentally regulated in the fetus. Therefore, the ghrelin ligand/receptor system may have a role (endocrine and/or paracrine) in the development (cellular proliferation) and function of the reproductive axis of the sheep. PMID:16259638

  12. Magnolol pretreatment prevents sepsis-induced intestinal dysmotility by maintaining functional interstitial cells of Cajal.

    PubMed

    Miao, Bin; Zhang, Shuwen; Wang, Hong; Yang, Tiecheng; Zhou, Deshan; Wang, Bao-en

    2013-08-01

    The purpose of this study was to investigate the mechanism by which magnolol treatment prevents lipopolysaccharide (LPS)-induced septic dysmotility in mice. Sepsis was induced by intravenous tail vein injection of LPS (4 mg/kg body weight). Animals were divided into three groups: the magnolol-treated septic group, the placebo-treated septic group, and the control group. Intestinal transit and circular smooth muscle contraction were measured 12 h after LPS injection, and immunocytochemisty was performed to study the morphology of interstitial cells of Cajal (ICCs). Stem cell factor (SCF) expression and c-kit phosphorylation were determined by Western blot analysis, and the mRNA levels of inducible NO synthase (iNOS) were determined by RT-PCR. Nitric oxide (NO) content, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) concentration were detected using commercial kits. Intestinal transit and muscular contractility were significantly lower in the LPS-treated group than in the control group. Immunocytochemical experiments showed that the total number of ICCs, and the total and average lengths of the ICC processes were significantly decreased in the LPS-treated group compared with those in the control group. In LPS-treated animals, magnolol pretreatment significantly accelerated intestinal transit, increased circular muscle contraction, and prevented ICC morphology changes. Phosphorylation of c-kit and expression of SCF were significantly downregulated in LPS-treated animals compared with control animals. Magnolol pretreatment prevented sepsis-induced decreases in c-kit phosphorylation and SCF expression in LPS-treated animals. Magnolol pretreatment prevented the sepsis-induced increase in NO concentration, iNOS expression, and MDA concentration, and decrease in SOD activity in LPS-treated animals. Our results suggest that magnolol treatment prevents sepsis-induced intestinal dysmotility by regulating SCF/c-kit and NO signaling to maintain functional ICCs.

  13. Mast cells and fibroblasts work in concert to aggravate pulmonary fibrosis: role of transmembrane SCF and the PAR-2/PKC-α/Raf-1/p44/42 signaling pathway.

    PubMed

    Wygrecka, Malgorzata; Dahal, Bhola K; Kosanovic, Djuro; Petersen, Frank; Taborski, Brigitte; von Gerlach, Susanne; Didiasova, Miroslava; Zakrzewicz, Dariusz; Preissner, Klaus T; Schermuly, Ralph T; Markart, Philipp

    2013-06-01

    Mast cell (MC) accumulation has been demonstrated in the lungs of idiopathic pulmonary fibrosis (IPF) patients. Mediators released from MCs may regulate tissue remodeling processes, thereby contributing to IPF pathogenesis. We investigated the role of MC-fibroblast interaction in the progression of lung fibrosis. Increased numbers of activated MCs, in close proximity to fibroblast foci and alveolar type II cells, were observed in IPF lungs. Correspondingly elevated tryptase levels were detected in IPF lung tissue samples. Coculture of human lung MCs with human lung fibroblasts (HLFs) induced MC activation, as evinced by tryptase release, and stimulated HLF proliferation; IPF HLFs exhibited a significantly higher growth rate, compared with control. Tryptase stimulated HLF growth in a PAR-2/PKC-α/Raf-1/p44/42-dependent manner and potentiated extracellular matrix production, but independent of PKC-α, Raf-1, and p44/42 activities. Proproliferative properties of tryptase were attenuated by knockdown or pharmacological inhibition of PAR-2, PKC-α, Raf-1, or p44/42. Expression of transmembrane SCF, but not soluble SCF, was elevated in IPF lung tissue and in fibroblasts isolated from IPF lungs. Coculture of IPF HLFs with MCs enhanced MC survival and proliferation. These effects were cell-contact dependent and could be inhibited by application of anti-SCF antibody or CD117 inhibitor. Thus, fibroblasts and MCs appear to work in concert to perpetuate fibrotic processes and so contribute to lung fibrosis progression. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  14. Glycogen Synthase Kinase-3β is a pro-survival signal for the maintenance of human mast cell homeostasis

    PubMed Central

    Rådinger, Madeleine; Smrž, Daniel; Metcalfe, Dean D.; Gilfillan, Alasdair M.

    2011-01-01

    Homeostasis of mature tissue-resident mast cells is dependent on the relative activation of pro- and anti-apoptotic regulators. In this study we investigated the role of Glycogen Synthase Kinase-3β (GSK3β) in the survival of neoplastic and non-neoplastic human mast cells. GSK3β was observed to be phosphorylated at the Y216 activating residue under resting conditions in both the neoplastic HMC1.2 cell line and in peripheral blood-derived primary human mast cells (HuMCs), suggesting constitutive activation of GSK3β in these cells. Lentiviral-transduced short hairpin RNA (shRNA) knockdown of GSK3β in both the HMC1.2 cells and HuMCs resulted in a significant reduction in cell survival as determined with the MTT assay. The decrease in SCF-mediated survival in the GSK3β knockdown HuMCs was reflected by enhancement of SCF-withdrawal-induced apoptosis, as determined by Annexin V staining and caspase cleavage; and this was associated with a pronounced reduction in SCF-mediated phosphorylation of Src homology 2 domain-containing phosphatase 2 (SHP2) and ERK1/2 and reduced expression of the anti-apoptotic proteins Bcl-xl and Bcl-2. These data show that GSK3β is an essential anti-apoptotic factor in both neopastic and non-transformed primary human mast cells through the regulation of SCF-mediated SHP2 and ERK activation. Our data suggest that targeting of GSK3β with small molecular weight inhibitors such as CHIR 99021 may thus provide a mechanism for limiting mast cell survival and thus subsequently decreasing the intensity of the allergic inflammatory response. PMID:22039301

  15. Dietary supplementation with zinc oxide decreases expression of the stem cell factor in the small intestine of weanling pigs.

    PubMed

    Ou, Deyuan; Li, Defa; Cao, Yunhe; Li, Xilong; Yin, Jingdong; Qiao, Shiyan; Wu, Guoyao

    2007-12-01

    Dietary supplementation with a high level of zinc oxide (ZnO) has been shown to reduce the incidence of diarrhea in weanling pigs, but the underlying mechanisms remain largely unknown. Intestinal-mucosal mast cells, whose maturation and proliferation is under the control of the stem cell factor (SCF), play an important role in the etiology of diarrhea by releasing histamine. The present study was conducted to test the novel hypothesis that supplementing ZnO to the diet for weanling piglets may inhibit SCF expression in the small intestine, thereby reducing the number of mast cells, histamine release, and diarrhea. In Experiment 1, 32 piglets (28 days of age) were weaned and fed diets containing 100 or 3000 mg zinc/kg (as ZnO) for 10 days (16 piglets per group). In Experiment 2, two groups of 28-day-old piglets (8 piglets per group) were fed the 100- or 3000-mg zinc/kg diet as in Experiment 1, except that they were pair-fed the same amounts of feed. Supplementation with a high level of ZnO reduced the incidence of diarrhea in weanling piglets. Dietary Zn supplementation reduced expression of the SCF gene at both mRNA and protein levels, the number of mast cells in the mucosa and submucosa of the small intestine and histamine release from mucosal mast cells. Collectively, our results indicate that dietary supplementation with ZnO inhibits SCF expression in the small intestine, leading to reductions in the number of mast cells and histamine release. These findings may have important implications for the prevention of weaning-associated diarrhea in piglets.

  16. GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.

    PubMed

    Subhash, Santhilal; Kanduri, Chandrasekhar

    2016-09-13

    High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance of the affected genes from these high-throughput studies. However, currently available functional enrichment tools need to be updated frequently to adapt to new entries from the functional database repositories. Hence there is a need for a simplified tool that can perform functional enrichment analysis by using updated information directly from the source databases such as KEGG, Reactome or Gene Ontology etc. In this study, we focused on designing a command-line tool called GeneSCF (Gene Set Clustering based on Functional annotations), that can predict the functionally relevant biological information for a set of genes in a real-time updated manner. It is designed to handle information from more than 4000 organisms from freely available prominent functional databases like KEGG, Reactome and Gene Ontology. We successfully employed our tool on two of published datasets to predict the biologically relevant functional information. The core features of this tool were tested on Linux machines without the need for installation of more dependencies. GeneSCF is more reliable compared to other enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. More importantly, GeneSCF can run multiple gene lists simultaneously on different organisms thereby saving time for the users. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures.

  17. Effects of nebivolol on endothelial function and exercise parameters in patients with slow coronary flow.

    PubMed

    Tiryakioglu, Selma; Tiryakioglu, Osman; Ari, Hasan; Basel, Mehmet C; Bozat, Tahsin

    2009-11-03

    Earlier studies have reported that a decrease in exercise capacity might indicate endothelial dysfunction. However, the effects of improvement of endothelial functions on exercise capacity have not been evaluated. The aim of the present study is to investigate the effects of nebivolol on flow-mediated dilatation (FMD), and on the exercise capacities of the patients with slow coronary flow (SCF). The study population included 25 subjects with SCF (Group 1) documented by the thrombolysis in myocardial infarction (TIMI) frame count, and 25 control group (Group 2) subjects with normal coronary angiography, for a total of 50 subjects who underwent coronary angiography due to several indications and had no coronary lesion. The TIMI frame count (TFC) values of the subjects in Group I for left anterior descending artery, right coronary, and circumflex coronary artery were 61.8 +/- 30.6, 37.2 +/- 17.4, and 34.6 +/- 17.4, respectively. All the subjects received nebivolol 5 mg/day. At the end of the first month of FMD, the mean exercise duration (MED) and the Duke Scores of the patients with SCF were significantly higher than the baseline values. However, the values by the sixth month did not differ from that at the first month. Although a numerical improvement compared to the baseline values was observed for the subjects in Group 2 by the measurements at the end of the first and the sixth month, this difference was not statistically significant. Nebivolol treatment increases FMD in the subjects with SCF. The difference in the exercise parameters of these subjects is particularly dramatic, and such an outcome may indirectly indicate long-term improvement in endothelial function.

  18. Is local or central adiposity more strongly associated with incident knee osteoarthritis than the body mass index in men or women?

    PubMed

    Culvenor, A G; Felson, D T; Wirth, W; Dannhauer, T; Eckstein, F

    2018-05-25

    To determine whether central (abdominal) or peripheral (thigh) adiposity measures are associated with incident radiographic knee osteoarthritis (RKOA) independent of body mass index (BMI) and whether their relation to RKOA was stronger than that of BMI. 161 Osteoarthritis Initiative (OAI) participants (62% female) with incident RKOA (Kellgren/Lawrence grade 0/1 at baseline, developing an osteophyte and joint space narrowing (JSN) grade ≥1 by year-4) were matched to 186 controls (58% female) without incident RKOA. Baseline waist-height-ratio (WHtR), and anatomical cross-sectional areas of thigh subcutaneous (SCF) and intermuscular fat (IMF) were measured, the latter using axial magnetic resonance images. Logistic regression assessed the relationship between each adiposity measure and incident RKOA before and after adjustment for BMI, and area under receiver operating characteristic curves (AUC) for each adiposity measure was compared to that of BMI using chi-squared tests. BMI, WHtR, subcutaneous fat (SCF) and IMF were all significantly associated with incident RKOA when analysed separately, with similar effect sizes (odds ratio range 1.30-1.53). After adjusting for BMI, odds ratios (ORs) for WHtR, SCF and IMF were attenuated and no longer statistically significant. No measure of central or peripheral adiposity was significantly more strongly associated with incident RKOA than BMI. Results were similar for men and women. Although both central (WHtR) and peripheral (SCF and IMF) adiposity were significantly associated with incident RKOA, neither was more strongly associated with incident RKOA than BMI. The simple measure of BMI appears sufficient to capture the elevated risk of RKOA associated with greater amounts of localised adiposity. Copyright © 2018 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  19. Accurate quasiparticle calculation of x-ray photoelectron spectra of solids

    NASA Astrophysics Data System (ADS)

    Aoki, Tsubasa; Ohno, Kaoru

    2018-05-01

    It has been highly desired to provide an accurate and reliable method to calculate core electron binding energies (CEBEs) of crystals and to understand the final state screening effect on a core hole in high resolution x-ray photoelectron spectroscopy (XPS), because the ΔSCF method cannot be simply used for bulk systems. We propose to use the quasiparticle calculation based on many-body perturbation theory for this problem. In this study, CEBEs of band-gapped crystals, silicon, diamond, β-SiC, BN, and AlP, are investigated by means of the GW approximation (GWA) using the full ω integration and compared with the preexisting XPS data. The screening effect on a deep core hole is also investigated in detail by evaluating the relaxation energy (RE) from the core and valence contributions separately. Calculated results show that not only the valence electrons but also the core electrons have an important contribution to the RE, and the GWA have a tendency to underestimate CEBEs due to the excess RE. This underestimation can be improved by introducing the self-screening correction to the GWA. The resulting C1s, B1s, N1s, Si2p, and Al2p CEBEs are in excellent agreement with the experiments within 1 eV absolute error range. The present self-screening corrected GW approach has the capability to achieve the highly accurate prediction of CEBEs without any empirical parameter for band-gapped crystals, and provide a more reliable theoretical approach than the conventional ΔSCF-DFT method.

  20. Accurate quasiparticle calculation of x-ray photoelectron spectra of solids.

    PubMed

    Aoki, Tsubasa; Ohno, Kaoru

    2018-05-31

    It has been highly desired to provide an accurate and reliable method to calculate core electron binding energies (CEBEs) of crystals and to understand the final state screening effect on a core hole in high resolution x-ray photoelectron spectroscopy (XPS), because the ΔSCF method cannot be simply used for bulk systems. We propose to use the quasiparticle calculation based on many-body perturbation theory for this problem. In this study, CEBEs of band-gapped crystals, silicon, diamond, β-SiC, BN, and AlP, are investigated by means of the GW approximation (GWA) using the full ω integration and compared with the preexisting XPS data. The screening effect on a deep core hole is also investigated in detail by evaluating the relaxation energy (RE) from the core and valence contributions separately. Calculated results show that not only the valence electrons but also the core electrons have an important contribution to the RE, and the GWA have a tendency to underestimate CEBEs due to the excess RE. This underestimation can be improved by introducing the self-screening correction to the GWA. The resulting C1s, B1s, N1s, Si2p, and Al2p CEBEs are in excellent agreement with the experiments within 1 eV absolute error range. The present self-screening corrected GW approach has the capability to achieve the highly accurate prediction of CEBEs without any empirical parameter for band-gapped crystals, and provide a more reliable theoretical approach than the conventional ΔSCF-DFT method.

  1. A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding.

    PubMed

    Scemama, Anthony; Renon, Nicolas; Rapacioli, Mathias

    2014-06-10

    We present an algorithm and its parallel implementation for solving a self-consistent problem as encountered in Hartree-Fock or density functional theory. The algorithm takes advantage of the sparsity of matrices through the use of local molecular orbitals. The implementation allows one to exploit efficiently modern symmetric multiprocessing (SMP) computer architectures. As a first application, the algorithm is used within the density-functional-based tight binding method, for which most of the computational time is spent in the linear algebra routines (diagonalization of the Fock/Kohn-Sham matrix). We show that with this algorithm (i) single point calculations on very large systems (millions of atoms) can be performed on large SMP machines, (ii) calculations involving intermediate size systems (1000-100 000 atoms) are also strongly accelerated and can run efficiently on standard servers, and (iii) the error on the total energy due to the use of a cutoff in the molecular orbital coefficients can be controlled such that it remains smaller than the SCF convergence criterion.

  2. First-principles real-space study of electronic and optical excitations in rutile TiO 2 nanocrystals

    DOE PAGES

    Hung, Linda; Baishya, Kopinjol; Öğüt, Serdar

    2014-10-17

    We model rutile titanium dioxide nanocrystals (NCs) up to ~1.5 nm in size to study the effects of quantum confinement on their electronic and optical properties. Ionization potentials (IPs) and electron affinities (EAs) are obtained via the perturbative GW approximation (G 0W 0) and ΔSCF method for NCs up to 24 and 64 TiO 2 formula units, respectively. These demanding GW computations are made feasible by using a real-space framework that exploits quantum confinement to reduce the number of empty states needed in GW summations. Time-dependent density functional theory (TDDFT) is used to predict the optical properties of NCs upmore » to 64 TiO 2 units. For a NC containing only 2 TiO 2 units, the offsets of the IP and the EA from the corresponding bulk limits are of similar magnitude. However, as NC size increases, the EA is found to converge more slowly to the bulk limit than the IP. The EA values computed at the G 0W 0 and ΔSCF levels of theory are found to agree fairly well with each other, while the IPs computed with ΔSCF are consistently smaller than those computed with G 0W 0 by a roughly constant amount. TDDFT optical gaps exhibit weaker size dependence than GW quasiparticle gaps, and result in exciton binding energies on the order of eV. Finally, altering the dimensions of a fixed-size NC can change electronic and optical excitations up to several tenths of an eV. The largest NCs modeled are still quantum confined and do not yet have quasiparticle levels or optical gaps at bulk values. Nevertheless, we find that classical Mie-Gans theory can quite accurately reproduce the line shape of TDDFT absorption spectra, even for (anisotropic) TiO 2 NCs of subnanometer size.« less

  3. First-principles real-space study of electronic and optical excitations in rutile TiO2 nanocrystals

    NASA Astrophysics Data System (ADS)

    Hung, Linda; Baishya, Kopinjol; Ã-ǧüt, Serdar

    2014-10-01

    We model rutile titanium dioxide nanocrystals (NCs) up to ˜1.5 nm in size to study the effects of quantum confinement on their electronic and optical properties. Ionization potentials (IPs) and electron affinities (EAs) are obtained via the perturbative GW approximation (G0W0) and ΔSCF method for NCs up to 24 and 64 TiO2 formula units, respectively. These demanding GW computations are made feasible by using a real-space framework that exploits quantum confinement to reduce the number of empty states needed in GW summations. Time-dependent density functional theory (TDDFT) is used to predict the optical properties of NCs up to 64 TiO2 units. For a NC containing only 2 TiO2 units, the offsets of the IP and the EA from the corresponding bulk limits are of similar magnitude. However, as NC size increases, the EA is found to converge more slowly to the bulk limit than the IP. The EA values computed at the G0W0 and ΔSCF levels of theory are found to agree fairly well with each other, while the IPs computed with ΔSCF are consistently smaller than those computed with G0W0 by a roughly constant amount. TDDFT optical gaps exhibit weaker size dependence than GW quasiparticle gaps, and result in exciton binding energies on the order of eV. Altering the dimensions of a fixed-size NC can change electronic and optical excitations up to several tenths of an eV. The largest NCs modeled are still quantum confined and do not yet have quasiparticle levels or optical gaps at bulk values. Nevertheless, we find that classical Mie-Gans theory can quite accurately reproduce the line shape of TDDFT absorption spectra, even for (anisotropic) TiO2 NCs of subnanometer size.

  4. Theoretical study of the electric dipole moment function of the ClO molecule

    NASA Technical Reports Server (NTRS)

    Pettersson, L. G. M.; Langhoff, S. R.; Chong, D. P.

    1986-01-01

    The potential energy function and electric dipole moment function (EDMF) are computed for ClO X 2Pi using several different techniques to include electron correlation. The EDMF is used to compute Einstein coefficients, vibrational lifetimes, and dipole moments in higher vibrational levels. The band strength of the 1-0 fundamental transition is computed to be 12 + or - 2 per sq cm atm determined from infrared heterodyne spectroscopy. The theoretical methods used include SCF, CASSCF, multireference singles plus doubles configuration interaction (MRCI) and contracted CI, coupled pair functional (CPF), and a modified version of the CPF method. The results obtained using the different methods are critically compared.

  5. Skp1 Independent Function of Cdc53/Cul1 in F-box Protein Homeostasis.

    PubMed

    Mathur, Radhika; Yen, James L; Kaiser, Peter

    2015-12-01

    Abundance of substrate receptor subunits of Cullin-RING ubiquitin ligases (CRLs) is tightly controlled to maintain the full repertoire of CRLs. Unbalanced levels can lead to sequestration of CRL core components by a few overabundant substrate receptors. Numerous diseases, including cancer, have been associated with misregulation of substrate receptor components, particularly for the largest class of CRLs, the SCF ligases. One relevant mechanism that controls abundance of their substrate receptors, the F-box proteins, is autocatalytic ubiquitylation by intact SCF complex followed by proteasome-mediated degradation. Here we describe an additional pathway for regulation of F-box proteins on the example of yeast Met30. This ubiquitylation and degradation pathway acts on Met30 that is dissociated from Skp1. Unexpectedly, this pathway required the cullin component Cdc53/Cul1 but was independent of the other central SCF component Skp1. We demonstrated that this non-canonical degradation pathway is critical for chromosome stability and effective defense against heavy metal stress. More importantly, our results assign important biological functions to a sub-complex of cullin-RING ligases that comprises Cdc53/Rbx1/Cdc34, but is independent of Skp1.

  6. Linking F-box protein 7 and parkin to neuronal degeneration in Parkinson's disease (PD).

    PubMed

    Zhou, Zhi Dong; Sathiyamoorthy, Sushmitha; Angeles, Dario C; Tan, Eng King

    2016-04-18

    Mutations of F-box protein 7 (FBXO7) and Parkin, two proteins in ubiquitin-proteasome system (UPS), are both implicated in pathogenesis of dopamine (DA) neuron degeneration in Parkinson's disease (PD). Parkin is a HECT/RING hybrid ligase that physically receives ubiquitin on its catalytic centre and passes ubiquitin onto its substrates, whereas FBXO7 is an adaptor protein in Skp-Cullin-F-box (SCF) SCF(FBXO7) ubiquitin E3 ligase complex to recognize substrates and mediate substrates ubiquitination by SCF(FBXO7) E3 ligase. Here, we discuss the overlapping pathophysiologic mechanisms and clinical features linking Parkin and FBXO7 with autosomal recessive PD. Both proteins play an important role in neuroprotective mitophagy to clear away impaired mitochondria. Parkin can be recruited to impaired mitochondria whereas cellular stress can promote FBXO7 mitochondrial translocation. PD-linked FBXO7 can recruit Parkin into damaged mitochondria and facilitate its aggregation. WT FBXO7, but not PD-linked FBXO7 mutants can rescue DA neuron degeneration in Parkin null Drosophila. A better understanding of the common pathophysiologic mechanisms of these two proteins could unravel specific pathways for targeted therapy in PD.

  7. Using SCC8, SCF27 and VMC7f2 markers in grapevine breeding for seedlessness via marker assisted selection.

    PubMed

    Akkurt, M; Çakır, A; Shidfar, M; Çelikkol, B P; Söylemezoğlu, G

    2012-08-13

    We used molecular markers associated with seedlessness in grapes, namely SCC8, SCF27 and VMC7f2, to improve the efficiency of seedless grapevine breeding via marker assisted selection (MAS). DNA from 372 F₁ hybrid progeny from the cross between seeded "Alphonse Lavallée" and seedless "Sultani" was amplified by PCR using three markers. After digestion of SCC8 marker amplification products by restriction enzyme BgIII, 40 individuals showed homozygous SCC8+/SCC8+ alleles at the seed development inhibitor (SdI) locus. DNA from 80 of the progeny amplified with the SCF27 marker produced bands; 174 individuals had 198-bp alleles of the VMC7f2 marker associated with seedlessness. In the second year, based on MAS, 183 F₁ hybrids were designated as seedless grapevine candidates because they were positive for a minimum of one marker. Twenty individuals were selected as genetic resources for future studies on seedless grapevine breeding because they carried alleles for the three markers associated with seedlessness. The VMC7f2 SSR marker was identified as the marker most associated with seedlessness.

  8. Design and process aspects of laboratory scale SCF particle formation systems.

    PubMed

    Vemavarapu, Chandra; Mollan, Matthew J; Lodaya, Mayur; Needham, Thomas E

    2005-03-23

    Consistent production of solid drug materials of desired particle and crystallographic morphologies under cGMP conditions is a frequent challenge to pharmaceutical researchers. Supercritical fluid (SCF) technology gained significant attention in pharmaceutical research by not only showing a promise in this regard but also accommodating the principles of green chemistry. Given that this technology attained commercialization in coffee decaffeination and in the extraction of hops and other essential oils, a majority of the off-the-shelf SCF instrumentation is designed for extraction purposes. Only a selective few vendors appear to be in the early stages of manufacturing equipment designed for particle formation. The scarcity of information on the design and process engineering of laboratory scale equipment is recognized as a significant shortcoming to the technological progress. The purpose of this article is therefore to provide the information and resources necessary for startup research involving particle formation using supercritical fluids. The various stages of particle formation by supercritical fluid processing can be broadly classified into delivery, reaction, pre-expansion, expansion and collection. The importance of each of these processes in tailoring the particle morphology is discussed in this article along with presenting various alternatives to perform these operations.

  9. PVDF-based semicrystalline-amorphous blends: Phase behavior and thermomechanical properties

    NASA Astrophysics Data System (ADS)

    Campo, Cheryl Josephine

    Poly(vinylidene fluoride) [PVDF]-based semicrystalline-amorphous blends were studied to better understand the degree to which transition temperatures and mechanical properties could be varied as a function of composition. Changes in the amorphous component, processing parameters, MW, and filler content were used to manipulate blend properties. Compositional and MW series of PVDF:poly(vinyl acetate) [PVAc] blends were prepared and characterized. Varying PVDF content led to appreciable changes in crystallinity. In contrast, the effect of composition on blend glass transition temperature, Tg, was manifested only at low PVDF contents. The effect of MWPVA, on the 30:70 PVDF:PVAc composition was manifested primarily in the materials' viscoelastic response to deformation. Ternary blends of PVDF, PVAc, and poly(methyl methacrylate) [PMMA] showed limited miscibility with both a PVAc- and PMMA-rich amorphous phase apparent in all the compositions tested. PVDF:PMMA blends on the other hand exhibited good miscibility characterized by tunable Tg values which were further exploited by varying the processing conditions in order to obtain thermomechanical properties ideal for bio-related shape memory applications. PVDF:poly(ethyl methacrylate) [PEMA] blends, despite having very broad transitions, similarly exhibited desirable transition temperatures for in vivo actuation. The effect of boron nitride (BN), short carbon fibers (SCF), and clay on blend properties was also assessed. SCF filler in 50:50 PVDF:PMMA led mainly to the formation of PVDF crystals in the alpha form, clay was observed to promote growth of the beta crystal form, and BN led to a mixture of crystal forms. BN also exhibited interesting effects in the creep behavior of this system as well as the crystallization behavior of the 50:50 PVDF:PEMA blend, suppressed kinetic crystallization competing with enhanced nucleation effect under isothermal conditions observed in the latter. Depending on the processing conditions used, SCF was found to have similar nucleation effects in the 50:50 PVDF:PMMA blend but diminished degrees of crystallinity overall. Finally, shape memory behavior of PVDF:PVAc blends as well as SCF-filled 50:50 PVDF:PMMA was characterized using single and multiple shape memory cycles. Increasing PVDF content had a negative impact on PVDF:PVAc shape memory properties while increasing stress was found to have an enhancing effect as did low SCF filler content in 50:50 PVDF:PMMA.

  10. Making ultrafine and highly-dispersive multimetallic nanoparticles in three-dimensional graphene with supercritical fluid as excellent electrocatalyst for oxygen reduction reaction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhou, Yazhou; Yen, Clive H.; Hu, Yun Hang

    2016-01-01

    Three-dimensional (3D) graphene showed an advanced support for designing porous electrode materials due to its high specific surface area, large pore volume, and excellent electronic property. However, the electrochemical properties of reported porous electrode materials still need to be improved further. The current challenge is how to deposit desirable nanoparticles (NPs) with controllable structure, loading and composition in 3D graphene while maintaining the high dispersion. Herein, we demonstrate a modified supercritical fluid (SCF) technique to address this issue by controlling the SCF system. Using this superior method, a series of Pt-based/3D graphene materials with the ultrafine-sized, highly dispersive and controllablemore » composition multimetallic NPs were successfully synthesized. Specifically, the resultant Pt40Fe60/3D graphene showed a significant enhancement in electrocatalytic performance for the oxygen reduction reaction (ORR), including a factor of 14.2 enhancement in mass activity (1.70 A mgPt 1), a factor of 11.9 enhancement in specific activity (1.55 mA cm 2), and higher durability compared with that of Pt/C catalyst. After careful comparison, the Pt40Fe60/3D graphene catalyst shows the higher ORR activity than most of the reported similar 3D graphene-based catalysts. The successful synthesis of such attractive materials by this method also paves the way to develop 3D graphene in widespread applications.« less

  11. Damage localization in aluminum plate with compact rectangular phased piezoelectric transducer array

    NASA Astrophysics Data System (ADS)

    Liu, Zenghua; Sun, Kunming; Song, Guorong; He, Cunfu; Wu, Bin

    2016-03-01

    In this work, a detection method for the damage in plate-like structure with a compact rectangular phased piezoelectric transducer array of 16 piezoelectric elements was presented. This compact array can not only detect and locate a single defect (through hole) in plate, but also identify multi-defects (through holes and surface defect simulated by an iron pillar glued to the plate). The experiments proved that the compact rectangular phased transducer array could detect the full range of plate structures and implement multiple-defect detection simultaneously. The processing algorithm proposed in this paper contains two parts: signal filtering and damage imaging. The former part was used to remove noise from signals. Continuous wavelet transform was applicable to signal filtering. Continuous wavelet transform can provide a plot of wavelet coefficients and the signal with narrow frequency band can be easily extracted from the plot. The latter part of processing algorithm was to implement damage detection and localization. In order to accurately locate defects and improve the imaging quality, two images were obtained from amplitude and phase information. One image was obtained with the Total Focusing Method (TFM) and another phase image was obtained with the Sign Coherence Factor (SCF). Furthermore, an image compounding technique for compact rectangular phased piezoelectric transducer array was proposed in this paper. With the proposed technique, the compounded image can be obtained by combining TFM image with SCF image, thus greatly improving the resolution and contrast of image.

  12. Preoptimised VB: a fast method for the ground and excited states of ionic clusters I. Localised preoptimisation for (ArCO) +, (ArN 2) + and N 4+

    NASA Astrophysics Data System (ADS)

    Langenberg, J. H.; Bucur, I. B.; Archirel, P.

    1997-09-01

    We show that in the simple case of van der Waals ionic clusters, the optimisation of orbitals within VB can be easily simulated with the help of pseudopotentials. The procedure yields the ground and the first excited states of the cluster simultaneously. This makes the calculation of potential energy surfaces for tri- and tetraatomic clusters possible, with very acceptable computation times. We give potential curves for (ArCO) +, (ArN 2) + and N 4+. An application to the simulation of the SCF method is shown for Na +H 2O.

  13. Theoretical investigation of polarization effects in solution: Importance of solvent collective motions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ishida, Tateki

    2015-01-22

    Recent theoretical studies on interesting topics related to polarization effects in solutions are presented. As one of interesting topics, ionic liquids (ILs) solvents are focused on. The collective dynamics of electronic polarizability through interionic dynamics and the effect of polarization in ILs, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF{sub 6}]), are studied with molecular dynamics simulation. Also, the time-dependent polarization effect on the probe betaine dye molecule, pyridinium N-phenoxide, in water is investigated by a time-dependent reference interaction site model self-consistent field (time-dependent RISM-SCF) approach. The importance of considering polarization effects on solution systems related to solvent collective motions is shown.

  14. The permanent electric dipole moment of CaOH

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Steimle, Timothy; Shirley, Jeffrey E.

    1990-01-01

    The X 2 Sigma(+), A 2Pi, and B 2Sigma(+) states of CaOH are characterized theoretically and experimentally, with a focus on the value of the permanent electric dipole moment (mu). Calculations based on SCF and SDCI studies of CaOH (Bauschlicher et al., 1984 and 1986) give mu values of 0.98, 0.49, and 0.11 D for the X, A, and B states, respectively, in good agreement with experiments in which the pure rotational spectra of these states were not detected. Modified Rittner (1951) and ligand-field models of these states are explored in detail, and the applicability of these results to observational searches for CaOH in circumstellar envelopes is indicated.

  15. Kinetics of polyelectrolyte adsorption

    NASA Astrophysics Data System (ADS)

    Cohen Stuart, M. A.; Hoogendam, C. W.; de Keizer, A.

    1997-09-01

    The kinetics of polyelectrolyte adsorption has been investigated theoretically. In analogy with Kramers' rate theory for chemical reactions we present a model which is based on the assumption that a polyelectrolyte encounters a barrier in its motion towards an adsorbing surface. The height of the barrier, which is of electrostatic origin, is calculated with a self-consistent-field (SCF) model. The salt concentration strongly affects the height of the barrier. At moderate salt concentrations (0953-8984/9/37/009/img1) equilibrium in the adsorption is attained; at low salt concentration (0953-8984/9/37/009/img2) equilibrium is not reached on the time scale of experiments. The attachment process shows resemblances to the classical DLVO theory.

  16. Higher-order finite-difference formulation of periodic Orbital-free Density Functional Theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ghosh, Swarnava; Suryanarayana, Phanish, E-mail: phanish.suryanarayana@ce.gatech.edu

    2016-02-15

    We present a real-space formulation and higher-order finite-difference implementation of periodic Orbital-free Density Functional Theory (OF-DFT). Specifically, utilizing a local reformulation of the electrostatic and kernel terms, we develop a generalized framework for performing OF-DFT simulations with different variants of the electronic kinetic energy. In particular, we propose a self-consistent field (SCF) type fixed-point method for calculations involving linear-response kinetic energy functionals. In this framework, evaluation of both the electronic ground-state and forces on the nuclei are amenable to computations that scale linearly with the number of atoms. We develop a parallel implementation of this formulation using the finite-difference discretization.more » We demonstrate that higher-order finite-differences can achieve relatively large convergence rates with respect to mesh-size in both the energies and forces. Additionally, we establish that the fixed-point iteration converges rapidly, and that it can be further accelerated using extrapolation techniques like Anderson's mixing. We validate the accuracy of the results by comparing the energies and forces with plane-wave methods for selected examples, including the vacancy formation energy in Aluminum. Overall, the suitability of the proposed formulation for scalable high performance computing makes it an attractive choice for large-scale OF-DFT calculations consisting of thousands of atoms.« less

  17. A pH-independent instantaneous release of flurbiprofen: a study of the preparation of complexes, their characterization and in vitro/in vivo evaluation.

    PubMed

    Wang, Han-Bing; Yang, Fei-Fei; Gai, Xiu-Mei; Cheng, Bing-Chao; Li, Jin-Yu; Pan, Hao; Yang, Xing-Gang; Pan, Wei-San

    2017-09-01

    In this study, furbiprofen/hydroxypropyl-β-cyclodextrin (HPβCD) inclusion complexes were prepared to improve the drug dissolution and facilitate its application in hydrophilic gels. Inclusion complexes were prepared using a supercritical fluid processing and a conventional optimized co-lypholization method was employed as a reference. The entrapment efficacy and drug loading of both methods were investigated. Evaluation of drug dissolution enhancement was conducted in deionized water as well as buffer solutions of different pH. Carbopol 940 gels of both flurbiprofen and flurbiprofen/HPβCD inclusion complexes, with or without penetration enhancers, were prepared and percutaneous permeation studies were performed using rat abdominal skin samples. Formation of flurbiprofen/HPβCD inclusion complexes was confirmed by Fourier transform-infrared spectroscopy, differential scanning calorimetry, X-ray diffraction and scanning electron microscopy. The results obtained showed that SCF processing produced a higher EE (81.91 ± 1.54%) and DL (6.96 ± 0.17%) compared with OCL with values of 69.11 ± 2.23% and 4.00 ± 1.01%, respectively. A marked instantaneous release of flurbiprofen/HPβCD inclusion complexes prepared by SCF processing (103.04 ± 2.66% cumulative release within 5 min, a 10-fold increase in comparison with flurbiprofen alone) was observed. In addition, this improvement in dissolution was shown to be pH-independent (the percentage cumulative release at pH 1.2, 4.5, 6.8 and 7.4 at 5 min was 95.19 ± 1.71, 101.75 ± 1.44, 105.37 ± 4.58 and 96.84 ± 0.56, respectively). Percutaneous permeability of flurbiprofen-in-HPβCD-in-gels could be significantly accelerated by turpentine oil and was related to the water content in the system. An in vivo pharmacokinetic study showed a 2-fold increase in C max and a shortened T max as well as a comparable relative bioavailability when compared with the commercial flurbiprofen Cataplasms (Zepolas ® ). With their superior dissolution, these flurbiprofen/HPβCD inclusion complexes prepared by SCF processing could provide improved applications for flurbiprofen.

  18. Natural gas content of geopressured aquifers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Randolph, Philip L.

    1977-01-01

    It is hypothesized that free, but immobile, natural gas is trapped in pores in geopressured aquifers and that this gas becomes mobile as aquifer pressure is reduced by water production. Computer simulation reveals this hypothesis is a plausible explanation for the high gas/water ratio observed from the No. 1 sand in the Edna Delcambre No. 1 well. In this Delcambre well test, the gas/water ratio increased from the solution gas value of less than 20 SCF/bbl to more than 50 SCF/bbl during production of 32,000 barrels of water in 10 days. Bottom hole pressure was reduced from 10,846 to 9,905more » psia. The computer simulation reveals that such increased gas production requires relative permeability to gas(k{sub rg}) increase from less than 10{sup -4} to about 10{sup -3} due to a decrease in fractional water saturation of pores (S{sub w}) of only about 0.001. Further, assuming drainage relative permeabilities are as calculated by the method of A.T. Corey{sup 1}, initial gas saturation of pores must be greater than 0.065. Means for achieving these initial conditions during geological time will be qualitatively discussed, and the effect of trapped gas upon long-term production will be described.« less

  19. Meta-analysis of incidence of early lung toxicity in 3-dimensional conformal irradiation of breast carcinomas

    PubMed Central

    2013-01-01

    Background This meta-analysis aims to ascertain the significance of early lung toxicity with 3-Dimensional (3D) conformal irradiation for breast carcinomas and identify the sub-groups of patients with increased risk. Methods Electronic databases, reference sections of major oncological textbooks and identified studies were searched for synonyms of breast radiotherapy and radiation pneumonitis (RP). Major studies in thoracic irradiation were reviewed to identify factors frequently associated with RP. Meta-analysis for RP incidence estimation and odds ratio calculation were carried out. Results The overall incidence of Clinical and Radiological RP is 14% and 42% respectively. Ten studies were identified. Dose-volume Histogram (DVH) related dosimetric factors (Volume of lung receiving certain dose, Vdose and Mean lung Dose, MLD), supraclavicular fossa (SCF) irradiation and age are significantly associated with RP, but not sequential chemotherapy and concomitant use of Tamoxifen. A poorly powered study in IMN group contributed to the negative finding. Smoking has a trend towards protective effect against RP. Conclusion Use of other modalities may be considered when Ipsilateral lung V20Gy > 30% or MLD > 15 Gy. Extra caution is needed in SCF and IMN irradiation as they are likely to influence these dosimetric parameters. PMID:24229418

  20. Potential surface for the collinear collision of Ne and H/sub 2//sup +/. [eendoergicity, surface parametrization

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hayes, E.F.; Siu, A.K.Q.; Chapman, F.M. Jr.

    1976-09-01

    A potential energy surface for the Ne--H/sub 2//sup +/ reaction has been obtained in the LCAO--MO--SCF approximation. Analysis of the surface indicates that the reaction Ne+H/sub 2//sup +/..-->..NeH/sup +/+H should proceed with an endoergicity of 12 kcal/mole, in agreement with the experimental results of Chupka and Russell. Several procedures for parameterizing a diatomics-in-molecules (DIM) representation of the NeH/sub 2//sup +/ surface are considered. The results show that an accurate representation of the SCF surface can be obtained from the DIM model using a minimum of diatomic and triatomic data. (AIP)

  1. New sesquiterpenes, JBIR-27 and -28, isolated from a tunicate-derived fungus, Penicillium sp. SS080624SCf1.

    PubMed

    Motohashi, Keiichiro; Hashimoto, Junko; Inaba, Shigeki; Khan, Shams Tabrez; Komaki, Hisayuki; Nagai, Aya; Takagi, Motoki; Shin-ya, Kazuo

    2009-05-01

    In the course of our screening program for novel metabolites from tunicate-derived fungi, novel sesquiterpenoids, named JBIR-27 (1) and -28 (2), together with known sporogen-AO1 and phomenone, were isolated from the culture broth of Penicillium sp. SS080624SCf1. The structures of 1 and 2 were determined to be eremophilane analogs on the basis of extensive NMR and MS analyses. Sporogen-AO1, phomenone and 2 showed cytotoxicity against human cervical carcinoma cell line HeLa at IC(50) values of 8.3, 19 and 92 microM, respectively, whereas 1 was inactive at a concentration of 80 microM.

  2. FES kinase participates in KIT-ligand induced chemotaxis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Voisset, Edwige, E-mail: Edwige.Voisset@inserm.fr; Institut Paoli-Calmettes, Marseille; Universite de la Mediterranee, Aix-Marseille II

    2010-02-26

    FES is a cytoplasmic tyrosine kinase activated by several membrane receptors, originally identified as a viral oncogene product. We have recently identified FES as a crucial effector of oncogenic KIT mutant receptor. However, FES implication in wild-type KIT receptor function was not addressed. We report here that FES interacts with KIT and is phosphorylated following activation by its ligand SCF. Unlike in the context of oncogenic KIT mutant, FES is not involved in wild-type KIT proliferation signal, or in cell adhesion. Instead, FES is required for SCF-induced chemotaxis. In conclusion, FES kinase is a mediator of wild-type KIT signalling implicatedmore » in cell migration.« less

  3. Deviations from idealised geometries part 3: approximately tetrahedral molecules of form MX 2Y 2 studied by SCF and MP2 calculations

    NASA Astrophysics Data System (ADS)

    Palmer, Michael H.

    1997-03-01

    The relatively minor deviations from true tetrahedral geometry for molecules of type MX 2Y 2 where M is tetravalent, and X, Y are either H, Me or halogen are discussed, in the light of ab initio calculations of equilibrium geometry with a large (triple zeta valence + polarisation) basis, at both the SCF and MP2 levels. The results are compared with known experimental structural and dipole moment data; in most cases a very close correlation with experiment is found, with slight improvements in the MP2 data. The study is coupled with a localised orbital study of relevance to Bent's Rule.

  4. Potential energy surfaces of the ground and low-lying states of HCCS and NCS: CASSCF, MRCI and CCSD(T) studies

    NASA Astrophysics Data System (ADS)

    Li, Yumin; Iwata, Suehiro

    1997-07-01

    For astronomically interesting molecules, HCCS and NCS, the equilibrium geometries and potential energy curves of three states (X 2Π, A 2Π and B 2Σ+) as well as vertical excitation energies are studied using complete active space SCF (CASSCF), multi-reference configuration interaction (MRCI) and coupled cluster (CCSD(T)) methods with cc-pVTZ basis sets. The difference and similarity in the three states of HCCS and NCS are illustrated. The results obtained are in good agreement with available experimental data.

  5. Second-Order Moller-Plesset Perturbation Theory for Molecular Dirac-Hartree-Fock Wave Functions

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Arnold, James O. (Technical Monitor)

    1994-01-01

    Moller-Plesset perturbation theory is developed to second order for a selection of Kramers restricted Dirac-Hartree-Fock closed and open-shell reference wave functions. The open-shell wave functions considered are limited to those with no more than two electrons in open shells, but include the case of a two-configuration SCF reference. Denominator shifts are included in the style of Davidson's OPT2 method. An implementation which uses unordered integrals with labels is presented, and results are given for a few test cases.

  6. Self-Consistent Field Theories for the Role of Large Length-Scale Architecture in Polymers

    NASA Astrophysics Data System (ADS)

    Wu, David

    At large length-scales, the architecture of polymers can be described by a coarse-grained specification of the distribution of branch points and monomer types within a molecule. This includes molecular topology (e.g., cyclic or branched) as well as distances between branch points or chain ends. Design of large length-scale molecular architecture is appealing because it offers a universal strategy, independent of monomer chemistry, to tune properties. Non-linear analogs of linear chains differ in molecular-scale properties, such as mobility, entanglements, and surface segregation in blends that are well-known to impact rheological, dynamical, thermodynamic and surface properties including adhesion and wetting. We have used Self-Consistent Field (SCF) theories to describe a number of phenomena associated with large length-scale polymer architecture. We have predicted the surface composition profiles of non-linear chains in blends with linear chains. These predictions are in good agreement with experimental results, including from neutron scattering, on a range of well-controlled branched (star, pom-pom and end-branched) and cyclic polymer architectures. Moreover, the theory allows explanation of the segregation and conformations of branched polymers in terms of effective surface potentials acting on the end and branch groups. However, for cyclic chains, which have no end or junction points, a qualitatively different topological mechanism based on conformational entropy drives cyclic chains to a surface, consistent with recent neutron reflectivity experiments. We have also used SCF theory to calculate intramolecular and intermolecular correlations for polymer chains in the bulk, dilute solution, and trapped at a liquid-liquid interface. Predictions of chain swelling in dilute star polymer solutions compare favorably with existing PRISM theory and swelling at an interface helps explain recent measurements of chain mobility at an oil-water interface. In collaboration with: Renfeng Hu, Colorado School of Mines, and Mark Foster, University of Akron. This work was supported by NSF Grants No. CBET- 0730692 and No. CBET-0731319.

  7. An automated exploration of the isomerization and dissociation pathways of (E)-1,2-dichloroethene cations and anions

    NASA Astrophysics Data System (ADS)

    Kishimoto, Naoki; Nishi, Yuito

    2017-04-01

    Isomerization and dissociation pathways after the photoionization or electron attachment of (E)-1,2-dichloroethene were calculated with an automated exploration method utilizing a scaled hypersphere search of the anharmonic downward distortion following algorithm at the UB3LYP/6-311G(2d,d,p) level of theory. The potential energies of transition states and dissociation channels were calculated by a composite method ((RO)CBS-QB3) and compared with the breakdown diagrams and electron attachment spectra observed in previous spectroscopic studies. The results of single point calculations with several DFT and post-SCF methods are compared using the root mean square deviations from the (RO)CBS-QB3 energies for six states of anionic dichloroethene.

  8. Feasibility of antihydrogen atom containment in helium: a problem of electron-positron correlation investigated by the Monte Carol method

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jackman, T.M.

    1987-01-01

    A theoretical investigation of the interaction potential between the helium atom and the antihydrogen atom was performed for the purpose of determining the feasibility of antihydrogen atom containment. The interaction potential showed an energy barrier to collapse of this system. A variational estimate of the height of this energy barrier and estimates of lifetime with respect to electron-positron annihilation were determined by the Variational Monte Carlo method. This calculation allowed for an improvement over an SCF result through the inclusion of explicit correlation factors in the trial wave function. An estimate of the correlation energy of this system was determinedmore » by the Green's Function Monte Carlo (GFMC) method.« less

  9. Localisation of stem cell factor, stanniocalcin-1, connective tissue growth factor and heparin-binding epidermal growth factor in the bovine uterus at the time of blastocyst formation.

    PubMed

    Muñoz, M; Martin, D; Carrocera, S; Alonso-Guervos, M; Mora, M I; Corrales, F J; Peynot, N; Giraud-Delville, C; Duranthon, V; Sandra, O; Gómez, E

    2017-10-01

    Early embryonic losses before implantation account for the highest rates of reproductive failure in mammals, in particular when in vitro-produced embryos are transferred. In the present study, we used molecular biology techniques (real-time quantitative polymerase chain reaction), classical immunohistochemical staining coupled with confocal microscopy and proteomic analysis (multiple reaction monitoring and western blot analysis) to investigate the role of four growth factors in embryo-uterine interactions during blastocyst development. Supported by a validated embryo transfer model, the study investigated: (1) the expression of stem cell factor (SCF), stanniocalcin-1 (STC1), connective tissue growth factor (CTGF) and heparin-binding epidermal growth factor-like growth factor (HB-EGF) in bovine uterine fluid; (2) the presence of SCF, STC1, CTGF and HB-EGF mRNA and protein in the bovine endometrium and embryos; and (3) the existence of reciprocal regulation between endometrial and embryonic expression of SCF, STC1, CTGF and HB-EGF. The results suggest that these growth factors most likely play an important role during preimplantation embryo development in cattle. The information obtained from the present study can contribute to improving the performance of in vitro culture technology in cattle and other species.

  10. SCF(JFK) is a bona fide E3 ligase for ING4 and a potent promoter of the angiogenesis and metastasis of breast cancer.

    PubMed

    Yan, Ruorong; He, Lin; Li, Zhongwu; Han, Xiao; Liang, Jing; Si, Wenzhe; Chen, Zhe; Li, Lei; Xie, Guojia; Li, Wanjin; Wang, Peiyan; Lei, Liandi; Zhang, Hongquan; Pei, Fei; Cao, Dengfeng; Sun, Luyang; Shang, Yongfeng

    2015-03-15

    Loss of function/dysregulation of inhibitor of growth 4 (ING4) and hyperactivation of NF-κB are frequent events in many types of human malignancies. However, the molecular mechanisms underlying these remarkable aberrations are not understood. Here, we report that ING4 is physically associated with JFK. We demonstrated that JFK targets ING4 for ubiquitination and degradation through assembly of an Skp1-Cul1-F-box (SCF) complex. We showed that JFK-mediated ING4 destabilization leads to the hyperactivation of the canonical NF-κB pathway and promotes angiogenesis and metastasis of breast cancer. Significantly, the expression of JFK is markedly up-regulated in breast cancer, and the level of JFK is negatively correlated with that of ING4 and positively correlated with an aggressive clinical behavior of breast carcinomas. Our study identified SCF(JFK) as a bona fide E3 ligase for ING4 and unraveled the JFK-ING4-NF-κB axis as an important player in the development and progression of breast cancer, supporting the pursuit of JFK as a potential target for breast cancer intervention. © 2015 Yan et al.; Published by Cold Spring Harbor Laboratory Press.

  11. Supercritical fluid processing: a new dry technique for photoresist developing

    NASA Astrophysics Data System (ADS)

    Gallagher-Wetmore, Paula M.; Wallraff, Gregory M.; Allen, Robert D.

    1995-06-01

    Supercritical fluid (SCF) technology is investigated as a dry technique for photoresist developing. Because of their unique combination of gaseous and liquid-like properties, these fluids offer comparative or improved efficiencies over liquid developers and, particularly carbon dioxide, would have tremendous beneficial impact on the environment and on worker safety. Additionally, SCF technology offers the potential for processing advanced resist systems which are currently under investigation as well as those that may have been abandoned due to problems associated with conventional developers. An investigation of various negative and positive photoresist systems is ongoing. Initially, supercritical carbon dioxide (SC CO2) as a developer for polysilane resists was explored because the exposure products, polysiloxanes, are generally soluble in this fluid. These initial studies demonstrated the viability of the SCF technique with both single layer and bilayer systems. Subsequently, the investigation focused on using SC CO2 to produce negative images with polymers that would typically be considered positive resists. Polymers such as styrenes and methacrylates were chemically modified by fluorination and/or copolymerization to render them soluble in SC CO2. Siloxane copolymers and siloxane-modified methacrylates were examined as well. The preliminary findings reported here indicate the feasibility of using SC CO2 for photoresist developing.

  12. Fault geometry and fluid-rock reaction: Combined controls on mineralization in the Xinli gold deposit, Jiaodong Peninsula, China

    NASA Astrophysics Data System (ADS)

    Yang, Lin; Zhao, Rui; Wang, Qingfei; Liu, Xuefei; Carranza, Emmanuel John M.

    2018-06-01

    The structures and fluid-rock reaction in the Xinli gold deposit, Jiaodong Peninsula, were investigated to further understand their combined controls on the development of permeability associated with ore-forming fluid migration. Orebodies in this deposit are hosted by the moderately SE-to S-dipping Sanshandao-Cangshang fault (SCF). Variations in both dip direction and dip angle along the SCF plane produced fault bends, which controlled the fluid accumulation and ore-shoot formation. Gold mineralizations occurred in early gold-quartz-pyrite and late gold-quartz-polymetallic sulphide stages following pervasive sericitization and silicification alterations. Theoretical calculation indicates that sericitization caused 8-57% volume decrease resulting in the development/enlargement of voids, further increase of grain-scale permeability, and resultant precipitation of the early gold-quartz-pyrite pods, which destroyed permeability. The rock softening produced by alterations promoted activities of SCF secondary faults and formation of new fractures, which rebuilt the permeability and controlled the late gold-quartz-polymetallic sulfide veins. Quantitative studies on permeability distributions show that the southwestern and northeastern bend areas with similar alteration and mineralization have persistent and anti-persistent permeability networks, respectively. These were likely caused by different processes of rebuilding permeability due to different stress states resulting from changes in fault geometry.

  13. Short-chain inulin-like fructans reduce endotoxin and bacterial translocations and attenuate development of TNBS-induced colitis in rats.

    PubMed

    Ito, Hiroyuki; Tanabe, Hiroki; Kawagishi, Hirokazu; Tadashi, Wada; Yasuhiko, Tomono; Sugiyama, Kimio; Kiriyama, Shuhachi; Morita, Tatsuya

    2009-10-01

    Anti-inflammatory effects of short-chain inulin-like fructans (SCF) on trinitrobenzene sulfonic acid (TNBS)-induced colitis were investigated in rats, focusing specifically on endotoxin and bacterial translocations. SCF with degrees of polymerization (DP) of 4 and 8 were used. Rats were fed either control diet or diets including 60 g DP4 or DP8 per kilogram for 7 days, and then received intracolonic TNBS and were fed the respective diets for a further 10 days. DP4 and DP8 significantly reduced colonic injuries as assessed by damage score, but the reduction of colonic myeloperoxidase activity was manifest solely with DP8. At 3 days after colitis induction, bacterial translocation to the mesenteric lymph node was significantly lower in the DP4 and DP8 groups, but significant reduction in the portal endotoxin concentration was achieved solely in the DP8 group. Immediately prior to colitis induction, cecal immunoglobulin A and mucin concentrations were higher in the DP4 and DP8 groups, but these changes were abolished at 10 days post colitis induction. The data suggest that SCF exert prophylactic effects against TNBS colitis, presumably as a result of inhibitory effects on endotoxin and bacterial translocations.

  14. Increased dissolution rate and oral bioavailability of hydrophobic drug glyburide tablets produced using supercritical CO₂ silica dispersion technology.

    PubMed

    Guan, Jibin; Han, Jihong; Zhang, Dong; Chu, Chunxia; Liu, Hongzhuo; Sun, Jin; He, Zhonggui; Zhang, Tianhong

    2014-04-01

    The aim of this study was to design a silica-supported solid dispersion of a water-insoluble drug, glyburide, to increase its dissolution rate and oral absorption using supercritical fluid (SCF) technology. DSC and PXRD results indicated that the encapsulated drug in the optimal solid dispersion was in an amorphous state and the product was stable for 6 months. Glyburide was adsorbed onto the porous silica, as confirmed by the SEM images and BET analysis. Furthermore, FT-IR spectroscopy confirmed that there was no change in the chemical structure of glyburide after the application of SCF. The glyburide silica-based dispersion could also be compressed into tablet form. In vitro drug release analysis of the silica solid dispersion tablets demonstrated faster release of glyburide compared with the commercial micronized tablet. In an in vivo test, the AUC of the tablets composed of the new glyburide silica-based solid dispersion was 2.01 times greater than that of the commercial micronized glyburide tablets. In conclusion, SCF technology presents a promising approach to prepare silica-based solid dispersions of hydrophobic drugs because of its ability to increase their release and oral bioavailability. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Endothelial cell-fatty acid binding protein 4 promotes angiogenesis: role of stem cell factor/c-kit pathway

    PubMed Central

    Elmasri, Harun; Ghelfi, Elisa; Yu, Chen-wei; Traphagen, Samantha; Cernadas, Manuela; Cao, Haiming; Shi, Guo-Ping; Plutzky, Jorge; Sahin, Mustafa; Hotamisligil, Gokhan; Cataltepe, Sule

    2013-01-01

    Fatty acid binding protein 4 (FABP4) plays an important role in regulation of glucose and lipid homeostasis as well as inflammation through its actions in adipocytes and macrophages. FABP4 is also expressed in a subset of endothelial cells, but its role in this cell type is not known. We found that FABP4-deficient human umbilical vein endothelial cells (HUVECs) demonstrate a markedly increased susceptibility to apoptosis as well as decreased migration and capillary network formation. Aortic rings from FABP4−/− mice demonstrated decreased angiogenic sprouting, which was recovered by reconstitution of FABP4. FABP4 was strongly regulated by mTORC1 and inhibited by Rapamycin. FABP4 modulated activation of several important signaling pathways in HUVECs, including downregulation of P38, eNOS, and stem cell factor (SCF)/c-kit signaling. Of these, the SCF/c-kit pathway was found to have a major role in attenuated angiogenic activity of FABP4-deficient ECs as provision of exogenous SCF resulted in a significant recovery in cell proliferation, survival, morphogenesis, and aortic ring sprouting. These data unravel a novel pro-angiogenic role for endothelial cell-FABP4 and suggest that it could be exploited as a potential target for diseases associated with pathological angiogenesis. PMID:22562362

  16. Itraconazole solid dispersion prepared by a supercritical fluid technique: preparation, in vitro characterization, and bioavailability in beagle dogs.

    PubMed

    Yin, Xuezhi; Daintree, Linda Sharon; Ding, Sheng; Ledger, Daniel Mark; Wang, Bing; Zhao, Wenwen; Qi, Jianping; Wu, Wei; Han, Jiansheng

    2015-01-01

    This research aimed to develop a supercritical fluid (SCF) technique for preparing a particulate form of itraconazole (ITZ) with good dissolution and bioavailability characteristics. The ITZ particulate solid dispersion was formulated with hydroxypropyl methylcellulose, Pluronic F-127, and L-ascorbic acid. Aggregated particles showed porous structure when examined by scanning electron microscopy. Powder X-ray diffraction and Fourier transform infrared spectra indicated an interaction between ITZ and excipients and showed that ITZ existed in an amorphous state in the composite solid dispersion particles. The solid dispersion obtained by the SCF process improved the dissolution of ITZ in media of pH 1.0, pH 4.5, and pH 6.8, compared with a commercial product (Sporanox(®)), which could be ascribed to the porous aggregated particle shape and amorphous solid state of ITZ. While the solid dispersion did not show a statistical improvement (P=0.50) in terms of oral bioavailability of ITZ compared with Sporanox(®), the C max (the maximum plasma concentration of ITZ in a pharmacokinetic curve) of ITZ was raised significantly (P=0.03) after oral administration. Thus, the SCF process has been shown to be an efficient, single step process to form ITZ-containing solid dispersion particles with good dissolution and oral bioavailability characteristics.

  17. Equivalence of chain conformations in the surface region of a polymer melt and a single Gaussian chain under critical conditions.

    PubMed

    Skvortsov, A M; Leermakers, F A M; Fleer, G J

    2013-08-07

    In the melt polymer conformations are nearly ideal according to Flory's ideality hypothesis. Silberberg generalized this statement for chains in the interfacial region. We check the Silberberg argument by analyzing the conformations of a probe chain end-grafted at a solid surface in a sea of floating free chains of concentration φ by the self-consistent field (SCF) method. Apart from the grafting, probe chain and floating chains are identical. Most of the results were obtained for a standard SCF model with freely jointed chains on a six-choice lattice, where immediate step reversals are allowed. A few data were generated for a five-choice lattice, where such step reversals are forbidden. These coarse-grained models describe the equilibrium properties of flexible atactic polymer chains at the scale of the segment length. The concentration was varied over the whole range from φ = 0 (single grafted chain) to φ = 1 (probe chain in the melt). The number of contacts with the surface, average height of the free end and its dispersion, average loop and train length, tail size distribution, end-point and overall segment distributions were calculated for a grafted probe chain as a function of φ, for several chain lengths and substrate∕polymer interactions, which were varied from strong repulsion to strong adsorption. The computations show that the conformations of the probe chain in the melt do not depend on substrate∕polymer interactions and are very similar to the conformations of a single end-grafted chain under critical conditions, and can thus be described analytically. When the substrate∕polymer interaction is fixed at the value corresponding to critical conditions, all equilibrium properties of a probe chain are independent of φ, over the whole range from a dilute solution to the melt. We believe that the conformations of all flexible chains in the surface region of the melt are close to those of an appropriate single chain in critical conditions, provided that one end of the single chain is fixed at the same point as a chain in the melt.

  18. Changes in the interstitial cells of Cajal and neuronal nitric oxide synthase positive neuronal cells with aging in the esophagus of F344 rats.

    PubMed

    Kim, Hee Jin; Kim, Nayoung; Kim, Yong Sung; Nam, Ryoung Hee; Lee, Sun Min; Park, Ji Hyun; Choi, Daeun; Hwang, Young-Jae; Lee, Jongchan; Lee, Hye Seung; Kim, Min-Seob; Lee, Moon Young; Lee, Dong Ho

    2017-01-01

    The aging-associated cellular and molecular changes in esophagus have not been established, yet. Thus we evaluated histological structure, interstitial cells of Cajal (ICCs), neuronal nitric oxide synthase (nNOS)-positive cells, and contractility in the esophagus of Fischer 344 rat at different ages (6-, 31-, 74-weeks, and 2-years). The lamina propria thickness and endomysial area were calculated. The immunoreactivity of c-Kit, nNOS and protein gene product (PGP) 9.5 was counted after immunohistochemistry. Expression of c-Kit, stem cell factor (SCF), nNOS and PGP 9.5 mRNA was measured by real-time PCR, and expression of c-Kit and nNOS protein was detected by Western blot. Isovolumetric contractile force measurement and electrical field stimulation (EFS) were conducted. The lamina propria thickness increased (6 week vs 2 year, P = 0.005) and the endomysial area of longitudinal muscle decreased with aging (6 week vs 2 year, P<0.001), while endomysial area of circular muscle did not significantly decrease. The proportions of NOS-immunoreactive cells and c-Kit-immunoreactive areas declined with aging (6 week vs 2 year; P<0.001 and P = 0.004, respectively), but there was no significant change of PGP 9.5-immunopositiviy. The expressions of nNOS, c-Kit and SCF mRNA also reduced with aging (6 week vs 2 year; P = 0.006, P = 0.001 and P = 0.006, respectively), while the change of PGP 9.5 mRNA expression was not significant. Western blot showed the significant decreases of nNOS and c-Kit protein expression with aging (6 week vs 2 year; P = 0.008 and P = 0.012, respectively). The EFS-induced esophageal contractions significantly decreased in 2-yr-old rat compared with 6-wk-old rats, however, L-NG-Nitroarginine methylester did not significantly increase the spontaneous and EFS-induced contractions in the 6-wk- and 2-yr-old rat esophagus. In conclusion, an increase of lamina propria thickness, a decrease of endomysial area, c-Kit, SCF and NOS expression with preserved total enteric neurons, and contractility in aged rat esophagus may explain the aging-associated esophageal dysmotility.

  19. Changes in the interstitial cells of Cajal and neuronal nitric oxide synthase positive neuronal cells with aging in the esophagus of F344 rats

    PubMed Central

    Kim, Hee Jin; Kim, Yong Sung; Nam, Ryoung Hee; Lee, Sun Min; Park, Ji Hyun; Choi, Daeun; Hwang, Young-Jae; Lee, Jongchan; Lee, Hye Seung; Kim, Min-Seob; Lee, Moon Young; Lee, Dong Ho

    2017-01-01

    The aging-associated cellular and molecular changes in esophagus have not been established, yet. Thus we evaluated histological structure, interstitial cells of Cajal (ICCs), neuronal nitric oxide synthase (nNOS)-positive cells, and contractility in the esophagus of Fischer 344 rat at different ages (6-, 31-, 74-weeks, and 2-years). The lamina propria thickness and endomysial area were calculated. The immunoreactivity of c-Kit, nNOS and protein gene product (PGP) 9.5 was counted after immunohistochemistry. Expression of c-Kit, stem cell factor (SCF), nNOS and PGP 9.5 mRNA was measured by real-time PCR, and expression of c-Kit and nNOS protein was detected by Western blot. Isovolumetric contractile force measurement and electrical field stimulation (EFS) were conducted. The lamina propria thickness increased (6 week vs 2 year, P = 0.005) and the endomysial area of longitudinal muscle decreased with aging (6 week vs 2 year, P<0.001), while endomysial area of circular muscle did not significantly decrease. The proportions of NOS-immunoreactive cells and c-Kit-immunoreactive areas declined with aging (6 week vs 2 year; P<0.001 and P = 0.004, respectively), but there was no significant change of PGP 9.5-immunopositiviy. The expressions of nNOS, c-Kit and SCF mRNA also reduced with aging (6 week vs 2 year; P = 0.006, P = 0.001 and P = 0.006, respectively), while the change of PGP 9.5 mRNA expression was not significant. Western blot showed the significant decreases of nNOS and c-Kit protein expression with aging (6 week vs 2 year; P = 0.008 and P = 0.012, respectively). The EFS-induced esophageal contractions significantly decreased in 2-yr-old rat compared with 6-wk-old rats, however, L-NG-Nitroarginine methylester did not significantly increase the spontaneous and EFS-induced contractions in the 6-wk- and 2-yr-old rat esophagus. In conclusion, an increase of lamina propria thickness, a decrease of endomysial area, c-Kit, SCF and NOS expression with preserved total enteric neurons, and contractility in aged rat esophagus may explain the aging-associated esophageal dysmotility. PMID:29182640

  20. Prediction of electronic structure of organic radicaloid anions using efficient, economical multireference gradient approach.

    PubMed

    Chattopadhyay, Sudip; Chaudhuri, Rajat K; Freed, Karl F

    2011-04-28

    The improved virtual orbital-complete active space configuration interaction (IVO-CASCI) method enables an economical and reasonably accurate treatment of static correlation in systems with significant multireference character, even when using a moderate basis set. This IVO-CASCI method supplants the computationally more demanding complete active space self-consistent field (CASSCF) method by producing comparable accuracy with diminished computational effort because the IVO-CASCI approach does not require additional iterations beyond an initial SCF calculation, nor does it encounter convergence difficulties or multiple solutions that may be found in CASSCF calculations. Our IVO-CASCI analytical gradient approach is applied to compute the equilibrium geometry for the ground and lowest excited state(s) of the theoretically very challenging 2,6-pyridyne, 1,2,3-tridehydrobenzene and 1,3,5-tridehydrobenzene anionic systems for which experiments are lacking, accurate quantum calculations are almost completely absent, and commonly used calculations based on single reference configurations fail to provide reasonable results. Hence, the computational complexity provides an excellent test for the efficacy of multireference methods. The present work clearly illustrates that the IVO-CASCI analytical gradient method provides a good description of the complicated electronic quasi-degeneracies during the geometry optimization process for the radicaloid anions. The IVO-CASCI treatment produces almost identical geometries as the CASSCF calculations (performed for this study) at a fraction of the computational labor. Adiabatic energy gaps to low lying excited states likewise emerge from the IVO-CASCI and CASSCF methods as very similar. We also provide harmonic vibrational frequencies to demonstrate the stability of the computed geometries.

  1. CRISPR/Cas9-mediated knockout of PiSSK1 reveals essential role of S-locus F-box protein-containing SCF complexes in recognition of non-self S-RNases during cross-compatible pollination in self-incompatible Petunia inflata.

    PubMed

    Sun, Linhan; Kao, Teh-Hui

    2018-06-01

    Function of Petunia PiSSK1. Self-incompatibility (SI), an inbreeding-preventing mechanism, is regulated in Petunia inflata by the polymorphic S-locus, which houses multiple pollen-specific S-locus F-box (SLF) genes and a single pistil-specific S-RNase gene. S 2 -haplotype and S 3 -haplotype possess the same 17 polymorphic SLF genes (named SLF1 to SLF17), and each SLF protein produced in pollen is assembled into an SCF (Skp1-Cullin1-F-box) E3 ubiquitin ligase complex. A complete suite of SLF proteins is thought to collectively interact with all non-self S-RNases to mediate their ubiquitination and degradation by the 26S proteasome, allowing cross-compatible pollination. For each SCF SLF complex, the Cullin1 subunit (named PiCUL1-P) and Skp1 subunit (named PiSSK1), like the F-box protein subunits (SLFs), are pollen-specific, raising the possibility that they also evolved specifically to function in SI. Here we used CRISPR/Cas9-meditated genome editing to generate frame-shift indel mutations in PiSSK1 and examined the SI behavior of a T 0 plant (S 2 S 3 ) with biallelic mutations in the pollen genome and two progeny plants (S 2 S 2 ) each homozygous for one of the indel alleles and not carrying the Cas9-containing T-DNA. Their pollen was completely incompatible with pistils of seven otherwise-compatible S-genotypes, but fully compatible with pistils of an S 3 S 3 transgenic plant in which production of S 3 -RNase was completely suppressed by an antisense S 3 -RNase gene, and with pistils of immature flower buds, which produce little S-RNase. These results suggest that PiSSK1 specifically functions in SI and support the hypothesis that SLF-containing SCF complexes are essential for compatible pollination.

  2. Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial.

    PubMed

    Holscher, Hannah D; Caporaso, J Gregory; Hooda, Seema; Brulc, Jennifer M; Fahey, George C; Swanson, Kelly S

    2015-01-01

    In our published randomized, double-blind, placebo-controlled, 3-period crossover trial, healthy adult men (n = 21) consumed bars containing no supplemental fiber (placebo; NFC), polydextrose (21 g/d), and soluble corn fiber (SCF; 21 g/d) for 21 d each. Fecal specimens were collected between days 16 and 21 for fermentative end-product analysis and 16S ribosomal RNA bacterial gene amplification for bacterial taxa identification. Fiber supplementation decreased fecal putrefaction compounds and shifted abundances of several bacterial taxa. The objective was to perform whole-genome shotgun 454 pyrosequencing on the same fecal specimens collected in that clinical trial to obtain comprehensive fecal bacterial genome sequencing coverage and explore the full range of bacterial genetic information in the fecal microbiome, thereby using a systematic approach to study the impact of dietary fiber supplementation on fecal metabolites, bacterial taxa, and bacterial metagenomes. Fecal samples were subjected to whole-genome shotgun 454 pyrosequencing to identify both fecal bacterial populations present and their functional genetic capacity. Whole-genome shotgun sequencing results revealed that fiber consumption shifted the Bacteroidetes:Firmicutes ratio, increasing the relative abundance of Bacteroidetes 12 ± 2% and 13 ± 2% with polydextrose and SCF, respectively, compared with NFC. Bivariate correlations showed a positive correlation between the Bacteroidetes:Firmicutes ratio and total dietary fiber intake but not body mass index. Principal coordinates analysis of Bray-Curtis distances indicated that bacterial gene composition was more similar in participants consuming fibers (polydextrose and SCF combined) in comparison with NFC. Shifts in bacterial gene abundances after polydextrose and SCF supplementation included genes associated with carbohydrate, amino acid, and lipid metabolism, as well as metabolism of cofactors and vitamins. This study conveys novel information about the impact of dietary fiber supplementation on the phylogenetic structure and functional capacity of the fecal microbiome of healthy adults. © 2015 American Society for Nutrition.

  3. Effects of atmospheric dynamics and aerosols on the fraction of supercooled water clouds

    NASA Astrophysics Data System (ADS)

    Li, Jiming; Lv, Qiaoyi; Zhang, Min; Wang, Tianhe; Kawamoto, Kazuaki; Chen, Siyu; Zhang, Beidou

    2017-02-01

    Based on 8 years of (January 2008-December 2015) cloud phase information from the GCM-Oriented Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) Cloud Product (GOCCP), aerosol products from CALIPSO and meteorological parameters from the ERA-Interim products, the present study investigates the effects of atmospheric dynamics on the supercooled liquid cloud fraction (SCF) during nighttime under different aerosol loadings at global scale to better understand the conditions of supercooled liquid water gradually transforming to ice phase. Statistical results indicate that aerosols' effect on nucleation cannot fully explain all SCF changes, especially in those regions where aerosols' effect on nucleation is not a first-order influence (e.g., due to low ice nuclei aerosol frequency). By performing the temporal and spatial correlations between SCFs and different meteorological factors, this study presents specifically the relationship between SCF and different meteorological parameters under different aerosol loadings on a global scale. We find that the SCFs almost decrease with increasing of aerosol loading, and the SCF variation is closely related to the meteorological parameters but their temporal relationship is not stable and varies with the different regions, seasons and isotherm levels. Obviously negative temporal correlations between SCFs versus vertical velocity and relative humidity indicate that the higher vertical velocity and relative humidity the smaller SCFs. However, the patterns of temporal correlation for lower-tropospheric static stability, skin temperature and horizontal wind are relatively more complex than those of vertical velocity and humidity. For example, their close correlations are predominantly located in middle and high latitudes and vary with latitude or surface type. Although these statistical correlations have not been used to establish a certain causal relationship, our results may provide a unique point of view on the phase change of mixed-phase cloud and have potential implications for further improving the parameterization of the cloud phase and determining the climate feedbacks.

  4. Early snow melts and biomass burning over Eastern Eurasia and their impacts on the air quality in Northern Japan

    NASA Astrophysics Data System (ADS)

    Yasunari, T. J.; daSilva, A.; Akiyama, M.; Hayasaki, M.; Murao, N.; Kim, K. M.

    2016-12-01

    We investigated monthly characteristics including a couple of large biomass burnings (BB) in Eastern Eurasia during 2003 and 2014, and the smoke impacts on Northern Japan. The new re-analyses data including the aerosol data assimilation, called MERRA-2, which was produced by the NASA's Global Modeling and Assimilation Office (GMAO), the monthly mean MODIS snow cover fraction (SCF) data (MOD10CM; further re-gridded), and the observations on PM2.5, elemental carbon (EC), and organic carbon (OC) in Sapporo city (Hokkaido, Japan), were used in our analyses. For the MERRA-2 and MODIS SCF data, we calculated 12-year climatology for each month and these anomalies from the climatology on the focused variables. Three-month means of the anomalies for the last three months until the BB months were calculated except for the SCF. For the SCF, the three-month mean anomalies until the one month before the BB months were also calculated. Here we start especially focusing on the identified fire months with the MERRA-2 data (May 2003, April 2008, and July 2014) in terms of these smoke impacts on the air qualities in Northern Japan (i.e., Hokkaido). We identified two types of biomass burning patterns within these three months. For the BBs in May 2003 and April 2008, the main BB areas were seen in the eastern part of the Lake Baikal. In July 2014, the main BB area was in the Sakha Republic and close to the Arctic region. Then, the MERRA-2 data overestimated the observations (EC, OC, and PM2.5) in Sapporo (Hokkaido, Japan) during the smoke transports, but the elevated timings were well reproduced. For all the three BB cases, abnormally reduced SCF were seen by the one month before the Eurasian BB generations (i.e., earlier than the BB generations). The positive and negative anomalies of 2-m temperature and surface soil wetness, covering the three-month until the BB months, were identified. These suggest that early snow-melting anomalies for these three years could make the following BB-ready environmental conditions around the regions where warmer temperature and dryer soil conditions were also maintained until setting on fire there. Therefore, the accurate grasp of Eurasian snow cover conditions in spring would be essential to project the following BB generations from spring to summer and the smoke impact from the fires on surrounding and remote areas.

  5. Computing sextic centrifugal distortion constants by DFT: A benchmark analysis on halogenated compounds

    NASA Astrophysics Data System (ADS)

    Pietropolli Charmet, Andrea; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi

    2017-05-01

    This work presents a benchmark study on the calculation of the sextic centrifugal distortion constants employing cubic force fields computed by means of density functional theory (DFT). For a set of semi-rigid halogenated organic compounds several functionals (B2PLYP, B3LYP, B3PW91, M06, M06-2X, O3LYP, X3LYP, ωB97XD, CAM-B3LYP, LC-ωPBE, PBE0, B97-1 and B97-D) were used for computing the sextic centrifugal distortion constants. The effects related to the size of basis sets and the performances of hybrid approaches, where the harmonic data obtained at higher level of electronic correlation are coupled with cubic force constants yielded by DFT functionals, are presented and discussed. The predicted values were compared to both the available data published in the literature and those obtained by calculations carried out at increasing level of electronic correlation: Hartree-Fock Self Consistent Field (HF-SCF), second order Møller-Plesset perturbation theory (MP2), and coupled-cluster single and double (CCSD) level of theory. Different hybrid approaches, having the cubic force field computed at DFT level of theory coupled to harmonic data computed at increasing level of electronic correlation (up to CCSD level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T)) were considered. The obtained results demonstrate that they can represent reliable and computationally affordable methods to predict sextic centrifugal terms with an accuracy almost comparable to that yielded by the more expensive anharmonic force fields fully computed at MP2 and CCSD levels of theory. In view of their reduced computational cost, these hybrid approaches pave the route to the study of more complex systems.

  6. Gas-phase infrared spectrum of phosphorus (III) oxycyanide, OPCN: experimental and theoretical investigations

    NASA Astrophysics Data System (ADS)

    Allaf, Abdul. W.; Kassem, M.; Alibrahim, M.; Boustani, Ihsan

    1999-03-01

    An attempt was made to observe the gas-phase infrared spectrum of Phosphorus (III) oxycyanide, OPCN for the first time. This molecule was produced by an on-line process using phosphorus (III) oxychloride, OPCl as precursor passed over heated AgCN. The products were characterised by the infrared spectra of their vapours. The low resolution gas-phase Fourier transform infrared spectrum shows two bands centered at 2165 and 1385 cm -1. These bands are assigned to, ν1 (CN stretch) and ν2 (OP stretch), respectively. Ab initio self-consistent-field (SCF) molecular orbital (MO) and Møller-Plesset second order perturbation theory (MP2) calculations were performed to determine the geometry, total energy and vibrational frequencies of OPCN.

  7. Diastereoselective reactions in glycine templates containing an ent-ardeemin fragment.

    PubMed

    Martín-Santamaría, Sonsoles; Corzo-Suárez, Raúl; Avendaño, Carmen; Espada, Modesta; Gago, Federico; García-Granda, Santiago; Rzepa, Henry S

    2002-04-05

    Self-consistent reaction field solvation models derived from SCF-MO calculations are shown to be reliable in modeling the diastereoselectivity of the reactions of the anion and cation derived from (4S)-2,4-dimethyl-2,4-dihydro-1H-pyrazino[2,1-b]quinazoline-3,6-dione (1) at C(1) with electrophiles and nucleophiles, respectively. The found anti/syn ratio of compound 8, which is a seco-ent-ardeemin analogue obtained by alkylation of 1 with gramine methiodide, confirms this computational model. A close similarity between the calculated geometry of the piperazine ring in the anti isomers of 1,2,4-trialkyl derivatives and that deduced from their (1)H NMR (solution) and X-ray data has been also established.

  8. Structure and stability of the N-hydroxyurea dimer: Post-Hartree-Fock quantum mechanical study

    NASA Astrophysics Data System (ADS)

    Jabalameli, Ali; Venkatraman, Ramaiyer; Nowek, Andrzej; Sullivan, Richard H.

    2000-10-01

    The potential energy surface (PES) search of the N-hydroxyurea dimer was searched with second-order Møller-Plesset perturbation theory (MP2) and the 6-31G(d,p) basis set. Eight local minimum energy structures have been found. Four of them have relatively strong (ΔE˜-10 to -13 kcal/mol) intermolecular interactions and the others are moderately strongly interacting species (ΔE˜-3 to -7 kcal/mol). Final estimation of interaction energies was performed using the larger 6-311G(df,pd) and 6-311G(2df,2pd) basis sets. The predicted interaction energies are ΔE=-14.26 kcal/mol and -3.43 kcal/mol for the strongest and the weakest interacting forms of the studied complex, respectively, at the MP2/6-311G(2df,2pd)//MP2/6-31G(d,p) level of theory. The self-consistent field (SCF) interaction energy decomposition indicates the important influence of the deformation term magnitude on ΔE(SCF). The calculated electron correlation contribution to ΔE(MP2) depends on the geometry of the system and varies from -0.5 to -5 kcal/mol. The estimated influence of water on the stability (free energy of hydration) of N-hydroxyurea dimers using the self-consistent isodensity polarized continuum (SCI-PCM) model of solvation varies from ˜-11 kcal/mol to ˜-21 kcal/mol. The forms predicted to be more strongly interacting species in gas phase are less influenced by hydration than the more weakly interacting ones.

  9. The correlated molecular electrostatic potential and electric field of 2 (1H)-pyrimidone and 2-hydroxypyrimidine

    NASA Astrophysics Data System (ADS)

    Leś, Andrzej; Adamowicz, Ludwik

    1991-06-01

    The molecular electrostatic potential and molecular electric field have been estimated by means of the expectation values of the respective one-electron operators. We used the molecular density matrix that includes the electron correlation effects up to the second-order of the many body perturbation theory. The results show that around the 2(1H)-pyrimidone molecule one may distinguish the electrophilic and nucleophilic regions, the latter characterized by two potential minima of -2.9 V. In the tautomeric form, 2-hydroxypyrimidine, a third potential minimum of -2.1 V appears close to the N1 nitrogen atom. For both molecules strong orientational forces acting on polar solvents are predicted in the vicinity of oxygen (O7) and nitrogen (N3) atoms. The electron correlation effects do not significantly alter the SCF values of the electrostatic potential and electric field at the distances within the van der Waals envelope of the pyrimidine bases. At larger distances, however, the correlation correction is significant, particularly in the direction facing the proton transfer path.

  10. Vertical multiphase flow correlations for high production rates and large tubulars

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Aggour, M.A.; Al-Yousef, H.Y.; Al-Muraikhi, A.J.

    1996-02-01

    Numerous correlations exist for predicting pressure drop in vertical multiphase flow. These correlations, however, were all developed and tested under limited operating conditions that do not match the high production rates and large tubulars normally found in the Middle East fields. This paper presents a comprehensive evaluation of existing correlations and modifications of some correlations to determine and recommend the best correlation or correlations for various field conditions. More than 400 field data sets covering tubing sizes from 2 3/8 to 7 inches, oil rates up to 23,200 B/D, water cuts up to 95%, and gas/oil ratio (GOR) up tomore » 927 scf/STB were used in this study. Considering all data combined, the Beggs and Brill correlation provided the best pressure predictions. However, the Hagedorn and Brown correlation was better for water cuts above 80%, while the Hasan and Kabir model was better for total liquid rates above 20,000 B/D. The Aziz correlation was significantly improved when the Orkiszewski flow-pattern transition criteria were used.« less

  11. Growth and characterization of Yb:Ho:YAG single crystal fiber

    NASA Astrophysics Data System (ADS)

    Yang, Yilun; Ye, Linhua; Bao, Renjie; Li, Shanming; Zhang, Peixiong; Xu, Min; Hang, Yin

    2018-06-01

    High quality Yb and Ho co-doped Y3Al5O12 single crystal fibers have been successfully grown by the laser heated pedestal growth method of up to 124 mm in length and 450 μm in diameter for the first time. The results of inductively coupled plasma-atomic emission spectrometry analysis, X-ray diffraction and Raman spectroscopy reveal that the lattice structure and doping concentrations of the SCF are the same as that of the bulk. Scanning electron microscopy microphotographs shows that the fibers only have minor diameter fluctuations within 0.5%.

  12. Chemical shifts of diamagnetic azafullerenes: (C 59N) 2 and C 59HN

    NASA Astrophysics Data System (ADS)

    Bühl, Michael; Curioni, Alessandro; Andreoni, Wanda

    1997-08-01

    13C and 15N chemical shifts have been calculated for the azafullerenes (C 59N) 2 and C 59HN using the GIAO (gauge including atomic orbitals)-SCF method based on the geometry obtained with the density functional theory BLYP scheme Our results are in good agreement with experimental data, in particular, for the "anomalous" shift of the saturated carbon. Combined with previous calculations of the structural stability and electronic as well as vibrational properties, the present findings confirm the calculated structures for both molecules and establish the [6,6]-closed configuration for the dimer.

  13. Tuning the nanostructures and optical properties of undoped and N-doped ZnO by supercritical fluid treatment

    NASA Astrophysics Data System (ADS)

    Li, Yaping; Wang, Hui-Qiong; Chu, Tian-Jian; Li, Yu-Chiuan; Li, Xiaojun; Liao, Xiaxia; Wang, Xiaodan; Zhou, Hua; Kang, Junyong; Chang, Kuan-Chang; Chang, Ting-Chang; Tsai, Tsung-Ming; Zheng, Jin-Cheng

    2018-05-01

    Treatment of ZnO films in a supercritical fluid (SCF) has been reported to improve the performance of devices in which the treated ZnO films are incorporated; however, the mechanism of this improvement remains unclear. In this paper, we study the transformation of the surface morphologies and emission properties of ZnO films before and after SCF treatment, establishing the relationship between the treated and untreated structures and thereby enabling tuning of the catalytic or opto-electronic performance of ZnO films or ZnO-film-based devices. Both undoped and N-doped ZnO nanostructures generated by SCF treatment of films are investigated using techniques to characterize their surface morphology (scanning electron microscopy (SEM) and atomic force microscopy (AFM)) as well as room-temperature photoluminescence (RT-PL) spectroscopy. The water-mixed supercritical CO2 (W-SCCO2) technology was found to form nanostructures in ZnO films through a self-catalyzed process enabled by the Zn-rich conditions in the ZnO films. The W-SCCO2 was also found to promote the inhibition of defect luminescence by introducing -OH groups onto the films. Two models are proposed to explain the effects of the treatment with W-SCCO2. This work demonstrates that the W-SCCO2 technology can be used as an effective tool for the nanodesign and property enhancement of functional metal oxides.

  14. The human ubiquitin-conjugating enzyme Cdc34 controls cellular proliferation through regulation of p27{sup Kip1} protein levels

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Butz, Nicole; Ruetz, Stephan; Natt, Francois

    2005-02-15

    Ubiquitin-mediated degradation of the cyclin-dependent kinase inhibitor p27{sup Kip1} was shown to be required for the activation of key cyclin-dependent kinases, thereby triggering the onset of DNA replication and cell cycle progression. Although the SCF{sup Skp2} ubiquitin ligase has been reported to mediate p27{sup Kip1} degradation, the nature of the human ubiquitin-conjugating enzyme involved in this process has not yet been determined at the cellular level. Here, we show that antisense oligonucleotides targeting the human ubiquitin-conjugating enzyme Cdc34 downregulate its expression, inhibit the degradation of p27{sup Kip1}, and prevent cellular proliferation. Elevation of p27{sup Kip1} protein level is found tomore » be the sole requirement for the inhibition of cellular proliferation induced upon downregulation of Cdc34. Indeed, reducing the expression of p27{sup Kip1} with a specific antisense oligonucleotide is sufficient to reverse the anti-proliferative phenotype elicited by the Cdc34 antisense. Furthermore, downregulation of Cdc34 is found to specifically increase the abundance of the SCF{sup Skp2} ubiquitin ligase substrate p27{sup Kip1}, but has no concomitant effect on the level of IkB{alpha} and {beta}-catenin, which are known substrates of a closely related SCF ligase.« less

  15. Th17 cell-mediated immune responses promote mast cell proliferation by triggering stem cell factor in keratinocytes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cho, Kyung-Ah; Park, Minhwa; Kim, Yu-Hee

    Although mast cells are traditionally thought to function as effector cells in allergic responses, they have increasingly been recognized as important regulators of various immune responses. Mast cells mature locally; thus, tissue-specific influences are important for promoting mast cell accumulation and survival in the skin and the gastrointestinal tract. In this study, we determined the effects of keratinocytes on mast cell accumulation during Th17-mediated skin inflammation. We observed increases in dermal mast cells in imiquimod-induced psoriatic dermatitis in mice accompanied by the expression of epidermal stem cell factor (SCF), a critical mast cell growth factor. Similar to mouse epidermal keratinocytes,more » SCF was highly expressed in the human HaCaT keratinocyte cell line following stimulation with IL−17. Further, keratinocytes promoted mast cell proliferation following stimulation with IL−17 in vitro. However, the effects of keratinocytes on mast cells were significantly diminished in the presence of anti−CD117 (stem cell factor receptor) blocking antibodies. Taken together, our results revealed that the Th17-mediated inflammatory environment promotes mast cell accumulation through keratinocyte-derived SCF. - Highlights: • Psoriasis-like skin inflammation increase dermal mast cells. • Keratinocyte produce stem cell factor in psoriasis-like skin inflammation. • Keratinocyte promote mast cell proliferation by stem cell factor dependent manner.« less

  16. Hunger mapping: food insecurity and vulnerability information.

    PubMed

    1997-12-01

    Save the Children Foundation (SCF), a nongovernmental organization (NGO), developed the "household food economy analysis" to assess the needs of an area or population facing acute food insecurity. This method considers all of the ways people secure access to food and illustrates the distribution of various food supplies in pie charts that allow comparison of the percentage contribution of each option during a normal year and a "bad" year. Data are gathered through the use of key informants, and the analysis permits identification of ways to support local initiatives and to target assistance. As a result of this work, SCF and another NGO, Helen Keller International, attended a March 1997 expert consultation organized by the UN Food and Agriculture Organization (FAO) to create a workplan for the Food Insecurity and Vulnerability Information and Mapping System (FIVIMS) called for in the World Food Summit Plan of Action. The consultation adopted use of the FAO's food and balance sheet approach, despite its limitations, and determined that indicators should be location- and time-specific as well as 1) simple and reliable, 2) readily available, 3) social and anthropometric, and 4) found at all levels. The consultation also recommended combination of the key informant and the indicator approach to data collection. Finally, the consultation identified appropriate actions that should be accomplished before the 1998 meeting of the FAO's Committee on World Food Security.

  17. Nonlinear Behavior of a Shim Coil in an LTS/HTS NMR Magnet With an HTS Insert Comprising Double-Pancake HTS-Tape Coils

    PubMed Central

    Hahn, Seung-yong; Ahn, Min Cheol; Bascuñán, Juan; Yao, Weijun; Iwasa, Yukikazu

    2010-01-01

    This paper reports results, experimental and analytical, of the nonlinear behavior of a shim coil in the presence of an HTS coil assembled with double-pancake (DP) HTS-tape coils. The experimental results are from: 1) operation of a 700 MHz LTS/HTS NMR magnet (LH700) consisting of a 600 MHz LTS NMR magnet (L600) equipped with superconducting shim coils and a 100 MHz DP-assembled HTS insert (H100) and; 2) an experiment with a room-temperature (RT) Z1 shim coil coupled to a 50 MHz DP-as-sembled HTS insert (H50). A field mapping theory with a harmonic analysis is applied to interpret both results. Based on experimental results and analyses, we conclude that the screening-current-induced field (SCF) generated by a DP-assembled HTS insert is primarily responsible for the nonlinear behavior, including strength degradation, of a shim coil. PMID:20383282

  18. Nuclear relaxation and vibrational contributions to the static electrical properties of polyatomic molecules: beyond the Hartree-Fock approximation

    NASA Astrophysics Data System (ADS)

    Luis, Josep M.; Martí, Josep; Duran, Miquel; Andrés, JoséL.

    1997-04-01

    Electronic and nuclear contributions to the static molecular electrical properties, along with the Stark tuning rate ( δνE ) and the infrared cross section changes ( δSE) have been calculated at the SCF level and at different correlated levels of theory, using a TZ2P basis set and finite field techniques. Nuclear contributions to these molecular properties have also been calculated using a recent analytical approach that allow both to check the accuracy of the finite field values, and to evaluate the importance of higher-order derivatives. The HF, CO, H 2O, H 2CO, and CH 4 molecules have been studied and the results compared to experimental date when available. The paper shows that nuclear relaxation and vibrational contributions must be included in order to obtain accurate values of the static electrical properties. Two different, combined approaches are proposed to predict experimental values of the electrical properties to an error smaller than 5%.

  19. Linear scaling computation of the Fock matrix. II. Rigorous bounds on exchange integrals and incremental Fock build

    NASA Astrophysics Data System (ADS)

    Schwegler, Eric; Challacombe, Matt; Head-Gordon, Martin

    1997-06-01

    A new linear scaling method for computation of the Cartesian Gaussian-based Hartree-Fock exchange matrix is described, which employs a method numerically equivalent to standard direct SCF, and which does not enforce locality of the density matrix. With a previously described method for computing the Coulomb matrix [J. Chem. Phys. 106, 5526 (1997)], linear scaling incremental Fock builds are demonstrated for the first time. Microhartree accuracy and linear scaling are achieved for restricted Hartree-Fock calculations on sequences of water clusters and polyglycine α-helices with the 3-21G and 6-31G basis sets. Eightfold speedups are found relative to our previous method. For systems with a small ionization potential, such as graphitic sheets, the method naturally reverts to the expected quadratic behavior. Also, benchmark 3-21G calculations attaining microhartree accuracy are reported for the P53 tetramerization monomer involving 698 atoms and 3836 basis functions.

  20. Fluctuation diamagnetism in two-band superconductors

    NASA Astrophysics Data System (ADS)

    Adachi, Kyosuke; Ikeda, Ryusuke

    2016-04-01

    Anomalously large fluctuation diamagnetism around the superconducting critical temperature has been recently observed in iron selenide (FeSe) [Kasahara et al. (unpublished)]. This indicates that superconducting fluctuations (SCFs) play a more significant role in FeSe, which supposedly has a two-band structure, than in the familiar single-band superconductors. Motivated by the data on FeSe, SCF-induced diamagnetism is examined in a two-band system, on the basis of a phenomenological approach with a Ginzburg-Landau functional. The obtained results indicate that the SCF-induced diamagnetism may be more enhanced than that in a single-band system due to the existence of two distinct fluctuation modes. Such enhancement of diamagnetism unique to a two-band system seems consistent with the large diamagnetism observed in FeSe, though still far from a quantitative agreement.

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