Generalized Jastrow variational method for liquid3He-4He mixtures at T=0 K

NASA Astrophysics Data System (ADS)

Mirabbaszadeh, K.

1989-07-01

The ground state energy of a dilute solution of mass-3 fermions in liquid4He is analyzed by a variational procedure based on the Jastrow many body theory. The antisymmetry of the wave function for fermions is incorporated following the procedure given by Lado, Inguva, and Smith. A set of coupled integrodifferential equations is solved in the hypernetted chain approximation yielding expressions for the binding energy of3He-4He mixtures; the radial distribution function is given together with the total energy for various values of density and the interparticle separation r s.

Nonlocal screening in metal surfaces

NASA Technical Reports Server (NTRS)

Krotscheck, E.; Kohn, W.

1986-01-01

Due to the effect of the nonuniform environment on the static screening of the Coulomb potential, the local-density approximation for the particle-hole interaction is found to be inadequate to determine the surface energy of simple metals. Use of the same set of single-particle states, and thus the same one-body density and the same work function, has eliminated the single-electron states in favor of the structure of the short-ranged correlations as the basis of this effect. A posteriori simplifications of the Fermi hypernetted-chain theory may be found to allow the same calculational accuracy with simpler computational tools.

Theory and computer simulation of hard-core Yukawa mixtures: thermodynamical, structural and phase coexistence properties.

PubMed

Mkanya, Anele; Pellicane, Giuseppe; Pini, Davide; Caccamo, Carlo

2017-09-13

We report extensive calculations, based on the modified hypernetted chain (MHNC) theory, on the hierarchical reference theory (HRT), and on Monte Carlo simulations, of thermodynamical, structural and phase coexistence properties of symmetric binary hard-core Yukawa mixtures (HCYM) with attractive interactions at equal species concentration. The obtained results are throughout compared with those available in the literature for the same systems. It turns out that the MHNC predictions for thermodynamic and structural quantities are quite accurate in comparison with the MC data. The HRT is equally accurate for thermodynamics, and slightly less accurate for structure. Liquid-vapor (LV) and liquid-liquid (LL) consolute coexistence conditions as emerging from simulations, are also highly satisfactorily reproduced by both the MHNC and HRT for relatively long ranged potentials. When the potential range reduces, the MHNC faces problems in determining the LV binodal line; however, the LL consolute line and the critical end point (CEP) temperature and density turn out to be still satisfactorily predicted within this theory. The HRT also predicts with good accuracy the CEP position. The possibility of employing liquid state theories HCYM for the purpose of reliably determining phase equilibria in multicomponent colloidal fluids of current technological interest, is discussed.

Theory and computer simulation of hard-core Yukawa mixtures: thermodynamical, structural and phase coexistence properties

NASA Astrophysics Data System (ADS)

Mkanya, Anele; Pellicane, Giuseppe; Pini, Davide; Caccamo, Carlo

2017-09-01

We report extensive calculations, based on the modified hypernetted chain (MHNC) theory, on the hierarchical reference theory (HRT), and on Monte Carlo simulations, of thermodynamical, structural and phase coexistence properties of symmetric binary hard-core Yukawa mixtures (HCYM) with attractive interactions at equal species concentration. The obtained results are throughout compared with those available in the literature for the same systems. It turns out that the MHNC predictions for thermodynamic and structural quantities are quite accurate in comparison with the MC data. The HRT is equally accurate for thermodynamics, and slightly less accurate for structure. Liquid-vapor (LV) and liquid-liquid (LL) consolute coexistence conditions as emerging from simulations, are also highly satisfactorily reproduced by both the MHNC and HRT for relatively long ranged potentials. When the potential range reduces, the MHNC faces problems in determining the LV binodal line; however, the LL consolute line and the critical end point (CEP) temperature and density turn out to be still satisfactorily predicted within this theory. The HRT also predicts with good accuracy the CEP position. The possibility of employing liquid state theories HCYM for the purpose of reliably determining phase equilibria in multicomponent colloidal fluids of current technological interest, is discussed.

Performance of Kobryn-Gusarov-Kovalenko closure from a thermodynamic viewpoint for one-component Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Miyata, Tatsuhiko; Tange, Kentaro

2018-05-01

The performance of Kobryn-Gusarov-Kovalenko (KGK) closure was examined in terms of the thermodynamics for one-component Lennard-Jones fluids. The result was compared to molecular dynamics simulation as well as to hypernetted chain, Kovalenko-Hirata (KH), Percus-Yevick and Verlet-modified closures. As the density increases, the error of KGK closure shows a turnover, regarding the excess internal energy, pressure and isothermal compressibility. On the other hand, it was numerically confirmed that the energy and the virial equations are consistent under both KH and KGK closures. The accuracies of density-derivative and temperature-derivative of the radial distribution function are also discussed.

A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution.

PubMed

Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro

2016-06-14

In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.

Theory of inhomogeneous quantum systems. III. Variational wave functions for Fermi fluids

NASA Astrophysics Data System (ADS)

Krotscheck, E.

1985-04-01

We develop a general variational theory for inhomogeneous Fermi systems such as the electron gas in a metal surface, the surface of liquid 3He, or simple models of heavy nuclei. The ground-state wave function is expressed in terms of two-body correlations, a one-body attenuation factor, and a model-system Slater determinant. Massive partial summations of cluster expansions are performed by means of Born-Green-Yvon and hypernetted-chain techniques. An optimal single-particle basis is generated by a generalized Hartree-Fock equation in which the two-body correlations screen the bare interparticle interaction. The optimization of the pair correlations leads to a state-averaged random-phase-approximation equation and a strictly microscopic determination of the particle-hole interaction.

Theoretical study of interactions of BSA protein in a NaCl aqueous solution

NASA Astrophysics Data System (ADS)

Pellicane, Giuseppe; Cavero, Miguel

2013-03-01

Bovine Serum Albumine (BSA) aqueous solutions in the presence of NaCl are investigated for different protein concentrations and low to intermediate ionic strengths. Protein interactions are modeled via a charge-screened colloidal model, in which the range of the potential is determined by the Debye-Hückel constant. We use Monte Carlo computer simulations to calculate the structure factor, and assume an oblate ellipsoidal form factor for BSA. The theoretical scattered intensities are found in good agreement with the experimental small angle X-ray scattering intensities available in the literature. The performance of well-known integral equation closures to the Ornstein-Zernike equation, namely the mean spherical approximation, the Percus-Yevick, and the hypernetted chain equations, is also assessed with respect to computer simulation.

Theoretical study of solvent effects on the coil-globule transition

NASA Astrophysics Data System (ADS)

Polson, James M.; Opps, Sheldon B.; Abou Risk, Nicholas

2009-06-01

The coil-globule transition of a polymer in a solvent has been studied using Monte Carlo simulations of a single chain subject to intramolecular interactions as well as a solvent-mediated effective potential. This solvation potential was calculated using several different theoretical approaches for two simple polymer/solvent models, each employing hard-sphere chains and hard-sphere solvent particles as well as attractive square-well potentials between some interaction sites. For each model, collapse is driven by variation in a parameter which changes the energy mismatch between monomers and solvent particles. The solvation potentials were calculated using two fundamentally different methodologies, each designed to predict the conformational behavior of polymers in solution: (1) the polymer reference interaction site model (PRISM) theory and (2) a many-body solvation potential (MBSP) based on scaled particle theory introduced by Grayce [J. Chem. Phys. 106, 5171 (1997)]. For the PRISM calculations, two well-studied solvation monomer-monomer pair potentials were employed, each distinguished by the closure relation used in its derivation: (i) a hypernetted-chain (HNC)-type potential and (ii) a Percus-Yevick (PY)-type potential. The theoretical predictions were each compared to results obtained from explicit-solvent discontinuous molecular dynamics simulations on the same polymer/solvent model systems [J. Chem. Phys. 125, 194904 (2006)]. In each case, the variation in the coil-globule transition properties with solvent density is mostly qualitatively correct, though the quantitative agreement between the theory and prediction is typically poor. The HNC-type potential yields results that are more qualitatively consistent with simulation. The conformational behavior of the polymer upon collapse predicted by the MBSP approach is quantitatively correct for low and moderate solvent densities but is increasingly less accurate for higher densities. At high solvent densities, the PRISM-HNC and MBSP approaches tend to overestimate, while the PRISM-PY approach underestimates the tendency of the solvent to drive polymer collapse.

Correlational and thermodynamic properties of finite-temperature electron liquids in the hypernetted-chain approximation.

PubMed

Tanaka, Shigenori

2016-12-07

Correlational and thermodynamic properties of homogeneous electron liquids at finite temperatures are theoretically analyzed in terms of dielectric response formalism with the hypernetted-chain (HNC) approximation and its modified version. The static structure factor and the local-field correction to describe the strong Coulomb-coupling effects beyond the random-phase approximation are self-consistently calculated through solution to integral equations in the paramagnetic (spin unpolarized) and ferromagnetic (spin polarized) states. In the ground state with the normalized temperature θ=0, the present HNC scheme well reproduces the exchange-correlation energies obtained by quantum Monte Carlo (QMC) simulations over the whole fluid phase (the coupling constant r s ≤100), i.e., within 1% and 2% deviations from putative best QMC values in the paramagnetic and ferromagnetic states, respectively. As compared with earlier studies based on the Singwi-Tosi-Land-Sjölander and modified convolution approximations, some improvements on the correlation energies and the correlation functions including the compressibility sum rule are found in the intermediate to strong coupling regimes. When applied to the electron fluids at intermediate Fermi degeneracies (θ≈1), the static structure factors calculated in the HNC scheme show good agreements with the results obtained by the path integral Monte Carlo (PIMC) simulation, while a small negative region in the radial distribution function is observed near the origin, which may be associated with a slight overestimation for the exchange-correlation hole in the HNC approximation. The interaction energies are calculated for various combinations of density and temperature parameters ranging from strong to weak degeneracy and from weak to strong coupling, and the HNC values are then parametrized as functions of r s and θ. The HNC exchange-correlation free energies obtained through the coupling-constant integration show reasonable agreements with earlier results including the PIMC-based fitting over the whole fluid region at finite degeneracies in the paramagnetic state. In contrast, a systematic difference between the HNC and PIMC results is observed in the ferromagnetic state, which suggests a necessity of further studies on the exchange-correlation free energies from both aspects of analytical theory and simulation.

Comparative study of the LOCV and the FHNC approaches for the nucleonic matter problem

NASA Astrophysics Data System (ADS)

Tafrihi, Azar; Modarres, Majid

2016-03-01

The nucleonic matter problem is investigated by comparing the lowest order constrained variational (LOCV) method with the Fermi hypernetted chain (FHNC) theory, emphasizing the role of the LOCV correlation functions. In this way, the central correlation functions are used in the LOCV formalism, for the Bethe homework problem. It is shown that the LOCV computations reasonably agree with those of FHNC. Moreover, the FHNC calculations are performed with the LOCV correlation functions. It is found that, assuming the LOCV or the parametrized correlation functions, the FHNC computations do not change significantly. So, one may conclude that the mentioned consistencies refer to the choice of the LOCV correlation functions. Because, the contribution of the many-body cluster terms can be ignored, if the LOCV correlation functions satisfy the normalization constraint. Then, using the AV 18 interaction, the operator-dependent (OD) correlation functions are employed in the LOCV calculations. Note that the LOCV OD correlation functions are obtained by averaging over the states. It turns out that the overall behaviour of the LOCV OD correlation functions are similar to those of FHNC. Although, due to the many-body effects which are considered in the FHNC calculations, the LOCV results fairly differ from those of FHNC. Finally, it is worth mentioning that, unlike the recent FHNC calculations, the spin-orbit-dependent correlation functions are included in the LOCV approach.

Theoretical study on the sound absorption of electrolytic solutions. I. Theoretical formulation.

PubMed

Yamaguchi, T; Matsuoka, T; Koda, S

2007-04-14

A theory is formulated that describes the sound absorption of electrolytic solutions due to the relative motion of ions, including the formation of ion pairs. The theory is based on the Kubo-Green formula for the bulk viscosity. The time correlation function of the pressure is projected onto the bilinear product of the density modes of ions. The time development of the product of density modes is described by the diffusive limit of the generalized Langevin equation, and approximate expressions for the three- and four-body correlation functions required are given with the hypernetted-chain integral equation theory. Calculations on the aqueous solutions of model electrolytes are performed. It is demonstrated that the theory describes both the activated barrier crossing between contact and solvent-separated ion pairs and the Coulombic correlation between ions.

Theoretical study on the sound absorption of electrolytic solutions. I. Theoretical formulation

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Matsuoka, T.; Koda, S.

2007-04-01

A theory is formulated that describes the sound absorption of electrolytic solutions due to the relative motion of ions, including the formation of ion pairs. The theory is based on the Kubo-Green formula for the bulk viscosity. The time correlation function of the pressure is projected onto the bilinear product of the density modes of ions. The time development of the product of density modes is described by the diffusive limit of the generalized Langevin equation, and approximate expressions for the three- and four-body correlation functions required are given with the hypernetted-chain integral equation theory. Calculations on the aqueous solutions of model electrolytes are performed. It is demonstrated that the theory describes both the activated barrier crossing between contact and solvent-separated ion pairs and the Coulombic correlation between ions.

Cooling without contact in bilayer dipolar Fermi gases

NASA Astrophysics Data System (ADS)

Tanatar, Bilal; Renklioglu, Basak; Oktel, M. Ozgur

2016-05-01

We consider two parallel layers of dipolar ultracold Fermi gases at different temperatures and calculate the heat transfer between them. The effective interactions describing screening and correlation effects between the dipoles in a single layer are modelled within the Euler-Lagrange Fermi-hypernetted chain approximation. The random-phase approximation is employed for the interactions across the layers. We investigate the amount of transferred power between the layers as a function of the temperature difference. Energy transfer proceeds via the long-range dipole-dipole interactions. A simple thermal model is developed to investigate the feasibility of using the contactless sympathetic cooling of the ultracold polar atoms/molecules. Our calculations indicate that dipolar heat transfer is effective for typical polar molecule experiments and may be utilized as a cooling process. Supported by TUBA and TUBITAK (112T974).

Average-atom model for two-temperature states and ionic transport properties of aluminum in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Hou, Yong; Fu, Yongsheng; Bredow, Richard; Kang, Dongdong; Redmer, Ronald; Yuan, Jianmin

2017-03-01

The average-atom model combined with the hyper-netted chain approximation is an efficient tool for electronic and ionic structure calculations for warm dense matter. Here we generalize this method in order to describe non-equilibrium states with different electron and ion temperature as produced in laser-matter interactions on ultra-short time scales. In particular, the electron-ion and ion-ion correlation effects are considered when calculating the electron structure. We derive an effective ion-ion pair-potential using the electron densities in the framework of temperature-depended density functional theory. Using this ion-ion potential we perform molecular dynamics simulations in order to determine the ionic transport properties such as the ionic diffusion coefficient and the shear viscosity through the ionic velocity autocorrelation functions.

Spin-dependent analysis of two-dimensional electron liquids

NASA Astrophysics Data System (ADS)

Bulutay, C.; Tanatar, B.

2002-05-01

Two-dimensional electron liquid (2D EL) at full Fermi degeneracy is revisited, giving special attention to the spin-polarization effects. First, we extend the recently proposed classical-map hypernetted-chain (CHNC) technique to the 2D EL, while preserving the simplicity of the original proposal. An efficient implementation of CHNC is given utilizing Lado's quadrature expressions for the isotropic Fourier transforms. Our results indicate that the paramagnetic phase stays to be the ground state until the Wigner crystallization density, even though the energy separation with the ferromagnetic and other partially polarized states become minute. We analyze compressibility and spin stiffness variations with respect to density and spin polarization, the latter being overlooked until now. Spin-dependent static structure factor and pair-distribution functions are computed; agreement with the available quantum Monte Carlo data persists even in the strong-coupling regime of the 2D EL.

Theory of the interface between a classical plasma and a hard wall

NASA Astrophysics Data System (ADS)

Ballone, P.; Pastore, G.; Tosi, M. P.

1983-09-01

The interfacial density profile of a classical one-component plasma confined by a hard wall is studied in planar and spherical geometries. The approach adapts to interfacial problems a modified hypernetted-chain approximation developed by Lado and by Rosenfeld and Ashcroft for the bulk structure of simple liquids. The specific new aim is to embody selfconsistently into the theory a contact theorem, fixing the plasma density at the wall through an equilibrium condition which involves the electrical potential drop across the interface and the bulk pressure. The theory is brought into fully quantitative contact with computer simulation data for a plasma confined in a spherical cavity of large but finite radius. The interfacial potential at the point of zero charge is accurately reproduced by suitably combining the contact theorem with relevant bulk properties in a simple, approximate representation of the interfacial charge density profile.

Theory of the interface between a classical plasma and a hard wall

NASA Astrophysics Data System (ADS)

Ballone, P.; Pastore, G.; Tosi, M. P.

1984-12-01

The interfacial density profile of a classical one-component plasma confined by a hard wall is studied in planar and spherical geometries. The approach adapts to interfacial problems a modified hypernetted-chain approximation developed by Lado and by Rosenfeld and Ashcroft for the bulk structure of simple liquids. The specific new aim is to embody self-consistently into the theory a “contact theorem”, fixing the plasma density at the wall through an equilibrium condition which involves the electrical potential drop across the interface and the bulk pressure. The theory is brought into fully quantitative contact with computer simulation data for a plasma confined in a spherical cavity of large but finite radius. It is also shown that the interfacial potential at the point of zero charge is accurately reproduced by suitably combining the contact theorem with relevant bulk properties in a simple, approximate representation of the interfacial charge density profile.

The force distribution probability function for simple fluids by density functional theory.

PubMed

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Pair potentials for warm dense matter and their application to x-ray Thomson scattering in aluminum and beryllium.

PubMed

Harbour, L; Dharma-Wardana, M W C; Klug, D D; Lewis, L J

2016-11-01

Ultrafast laser experiments yield increasingly reliable data on warm dense matter, but their interpretation requires theoretical models. We employ an efficient density functional neutral-pseudoatom hypernetted-chain (NPA-HNC) model with accuracy comparable to ab initio simulations and which provides first-principles pseudopotentials and pair potentials for warm-dense matter. It avoids the use of (i) ad hoc core-repulsion models and (ii) "Yukawa screening" and (iii) need not assume ion-electron thermal equilibrium. Computations of the x-ray Thomson scattering (XRTS) spectra of aluminum and beryllium are compared with recent experiments and with density-functional-theory molecular-dynamics (DFT-MD) simulations. The NPA-HNC structure factors, compressibilities, phonons, and conductivities agree closely with DFT-MD results, while Yukawa screening gives misleading results. The analysis of the XRTS data for two of the experiments, using two-temperature quasi-equilibrium models, is supported by calculations of their temperature relaxation times.

Demixing in simple dipolar mixtures: Integral equation versus density functional results

NASA Astrophysics Data System (ADS)

Range, Gabriel M.; Klapp, Sabine H. L.

2004-09-01

Using reference hypernetted chain (RHNC) integral equations and density functional theory in the modified mean-field (MMF) approximation we investigate the phase behavior of binary mixtures of dipolar hard spheres. The two species ( A and B ) differ only in their dipole moments mA and mB , and the central question investigated is under which conditions these asymmetric mixtures can exhibit demixing phase transitions in the fluid phase regime. Results from our two theoretical approaches turn out to strongly differ. Within the RHNC (which we apply to the isotropic high-temperature phase) demixing does indeed occur for dense systems with small interaction parameters Γ=mB2/mA2 . This result generalizes previously reported observations on demixing in mixtures of dipolar and neutral hard spheres (Γ=0) to the case of true dipolar hard sphere mixtures. The RHNC approach also indicates that these demixed fluid phases are isotropic at temperatures accessible by the theory, whereas isotropic-to-ferroelectric transitions occur only at larger Γ . The MMF theory, on the other hand, yields a different picture in which demixing occurs in combination with spontaneous ferroelectricity at all Γ considered. This discrepancy underlines the relevance of correlational effects for the existence of demixing transitions in dipolar systems without dispersive interactions. Indeed, supplementing the dipolar interactions by small, asymmetric amounts of van der Waals-like interactions (and thereby supporting the systems tendency to demix) one finally reaches good agreement between MMF and RHNC results.

Advances in visual representation of molecular potentials.

PubMed

Du, Qi-Shi; Huang, Ri-Bo; Chou, Kuo-Chen

2010-06-01

The recent advances in visual representations of molecular properties in 3D space are summarized, and their applications in molecular modeling study and rational drug design are introduced. The visual representation methods provide us with detailed insights into protein-ligand interactions, and hence can play a major role in elucidating the structure or reactivity of a biomolecular system. Three newly developed computation and visualization methods for studying the physical and chemical properties of molecules are introduced, including their electrostatic potential, lipophilicity potential and excess chemical potential. The newest application examples of visual representations in structure-based rational drug are presented. The 3D electrostatic potentials, calculated using the empirical method (EM-ESP), in which the classical Coulomb equation and traditional atomic partial changes are discarded, are highly consistent with the results by the higher level quantum chemical method. The 3D lipophilicity potentials, computed by the heuristic molecular lipophilicity potential method based on the principles of quantum mechanics and statistical mechanics, are more accurate and reliable than those by using the traditional empirical methods. The 3D excess chemical potentials, derived by the reference interaction site model-hypernetted chain theory, provide a new tool for computational chemistry and molecular modeling. For structure-based drug design, the visual representations of molecular properties will play a significant role in practical applications. It is anticipated that the new advances in computational chemistry will stimulate the development of molecular modeling methods, further enriching the visual representation techniques for rational drug design, as well as other relevant fields in life science.

Universality of bridge functions and its relation to variational perturbation theory and additivity of equations of state

NASA Astrophysics Data System (ADS)

Rosenfeld, Yaakov

1984-05-01

Featuring the modified hypernetted-chain (MHNC) scheme as a variational fitting procedure, we demonstrate that the accuracy of the variational perturbation theory (VPT) and of the method based on additivity of equations of state is determined by the excess entropy dependence of the bridge-function parameters [i.e., η(s) when the Percus-Yevick hard-sphere bridge functions are employed]. It is found that η(s) is nearly universal for all soft (i.e., "physical") potentials while it is distinctly different for the hard spheres, providing a graphical display of the "jump" in pair-potential space (with respect to accuracy of VPT) from "hard" to "soft" behavior. The universality of η(s) provides a local criterion for the MHNC scheme that should be useful for inverting structure-factor data in order to obtain the potential. An alternative local MHNC criterion due to Lado is rederived and extended, and it is also analyzed in light of the plot of η(s).

Dressed ion theory of size-asymmetric electrolytes: effective ionic charges and the decay length of screened Coulomb potential and pair correlations.

PubMed

Forsberg, Björn; Ulander, Johan; Kjellander, Roland

2005-02-08

The effects of ionic size asymmetry on long-range electrostatic interactions in electrolyte solutions are investigated within the primitive model. Using the formalism of dressed ion theory we analyze correlation functions from Monte Carlo simulations and the hypernetted chain approximation for size asymmetric 1:1 electrolytes. We obtain decay lengths of the screened Coulomb potential, effective charges of ions, and effective permittivity of the solution. It is found that the variation of these quantities with the degree of size asymmetry depends in a quite intricate manner on the interplay between the electrostatic coupling and excluded volume effects. In most cases the magnitude of the effective charge of the small ion species is larger than that of the large species; the difference increases with increasing size asymmetry. The effective charges of both species are larger (in absolute value) than the bare ionic charge, except for high asymmetry where the effective charge of the large ions can become smaller than the bare charge.

Coulomb Logarithm in Nonideal and Degenerate Plasmas

NASA Astrophysics Data System (ADS)

Filippov, A. V.; Starostin, A. N.; Gryaznov, V. K.

2018-03-01

Various methods for determining the Coulomb logarithm in the kinetic theory of transport and various variants of the choice of the plasma screening constant, taking into account and disregarding the contribution of the ion component and the boundary value of the electron wavevector are considered. The correlation of ions is taken into account using the Ornstein-Zernike integral equation in the hypernetted-chain approximation. It is found that the effect of ion correlation in a nondegenerate plasma is weak, while in a degenerate plasma, this effect must be taken into account when screening is determined by the electron component alone. The calculated values of the electrical conductivity of a hydrogen plasma are compared with the values determined experimentally in the megabar pressure range. It is shown that the values of the Coulomb logarithm can indeed be smaller than unity. Special experiments are proposed for a more exact determination of the Coulomb logarithm in a magnetic field for extremely high pressures, for which electron scattering by ions prevails.

Optimized theory for simple and molecular fluids.

PubMed

Marucho, M; Montgomery Pettitt, B

2007-03-28

An optimized closure approximation for both simple and molecular fluids is presented. A smooth interpolation between Perkus-Yevick and hypernetted chain closures is optimized by minimizing the free energy self-consistently with respect to the interpolation parameter(s). The molecular version is derived from a refinement of the method for simple fluids. In doing so, a method is proposed which appropriately couples an optimized closure with the variant of the diagrammatically proper integral equation recently introduced by this laboratory [K. M. Dyer et al., J. Chem. Phys. 123, 204512 (2005)]. The simplicity of the expressions involved in this proposed theory has allowed the authors to obtain an analytic expression for the approximate excess chemical potential. This is shown to be an efficient tool to estimate, from first principles, the numerical value of the interpolation parameters defining the aforementioned closure. As a preliminary test, representative models for simple fluids and homonuclear diatomic Lennard-Jones fluids were analyzed, obtaining site-site correlation functions in excellent agreement with simulation data.

Stability of the iterative solutions of integral equations as one phase freezing criterion.

PubMed

Fantoni, R; Pastore, G

2003-10-01

A recently proposed connection between the threshold for the stability of the iterative solution of integral equations for the pair correlation functions of a classical fluid and the structural instability of the corresponding real fluid is carefully analyzed. Direct calculation of the Lyapunov exponent of the standard iterative solution of hypernetted chain and Percus-Yevick integral equations for the one-dimensional (1D) hard rods fluid shows the same behavior observed in 3D systems. Since no phase transition is allowed in such 1D system, our analysis shows that the proposed one phase criterion, at least in this case, fails. We argue that the observed proximity between the numerical and the structural instability in 3D originates from the enhanced structure present in the fluid but, in view of the arbitrary dependence on the iteration scheme, it seems uneasy to relate the numerical stability analysis to a robust one-phase criterion for predicting a thermodynamic phase transition.

Heat Transfer Through Dipolar Coupling: Sympathetic cooling without contact

NASA Astrophysics Data System (ADS)

Oktel, Mehmet; Renklioglu, Basak; Tanatar, Bilal

We consider two parallel layers of dipolar ultracold gases at different temperatures and calculate the heat transfer through dipolar coupling. As the simplest model we consider a system in which both of the layers contain two-dimensional spin-polarized Fermi gases. The effective interactions describing the correlation effects and screening between the dipoles are obtained by the Euler-Lagrange Fermi-hypernetted-chain approximation in a single layer. We use the random-phase approximation (RPA) for the interactions across the layers. We find that heat transfer through dipolar coupling becomes efficient when the layer separation is comparable to dipolar interaction length scale. We characterize the heat transfer by calculating the time constant for temperature equilibration between the layers and find that for the typical experimental parameter regime of dipolar molecules this is on the order of milliseconds. We generalize the initial model to Boson-Boson and Fermion-Boson layers and suggest that contactless sympathetic cooling may be used for ultracold dipolar molecules. Supported by TUBITAK 1002-116F030.

Models of the elastic x-ray scattering feature for warm dense aluminum

DOE PAGES

Starrett, Charles Edward; Saumon, Didier

2015-09-03

The elastic feature of x-ray scattering from warm dense aluminum has recently been measured by Fletcher et al. [Nature Photonics 9, 274 (2015)] with much higher accuracy than had hitherto been possible. This measurement is a direct test of the ionic structure predicted by models of warm dense matter. We use the method of pseudoatom molecular dynamics to predict this elastic feature for warm dense aluminum with temperatures of 1–100 eV and densities of 2.7–8.1g/cm 3. We compare these predictions to experiments, finding good agreement with Fletcher et al. and corroborating the discrepancy found in analyses of an earlier experimentmore » of Ma et al. [Phys. Rev. Lett. 110, 065001 (2013)]. Lastly, we also evaluate the validity of the Thomas-Fermi model of the electrons and of the hypernetted chain approximation in computing the elastic feature and find them both wanting in the regime currently probed by experiments.« less

Simple electrolyte solutions: Comparison of DRISM and molecular dynamics results for alkali halide solutions

PubMed Central

Joung, In Suk; Luchko, Tyler; Case, David A.

2013-01-01

Using the dielectrically consistent reference interaction site model (DRISM) of molecular solvation, we have calculated structural and thermodynamic information of alkali-halide salts in aqueous solution, as a function of salt concentration. The impact of varying the closure relation used with DRISM is investigated using the partial series expansion of order-n (PSE-n) family of closures, which includes the commonly used hypernetted-chain equation (HNC) and Kovalenko-Hirata closures. Results are compared to explicit molecular dynamics (MD) simulations, using the same force fields, and to experiment. The mean activity coefficients of ions predicted by DRISM agree well with experimental values at concentrations below 0.5 m, especially when using the HNC closure. As individual ion activities (and the corresponding solvation free energies) are not known from experiment, only DRISM and MD results are directly compared and found to have reasonably good agreement. The activity of water directly estimated from DRISM is nearly consistent with values derived from the DRISM ion activities and the Gibbs-Duhem equation, but the changes in the computed pressure as a function of salt concentration dominate these comparisons. Good agreement with experiment is obtained if these pressure changes are ignored. Radial distribution functions of NaCl solution at three concentrations were compared between DRISM and MD simulations. DRISM shows comparable water distribution around the cation, but water structures around the anion deviate from the MD results; this may also be related to the high pressure of the system. Despite some problems, DRISM-PSE-n is an effective tool for investigating thermodynamic properties of simple electrolytes. PMID:23387564

Water based on a molecular model behaves like a hard-sphere solvent for a nonpolar solute when the reference interaction site model and related theories are employed

NASA Astrophysics Data System (ADS)

Hayashi, Tomohiko; Oshima, Hiraku; Harano, Yuichi; Kinoshita, Masahiro

2016-09-01

For neutral hard-sphere solutes, we compare the reduced density profile of water around a solute g(r), solvation free energy μ, energy U, and entropy S under the isochoric condition predicted by the two theories: dielectrically consistent reference interaction site model (DRISM) and angle-dependent integral equation (ADIE) theories. A molecular model for water pertinent to each theory is adopted. The hypernetted-chain (HNC) closure is employed in the ADIE theory, and the HNC and Kovalenko-Hirata (K-H) closures are tested in the DRISM theory. We also calculate g(r), U, S, and μ of the same solute in a hard-sphere solvent whose molecular diameter and number density are set at those of water, in which case the radial-symmetric integral equation (RSIE) theory is employed. The dependences of μ, U, and S on the excluded volume and solvent-accessible surface area are analyzed using the morphometric approach (MA). The results from the ADIE theory are in by far better agreement with those from computer simulations available for g(r), U, and μ. For the DRISM theory, g(r) in the vicinity of the solute is quite high and becomes progressively higher as the solute diameter d U increases. By contrast, for the ADIE theory, it is much lower and becomes further lower as d U increases. Due to unphysically positive U and significantly larger |S|, μ from the DRISM theory becomes too high. It is interesting that μ, U, and S from the K-H closure are worse than those from the HNC closure. Overall, the results from the DRISM theory with a molecular model for water are quite similar to those from the RSIE theory with the hard-sphere solvent. Based on the results of the MA analysis, we comparatively discuss the different theoretical methods for cases where they are applied to studies on the solvation of a protein.

Penetrable square-well fluids: exact results in one dimension.

PubMed

Santos, Andrés; Fantoni, Riccardo; Giacometti, Achille

2008-05-01

We introduce a model of attractive penetrable spheres by adding a short-range attractive square well outside a penetrable core, and we provide a detailed analysis of structural and thermodynamical properties in one dimension using the exact impenetrable counterpart as a starting point. The model is expected to describe star polymers in regimes of good and moderate solvent under dilute conditions. We derive the exact coefficients of a low-density expansion up to second order for the radial distribution function and up to fourth order in the virial expansion. These exact results are used as a benchmark to test the reliability of approximate theories (Percus-Yevick and hypernetted chain). Notwithstanding the lack of an exact solution for arbitrary densities, our results are expected to be rather precise within a wide range of temperatures and densities. A detailed analysis of some limiting cases is carried out. In particular, we provide a complete solution of the sticky penetrable-sphere model in one dimension up to the same order in density. The issue of Ruelle's thermodynamics stability is analyzed and the region of a well-defined thermodynamic limit is identified.

Thermodynamic Theory of Spherically Trapped Coulomb Clusters

NASA Astrophysics Data System (ADS)

Wrighton, Jeffrey; Dufty, James; Bonitz, Michael; K"{A}Hlert, Hanno

2009-11-01

The radial density profile of a finite number of identical charged particles confined in a harmonic trap is computed over a wide ranges of temperatures (Coulomb coupling) and particle numbers. At low temperatures these systems form a Coulomb crystal with spherical shell structure which has been observed in ultracold trapped ions and in dusty plasmas. The shell structure is readily reproduced in simulations. However, analytical theories which used a mean field approachfootnotetext[1]C. Henning et al., Phys. Rev. E 74, 056403 (2006) or a local density approximationfootnotetext[2]C. Henning et al., Phys. Rev. E 76, 036404 (2007) have, so far, only been able to reproduce the average density profile. Here we present an approach to Coulomb correlations based on the hypernetted chain approximation with additional bridge diagrams. It is demonstrated that this model reproduces the correct shell structure within a few percent and provides the basis for a thermodynamic theory of Coulomb clusters in the strongly coupled fluid state.footnotetext[3]J. Wrighton, J.W. Dufty, H. K"ahlert and M. Bonitz, J. Phys. A 42, 214052 (2009) and Phys. Rev. E (2009) (to be submitted)

Algorithms for the computation of solutions of the Ornstein-Zernike equation.

PubMed

Peplow, A T; Beardmore, R E; Bresme, F

2006-10-01

We introduce a robust and efficient methodology to solve the Ornstein-Zernike integral equation using the pseudoarc length (PAL) continuation method that reformulates the integral equation in an equivalent but nonstandard form. This enables the computation of solutions in regions where the compressibility experiences large changes or where the existence of multiple solutions and so-called branch points prevents Newton's method from converging. We illustrate the use of the algorithm with a difficult problem that arises in the numerical solution of integral equations, namely the evaluation of the so-called no-solution line of the Ornstein-Zernike hypernetted chain (HNC) integral equation for the Lennard-Jones potential. We are able to use the PAL algorithm to solve the integral equation along this line and to connect physical and nonphysical solution branches (both isotherms and isochores) where appropriate. We also show that PAL continuation can compute solutions within the no-solution region that cannot be computed when Newton and Picard methods are applied directly to the integral equation. While many solutions that we find are new, some correspond to states with negative compressibility and consequently are not physical.

Radial Distribution Functions of Strongly Coupled Two-Temperature Plasmas

NASA Astrophysics Data System (ADS)

Shaffer, Nathaniel R.; Tiwari, Sanat Kumar; Baalrud, Scott D.

2017-10-01

We present tests of three theoretical models for the radial distribution functions (RDFs) in two-temperature strongly coupled plasmas. RDFs are useful in extending plasma thermodynamics and kinetic theory to strong coupling, but they are usually known only for thermal equilibrium or for approximate one-component model plasmas. Accurate two-component modeling is necessary to understand the impact of strong coupling on inter-species transport, e.g., ambipolar diffusion and electron-ion temperature relaxation. We demonstrate that the Seuferling-Vogel-Toeppfer (SVT) extension of the hypernetted chain equations not only gives accurate RDFs (as compared with classical molecular dynamics simulations), but also has a simple connection with the Yukawa OCP model. This connection gives a practical means to recover the structure of the electron background from knowledge of the ion-ion RDF alone. Using the model RDFs in Effective Potential Theory, we report the first predictions of inter-species transport coefficients of strongly coupled plasmas far from equilibrium. This work is supported by NSF Grant No. PHY-1453736, AFSOR Award No. FA9550-16-1-0221, and used XSEDE computational resources.

Generalized Jastrow Variational Method for Liquid HELIUM-3-HELIUM-4 Mixtures at T = 0 K.

NASA Astrophysics Data System (ADS)

Mirabbaszadeh, Kavoos

Microscopic theory of dilute liquid { ^3 He}-{^4 He} mixtures is of great interest, because it provides a physical realization of a nearly degenerate weakly interacting Fermion system. An understanding of properties of the mixtures has received considerable attention both theoretically and experimentally over the past thirty years. We present here a variational procedure based on the Jastrow function for the ground state of {^3 He}- {^4 He} mixtures by minimizing the total energy of the mixture using the hypernetted-chain (HNC) approximation and the Percus-Yevick (PY) approximation for the two body correlation functions. Our goal is to compute from first principles the internal energy of the system and the various two body correlation functions at various densities and compare the results with experiment. The Jastrow variational method for the ground state energy of liquid {^4 He} consists of the following ansatz for the wave function Psi_alpha {rm(vec r_{1 alpha},} {vec r_{2alpha},} dots, {vec r_{N _alpha})} = prod _{rm i < j} {rm f_ {alphaalpha}(r_{ij}). } For a {^3 He } system the corresponding ansatz is Psi_beta {rm( vec r_{1beta},} {vec r_{2beta },} dots, {vec r_{N_beta})} = {[prod _{i < j} f_{betabeta }(r_{ij})]} Phi {rm( vec r_{1beta},} {vec r_{2beta },} dots, {vec r_{Nbeta}),} where Phi is a Slater determinant of plane waves for the ground state of the Fermion system. The total energy per particle can be written in the form: E = x_sp{alpha}{2} E_{alphaalpha} + x_sp{beta}{2 }E_{betabeta } + 2x_{alpha} x_{beta}E _{alphabeta}, where E_{alphaalpha} , E_{betabeta} , E_{alphabeta} are unknown parameters to be determined from a microscopic theory. Using the Jastrow wave function Psi for the mixture, a general expression is given for the ground state energy in terms of the two body potential and two and three body correlation functions. The Kirkwood Super-position Approximation (KSA) is used for the three-body correlation functions. The antisymmetry of the wave function for Fermions is incorporated following the procedure given earlier by Lado, Inguva and Smith. This procedure for treating the antisymmetry of the wave function simplifies the equations for the two-body correlation functions considerably. The equations for the correlation functions are solved in the hypernetted-chain approximation. Once the two-particle correlation functions for the mixture ( ^3He-^4He) have been obtained, the energy is minimized with respect to the variational parameters involved in the Jastrow wave function. The binding energy and the optimal correlation functions are then obtained as a function of the concentration of ^3He atoms in the mixture. (Abstract shortened with permission of author.).

Efficient molecular density functional theory using generalized spherical harmonics expansions.

PubMed

Ding, Lu; Levesque, Maximilien; Borgis, Daniel; Belloni, Luc

2017-09-07

We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density ρ(r,Ω) around the solute is a function of the position r≡(x,y,z) and of the three Euler angles Ω≡(θ,ϕ,ψ) describing the solvent orientation. The standard density functional, equivalent to the hypernetted-chain closure for the solute-solvent correlations in the liquid theory, is minimized with respect to ρ(r,Ω). The up-to-now very expensive angular convolution products are advantageously replaced by simple products between projections onto generalized spherical harmonics. The dramatic gain in speed of resolution enables to explore in a systematic way molecular solutes of up to nanometric sizes in arbitrary solvents and to calculate their solvation free energy and associated microscopic solvent structure in at most a few minutes. We finally illustrate the formalism by tackling the solvation of molecules of various complexities in water.

The LOCV asymmetric nuclear matter two-body density distributions versus those of FHNC

NASA Astrophysics Data System (ADS)

Tafrihi, Azar

2018-05-01

The theoretical computations of the electron-nucleus scattering can be improved, by employing the asymmetric nuclear matter (ASM) two-body density distributions (TBDD) . But, due to the sophistications of the calculations, the TBDD with arbitrary isospin asymmetry have not yet been computed in the Fermi Hypernetted Chain (FHNC) or the Monte Carlo (MC) approaches. So, in the present work, we intend to find the ASM TBDD, in the states with isospin T, spin S and spin projection Sz, in the Lowest Order Constrained Variational (LOCV) method. It is demonstrated that, at small relative distances, independent of the proton to neutron ratio β, the state-dependent TBDD have a universal shape. Expectedly, it is observed that, at low (high) β values, the nucleons prefer to make a pair in the T = 1(0) states. In addition, the strength of the tensor-dependent correlations is investigated, using the ratio of the TBDD in the TSSz = 010 state with θ = π / 2 and that of θ = 0. The mentioned ratios peak at r ∼ 0 . 9 fm, considering different β values. It is hoped that, the present results could help a better reproduction of the experimental data of the electron-nucleus scattering.

Electron and Nuclear Pressures in Electron-Nucleus Mixtures

NASA Astrophysics Data System (ADS)

Chihara, J.; Yamagiwa, M.

2007-12-01

For a solid metal with frozen nuclei, the density-functional theory provides a unique definition of the electron pressure in an electron-nucleus mixture, and the total pressure of this mixture is represented as the sum of the electron and nuclear pressures. This fact leads to definitions of the electron and nuclear pressures on the basis of the virial theorem in terms of the wall potentials confining the electrons and nuclei. These definitions take a general form applicable without use of the adiabatic approximation. In this situation, we show that Janak's definition of the electron pressure in terms of the nuclear virial term is inappropriate; a similar statement holds for the definition of the stress tensor in this mixture. It is also demonstrated that both the electron and nuclear pressures become zero individually for a metal in vacuum, in contrast to the conventional understanding, according to which zero pressure is realized as a result of a cancellation of the elect ron and nuclear pressures. On the basis of these facts, a simple equation of state for liquid metals is derived, and it is examined numerically for the case of liquid alkaline metals by use of the quantum hypernetted chain equation and the Ashcroft model potential.

The A in SAFT: developing the contribution of association to the Helmholtz free energy within a Wertheim TPT1 treatment of generic Mie fluids

NASA Astrophysics Data System (ADS)

Dufal, Simon; Lafitte, Thomas; Haslam, Andrew J.; Galindo, Amparo; Clark, Gary N. I.; Vega, Carlos; Jackson, George

2015-05-01

An accurate representation of molecular association is a vital ingredient of advanced equations of state (EOSs), providing a description of thermodynamic properties of complex fluids where hydrogen bonding plays an important role. The combination of the first-order thermodynamic perturbation theory (TPT1) of Wertheim for associating systems with an accurate description of the structural and thermodynamic properties of the monomer fluid forms the basis of the statistical associating fluid theory (SAFT) family of EOSs. The contribution of association to the free energy in SAFT and related EOSs is very sensitive to the nature of intermolecular potential used to describe the monomers and, crucially, to the accuracy of the representation of the thermodynamic and structural properties. Here we develop an accurate description of the association contribution for use within the recently developed SAFT-VR Mie framework for chain molecules formed from segments interacting through a Mie potential [T. Lafitte, A. Apostolakou, C. Avendaño, A, Galindo, C. S. Adjiman, E. A. Müller, and G. Jackson, J. Chem. Phys. 139, 154504 (2013)]. As the Mie interaction represents a soft-core potential model, a method similar to that adopted for the Lennard-Jones potential [E. A. Müller and K. E. Gubbins, Ind. Eng. Chem. Res. 34, 3662 (1995)] is employed to describe the association contribution to the Helmholtz free energy. The radial distribution function (RDF) of the Mie fluid (which is required for the evaluation of the integral at the heart of the association term) is determined for a broad range of thermodynamic conditions (temperatures and densities) using the reference hyper-netted chain (RHNC) integral-equation theory. The numerical data for the association kernel of Mie fluids with different association geometries are then correlated for a range of thermodynamic states to obtain a general expression for the association contribution which can be applied for varying values of the Mie repulsive exponent. The resulting SAFT-VR Mie EOS allows for a much improved description of the vapour-liquid equilibria and single-phase properties of associating fluids such as water, methanol, ammonia, hydrogen sulphide, and their mixtures. A comparison is also made between the theoretical predictions of the degree of association for water and the extent of hydrogen bonding obtained from molecular simulations of the SPC/E and TIP4P/2005 atomistic models.

Fluids Density Functional Theory of Salt-Doped Block Copolymers

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; Hall, Lisa M.

Block copolymers have attracted a great deal of recent interest as potential non-flammable, solid-state, electrolyte materials for batteries or other charge carrying applications. The microphase separation in block copolymers combines the properties of a conductive (though mechanically soft) polymer with a mechanically robust (though non-conductive) polymer. We use fluids density functional theory (fDFT) to study the phase behavior of salt-doped block copolymers. Because the salt prefers to preferentially solvate into the conductive phase, salt doping effectively enhances the segregation strength between the two polymer types. We consider the effects of this preferential solvation and of charge correlations by separately modeling the ion-rich phase, without bonding, using the Ornstein-Zernike equation and the hypernetted-chain closure. We use the correlations from this subsystem in the inhomogeneous fDFT calculations. Initial addition of salt increases the domain spacing and sharpens the interfacial region, but for high salt loadings the interface can broaden. Addition of salt can also drive a system with a low copolymer segregation strength to order by first passing through a two phase regime with a salt-rich ordered phase and a salt-poor disordered phase. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Award Number DE-SC0014209.

Theory and simulation of electrolyte mixtures

NASA Astrophysics Data System (ADS)

Lee, B. Hribar; Vlachy, V.; Bhuiyan, L. B.; Outhwaite, C. W.; Molero, M.

Monte Carlo simulation and theoretical results on some aspects of thermodynamics of mixtures of electrolytes with a common species are presented. Both charge symmetric mixtures, where ions differ only in size, and charge asymmetric but size symmetric mixtures at ionic strength ranging generally from I = 10-4 to 1.0 M, and in a few cases up to I = M, are examined. The theoretical methods explored are: (i) the symmetric Poisson-Boltzmann theory, (ii) the modified Poisson-Boltzmann theory and (iii) the hypernetted-chain integral equation. The first two electrolyte mixing coefficients w0 and w1 of the various mixtures are calculated from an accurate determination of their osmotic pressure data. The theories are seen to be consistent among themselves, and with certain limiting laws in the literature, in predicting the trends of the mixing coefficients with respect to ionic strength. Some selected relevant experimental data have been analysed and compared with the theoretical and simulation trends. In addition the mean activity coefficients for a model mimicking the mixture of KCl and KF electrolytes are calculated and hence the Harned coefficients obtained for this system. These calculations are compared with the experimental data and Monte Carlo results available in the literature. The theoretically predicted Harned coefficients are in good agreement with the simulation results for the model KCl-KF mixture.

Use of Two-Body Correlated Basis Functions with van der Waals Interaction to Study the Shape-Independent Approximation for a Large Number of Trapped Interacting Bosons

NASA Astrophysics Data System (ADS)

Lekala, M. L.; Chakrabarti, B.; Das, T. K.; Rampho, G. J.; Sofianos, S. A.; Adam, R. M.; Haldar, S. K.

2017-05-01

We study the ground-state and the low-lying excitations of a trapped Bose gas in an isotropic harmonic potential for very small (˜ 3) to very large (˜ 10^7) particle numbers. We use the two-body correlated basis functions and the shape-dependent van der Waals interaction in our many-body calculations. We present an exhaustive study of the effect of inter-atomic correlations and the accuracy of the mean-field equations considering a wide range of particle numbers. We calculate the ground-state energy and the one-body density for different values of the van der Waals parameter C6. We compare our results with those of the modified Gross-Pitaevskii results, the correlated Hartree hypernetted-chain equations (which also utilize the two-body correlated basis functions), as well as of the diffusion Monte Carlo for hard sphere interactions. We observe the effect of the attractive tail of the van der Waals potential in the calculations of the one-body density over the truly repulsive zero-range potential as used in the Gross-Pitaevskii equation and discuss the finite-size effects. We also present the low-lying collective excitations which are well described by a hydrodynamic model in the large particle limit.

Elementary diagrams in nuclear and neutron matter

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

Wiringa, R.B.

1995-08-01

Variational calculations of nuclear and neutron matter are currently performed using a diagrammatic cluster expansion with the aid of nonlinear integral equations for evaluating expectation values. These are the Fermi hypernetted chain (FHNC) and single-operator chain (SOC) equations, which are a way of doing partial diagram summations to infinite order. A more complete summation can be made by adding elementary diagrams to the procedure. The simplest elementary diagrams appear at the four-body cluster level; there is one such E{sub 4} diagram in Bose systems, but 35 diagrams in Fermi systems, which gives a level of approximation called FHNC/4. We developedmore » a novel technique for evaluating these diagrams, by computing and storing 6 three-point functions, S{sub xyz}(r{sub 12}, r{sub 13}, r{sub 23}), where xyz (= ccd, cce, ddd, dde, dee, or eee) denotes the exchange character at the vertices 1, 2, and 3. All 35 Fermi E{sub 4} diagrams can be constructed from these 6 functions and other two-point functions that are already calculated. The elementary diagrams are known to be important in some systems like liquid {sup 3}He. We expect them to be small in nuclear matter at normal density, but they might become significant at higher densities appropriate for neutron star calculations. This year we programmed the FHNC/4 contributions to the energy and tested them in a number of simple model cases, including liquid {sup 3}He and Bethe`s homework problem. We get reasonable, but not exact agreement with earlier published work. In nuclear and neutron matter with the Argonne v{sub 14} interaction these contributions are indeed small corrections at normal density and grow to only 5-10 MeV/nucleon at 5 times normal density.« less

Thomson scattering from a three-component plasma.

PubMed

Johnson, W R; Nilsen, J

2014-02-01

A model for a three-component plasma consisting of two distinct ionic species and electrons is developed and applied to study x-ray Thomson scattering. Ions of a specific type are assumed to be identical and are treated in the average-atom approximation. Given the plasma temperature and density, the model predicts mass densities, effective ionic charges, and cell volumes for each ionic type, together with the plasma chemical potential and free-electron density. Additionally, the average-atom treatment of individual ions provides a quantum-mechanical description of bound and continuum electrons. The model is used to obtain parameters needed to determine the dynamic structure factors for x-ray Thomson scattering from a three-component plasma. The contribution from inelastic scattering by free electrons is evaluated in the random-phase approximation. The contribution from inelastic scattering by bound electrons is evaluated using the bound-state and scattering wave functions obtained from the average-atom calculations. Finally, the partial static structure factors for elastic scattering by ions are evaluated using a two-component version of the Ornstein-Zernike equations with hypernetted chain closure, in which electron-ion interactions are accounted for using screened ion-ion interaction potentials. The model is used to predict the x-ray Thomson scattering spectrum from a CH plasma and the resulting spectrum is compared with experimental results obtained by Feltcher et al. [Phys. Plasmas 20, 056316 (2013)].

Spin polarization of two-dimensional electron system in parabolic potential

NASA Astrophysics Data System (ADS)

Miyake, Takashi; Totsuji, Chieko; Nakanishi, Kenta; Tsuruta, Kenji; Totsuji, Hiroo

2008-09-01

We analyze the ground state of the two-dimensional quantum system of electrons confined in a parabolic potential with the system size around 100 at 0 K. We map the system onto a classical system on the basis of the classical-map hypernetted-chain (CHNC) method which has been proven to work in the integral-equation-based analyses of uniform systems and apply classical Monte Carlo and molecular dynamics simulations. We find that, when we decrease the strength of confinement keeping the number of confined electrons fixed, the energy of the spin-polarized state with somewhat lower average density becomes smaller than that of the spin-unpolarized state with somewhat higher average density. This system thus undergoes the transition from the spin-unpolarized state to the spin polarized state and the corresponding critical value of r estimated from the average density is as low as r∼0.4 which is much smaller than the r value for the Wigner lattice formation. When we compare the energies of spin-unpolarized and spin-polarized states for given average density, our data give the critical r value for the transition between unpolarized and polarized states around 10 which is close to but still smaller than the known possibility of polarization at r∼27. The advantage of our method is a direct applicability to geometrically complex systems which are difficult to analyze by integral equations and this is an example.

Historical Semantic Chaining and Efficient Communication: The Case of Container Names

ERIC Educational Resources Information Center

Xu, Yang; Regier, Terry; Malt, Barbara C.

2016-01-01

Semantic categories in the world's languages often reflect a historical process of "chaining": A name for one referent is extended to a conceptually related referent, and from there on to other referents, producing a chain of exemplars that all bear the same name. The beginning and end points of such a chain might in principle be rather…

Why do ultrasoft repulsive particles cluster and crystallize? Analytical results from density-functional theory.

PubMed

Likos, Christos N; Mladek, Bianca M; Gottwald, Dieter; Kahl, Gerhard

2007-06-14

We demonstrate the accuracy of the hypernetted chain closure and of the mean-field approximation for the calculation of the fluid-state properties of systems interacting by means of bounded and positive pair potentials with oscillating Fourier transforms. Subsequently, we prove the validity of a bilinear, random-phase density functional for arbitrary inhomogeneous phases of the same systems. On the basis of this functional, we calculate analytically the freezing parameters of the latter. We demonstrate explicitly that the stable crystals feature a lattice constant that is independent of density and whose value is dictated by the position of the negative minimum of the Fourier transform of the pair potential. This property is equivalent with the existence of clusters, whose population scales proportionally to the density. We establish that regardless of the form of the interaction potential and of the location on the freezing line, all cluster crystals have a universal Lindemann ratio Lf=0.189 at freezing. We further make an explicit link between the aforementioned density functional and the harmonic theory of crystals. This allows us to establish an equivalence between the emergence of clusters and the existence of negative Fourier components of the interaction potential. Finally, we make a connection between the class of models at hand and the system of infinite-dimensional hard spheres, when the limits of interaction steepness and space dimension are both taken to infinity in a particularly described fashion.

Solute-solvent cavity and bridge functions. I. Varying size of the solute

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

Vyalov, I., E-mail: ivan.vyalov@iit.it; Chuev, G., E-mail: genchuev@rambler.ru; Georgi, N., E-mail: georgi@mis.mpg.de

2014-08-21

In this work we present the results of the extensive molecular simulations of solute-solvent cavity and bridge functions. The mixtures of Lennard-Jones solvent with Lennard-Jones solute at infinite dilution are considered for different solute-solvent size ratios—up to 4:1. The Percus-Yevick and hypernetted chain closures deviate substantially from simulation results in the investigated temperature and density ranges. We also find that the behavior of the indirect and cavity correlation functions is non-monotonous within the hard-core region, but the latter can be successfully approximated by mean-field theory if the solute-solvent interaction energy is divided into repulsive and attractive contribution, according to Weeks-Chandler-Andersenmore » theory. Furthermore, in spite of the non-monotonous behavior of logarithm of the cavity function and the indirect correlation function, their difference, i.e., the bridge function remains constant within the hard-core region. Such behavior of the bridge and indirect correlation functions at small distances and for small values of indirect correlation function is well known from the Duh-Haymet plots, where the non-unique relationship results in loops of the bridge function vs. indirect correlation function graphs. We show that the same pathological behavior appears also when distance is small and indirect correlation function is large. We further show that the unique functional behavior of the bridge function can be established when bridge is represented as a function of the renormalized, repulsive indirect correlation function.« less

A pressure consistent bridge correction of Kovalenko-Hirata closure in Ornstein-Zernike theory for Lennard-Jones fluids by apparently adjusting sigma parameter

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

Ebato, Yuki; Miyata, Tatsuhiko, E-mail: miyata.tatsuhiko.mf@ehime-u.ac.jp

Ornstein-Zernike (OZ) integral equation theory is known to overestimate the excess internal energy, U{sup ex}, pressure through the virial route, P{sub v}, and excess chemical potential, μ{sup ex}, for one-component Lennard-Jones (LJ) fluids under hypernetted chain (HNC) and Kovalenko-Hirata (KH) approximatons. As one of the bridge correction methods to improve the precision of these thermodynamic quantities, it was shown in our previous paper that the method to apparently adjust σ parameter in the LJ potential is effective [T. Miyata and Y. Ebato, J. Molec. Liquids. 217, 75 (2016)]. In our previous paper, we evaluated the actual variation in the σmore » parameter by using a fitting procedure to molecular dynamics (MD) results. In this article, we propose an alternative method to determine the actual variation in the σ parameter. The proposed method utilizes a condition that the virial and compressibility pressures coincide with each other. This method can correct OZ theory without a fitting procedure to MD results, and possesses characteristics of keeping a form of HNC and/or KH closure. We calculate the radial distribution function, pressure, excess internal energy, and excess chemical potential for one-component LJ fluids to check the performance of our proposed bridge function. We discuss the precision of these thermodynamic quantities by comparing with MD results. In addition, we also calculate a corrected gas-liquid coexistence curve based on a corrected KH-type closure and compare it with MD results.« less

Diagnostic reference range of κ/λ free light chain ratio to screen for Bence Jones proteinuria is not significantly influenced by GFR.

PubMed

Schmidt-Hieltjes, Yvonne; Elshof, Clemens; Roovers, Lian; Ruinemans-Koerts, Janneke

2016-05-01

The aim of our study was to analyse whether the κ/λ free light chain ratio reference range for screening for Bence Jones proteinuria should be dependent on the estimated glomerular filtration rate (eGFR). The serum κ/λ free light chain ratio, eGFR, serum M-protein and Bence Jones protein were measured in 544 patients for whom Bence Jones protein analysis was ordered. In the population of patients without Bence Jones proteinuria or a M-protein (n = 402), there is no gradual increase in κ/λ free light chain ratio with diminishing eGFR. The κ/λ free light chain ratio in this group was 0.56-1.86 (95% interval). With this diagnostic reference range of the κ/λ ratio, 105 of the 110 patients with Bence Jones protein could be identified correctly. Only five patients with Bence Jones proteinuria (<0.17 g/L) were missed, without diagnostic or therapeutic consequences. In 36 patients (6.6%), an abnormal κ/λ free light chain ratio was measured without the presence of Bence Jones proteinuria. A κ/λ free light chain ratio in serum can be used safely and efficiently to select urine samples which should be analysed for Bence Jones proteinuria with an electrophoresis/immunofixation technique. Using this diagnostic reference range, the number of urine samples which should be analysed by electrophoresis/immunofixation could be reduced by 74%. The diagnostic reference interval can be determined best in a group of patients for whom Bence Jones analysis is indicated. For calculation of this reference range, the eGFR value does not need to be taken into account. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Performance analysis of Supply Chain Management with Supply Chain Operation reference model

NASA Astrophysics Data System (ADS)

Hasibuan, Abdurrozzaq; Arfah, Mahrani; Parinduri, Luthfi; Hernawati, Tri; Suliawati; Harahap, Bonar; Rahmah Sibuea, Siti; Krianto Sulaiman, Oris; purwadi, Adi

2018-04-01

This research was conducted at PT. Shamrock Manufacturing Corpora, the company is required to think creatively to implement competition strategy by producing goods/services that are more qualified, cheaper. Therefore, it is necessary to measure the performance of Supply Chain Management in order to improve the competitiveness. Therefore, the company is required to optimize its production output to meet the export quality standard. This research begins with the creation of initial dimensions based on Supply Chain Management process, ie Plan, Source, Make, Delivery, and Return with hierarchy based on Supply Chain Reference Operation that is Reliability, Responsiveness, Agility, Cost, and Asset. Key Performance Indicator identification becomes a benchmark in performance measurement whereas Snorm De Boer normalization serves to equalize Key Performance Indicator value. Analiytical Hierarchy Process is done to assist in determining priority criteria. Measurement of Supply Chain Management performance at PT. Shamrock Manufacturing Corpora produces SC. Responsiveness (0.649) has higher weight (priority) than other alternatives. The result of performance analysis using Supply Chain Reference Operation model of Supply Chain Management performance at PT. Shamrock Manufacturing Corpora looks good because its monitoring system between 50-100 is good.

The solvation of ions in acetonitrile and acetone. II. Monte Carlo simulations using polarizable solvent models

NASA Astrophysics Data System (ADS)

Fischer, R.; Richardi, J.; Fries, P. H.; Krienke, H.

2002-11-01

Structural properties and energies of solvation are simulated for alkali and halide ions. The solvation structure is discussed in terms of various site-site distribution functions, of solvation numbers, and of orientational correlation functions of the solvent molecules around the ions. The solvent polarizability has notable effects which cannot be intuitively predicted. In particular, it is necessary to reproduce the experimental solvation numbers of small ions. The changes of solvation properties are investigated along the alkali and halide series. By comparing the solvation of ions in acetone to that in acetonitrile, it is shown that the spatial correlations among the solvent molecules around an ion result in a strong screening of the ion-solvent direct intermolecular potential and are essential to understand the changes in the solvation structures and energies between different solvents. The solvation properties derived from the simulations are compared to earlier predictions of the hypernetted chain (HNC) approximation of the molecular Ornstein-Zernike (MOZ) theory [J. Richardi, P. H. Fries, and H. Krienke, J. Chem. Phys. 108, 4079 (1998)]. The MOZ(HNC) formalism gives an overall qualitatively correct picture of the solvation and its various unexpected findings are corroborated. For the larger ions, its predictions become quantitative. The MOZ approach allows to calculate solvent-solvent and ion-solvent potentials of mean force, which shed light on the 3D labile molecular and ionic architectures in the solution. These potentials of mean force convey a unique information which is necessary to fully interpret the angle-averaged structural functions computed from the simulations. Finally, simulations of solutions at finite concentrations show that the solvent-solvent and ion-solvent spatial correlations at infinite dilution are marginally altered by the introduction of fair amounts of ions.

The Technology Introduction of Chain Boiler Energy Conservation Transformation

NASA Astrophysics Data System (ADS)

Li, Henan; Liu, Xiwen; Yuan, Hong; Lin, Jiadai; Zhang, Yu

2017-12-01

Introduced the present status of chain boiler efficiency is low, the system analysis of the chain boiler optimization and upgrading of technology, for the whole progress of chain boiler to provide some ideas and reference.

Validation of serum free light chain reference ranges in primary care.

PubMed

Galvani, Luca; Flanagan, Jane; Sargazi, Mansour; Neithercut, William D

2016-05-01

The demand for measurement of serum immunoglobulin free kappa (κ) and lambda (λ) light chains has increased. The κ:λ ratio is used to assist in diagnosis/monitoring of plasma cell disorders. The binding site reference range for serum-free light chain κ:λ ratios of 0.26-1.65 was derived from healthy volunteers. Subsequently, a reference range of 0.37-3.1 for patients with chronic kidney disease has been proposed. Elevated free light chain concentrations and borderline raised free light chain ratios also may be found in polyclonal gammopathies and with other non-renal illnesses. This assessment was conducted to validate the established free light chain reference ranges in individuals from primary care. A total of 130 samples were identified from routine blood samples collected in primary care for routine biochemistry testing and estimated glomerular filtration rate calculation. The median and range of κ:λ ratios found in each estimated glomerular filtration rate group used for chronic kidney disease classification were higher than previously described. This was the case for individuals with normal or essentially normal renal function with estimated glomerular filtration rates>90, (0.58-1.76) and estimated glomerular filtration rate of 60-90 mL/min/1.73 m(2), (0.71-1.93). Individuals with estimated glomerular filtration rate 15-30, (0.72-4.50) and estimated glomerular filtration rate <15 ml/min/1.73 m(2) (0.71-4.95) also had higher values when compared to the current renal reference range of 0.37-3.10. Elevation of free light chain-κ:λ ratios may occur in the absence of a reduced renal function shown by a normal estimated glomerular filtration rate and in the presence of reduced renal function by estimated glomerular filtration rate when comparing results with the established reference ranges. Explanations include choice of analytical systems or the presence of other concurrent non-plasma cell illness. © The Author(s) 2016.

Supply-Chain Optimization Template

NASA Technical Reports Server (NTRS)

Quiett, William F.; Sealing, Scott L.

2009-01-01

The Supply-Chain Optimization Template (SCOT) is an instructional guide for identifying, evaluating, and optimizing (including re-engineering) aerospace- oriented supply chains. The SCOT was derived from the Supply Chain Council s Supply-Chain Operations Reference (SCC SCOR) Model, which is more generic and more oriented toward achieving a competitive advantage in business.

An approach for formalising the supply chain operations

NASA Astrophysics Data System (ADS)

Zdravković, Milan; Panetto, Hervé; Trajanović, Miroslav; Aubry, Alexis

2011-11-01

Reference models play an important role in the knowledge management of the various complex collaboration domains (such as supply chain networks). However, they often show a lack of semantic precision and, they are sometimes incomplete. In this article, we present an approach to overcome semantic inconsistencies and incompleteness of the Supply Chain Operations Reference (SCOR) model and hence improve its usefulness and expand the application domain. First, we describe a literal web ontology language (OWL) specification of SCOR concepts (and related tools) built with the intention to preserve the original approach in the classification of process reference model entities, and hence enable the effectiveness of usage in original contexts. Next, we demonstrate the system for its exploitation, in specific - tools for SCOR framework browsing and rapid supply chain process configuration. Then, we describe the SCOR-Full ontology, its relations with relevant domain ontology and show how it can be exploited for improvement of SCOR ontological framework competence. Finally, we elaborate the potential impact of the presented approach, to interoperability of systems in supply chain networks.

Teaching Supply Chain Management Complexities: A SCOR Model Based Classroom Simulation

ERIC Educational Resources Information Center

Webb, G. Scott; Thomas, Stephanie P.; Liao-Troth, Sara

2014-01-01

The SCOR (Supply Chain Operations Reference) Model Supply Chain Classroom Simulation is an in-class experiential learning activity that helps students develop a holistic understanding of the processes and challenges of supply chain management. The simulation has broader learning objectives than other supply chain related activities such as the…

Polymer Chain Conformation and Dynamical Confinement in a Model One-Component Nanocomposite

NASA Astrophysics Data System (ADS)

Mark, C.; Holderer, O.; Allgaier, J.; Hübner, E.; Pyckhout-Hintzen, W.; Zamponi, M.; Radulescu, A.; Feoktystov, A.; Monkenbusch, M.; Jalarvo, N.; Richter, D.

2017-07-01

We report a neutron-scattering investigation on the structure and dynamics of a single-component nanocomposite based on SiO2 particles that were grafted with polyisoprene chains at the entanglement limit. By skillful labeling, we access both the monomer density in the corona as well as the conformation of the grafted chains. While the corona profile follows a r-1 power law, the conformation of a grafted chain is identical to that of a chain in a reference melt, implying a high mutual penetration of the coronas from different particles. The brush crowding leads to topological confinement of the chain dynamics: (i) At local scales, the segmental dynamics is unchanged compared to the reference melt, while (ii) at the scale of the chain, the dynamics appears to be slowed down; (iii) by performing a mode analysis in terms of end-fixed Rouse chains, the slower dynamics is tracked to topological confinement within the cone spanned by the adjacent grafts; (iv) by adding 50% matrix chains, the topological confinement sensed by the grafted chain is lifted partially and the apparent chain motion is accelerated. We observe a crossover from pure Rouse motion at short times to topological confined motion beyond the time when the segmental mean squared displacement has reached the distance to the next graft.

Dual chain perturbation theory: A new equation of state for polyatomic molecules

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

Marshall, Bennett D., E-mail: bennett.d.marshall@exxonmobil.com

In the development of equations of state for polyatomic molecules, thermodynamic perturbation theory (TPT) is widely used to calculate the change in free energy due to chain formation. TPT is a simplification of a more general and exact multi-density cluster expansion for associating fluids. In TPT, all contributions to the cluster expansion which contain chain–chain interactions are neglected. That is, all inter-chain interactions are treated at the reference fluid level. This allows for the summation of the cluster theory in terms of reference system correlation functions only. The resulting theory has been shown to be accurate and has been widelymore » employed as the basis of many engineering equations of state. While highly successful, TPT has many handicaps which result from the neglect of chain–chain contributions. The subject of this document is to move beyond the limitations of TPT and include chain–chain contributions to the equation of state.« less

Comparison of two optimized readout chains for low light CIS

NASA Astrophysics Data System (ADS)

Boukhayma, A.; Peizerat, A.; Dupret, A.; Enz, C.

2014-03-01

We compare the noise performance of two optimized readout chains that are based on 4T pixels and featuring the same bandwidth of 265kHz (enough to read 1Megapixel with 50frame/s). Both chains contain a 4T pixel, a column amplifier and a single slope analog-to-digital converter operating a CDS. In one case, the pixel operates in source follower configuration, and in common source configuration in the other case. Based on analytical noise calculation of both readout chains, an optimization methodology is presented. Analytical results are confirmed by transient simulations using 130nm process. A total input referred noise bellow 0.4 electrons RMS is reached for a simulated conversion gain of 160μV/e-. Both optimized readout chains show the same input referred 1/f noise. The common source based readout chain shows better performance for thermal noise and requires smaller silicon area. We discuss the possible drawbacks of the common source configuration and provide the reader with a comparative table between the two readout chains. The table contains several variants (column amplifier gain, in-pixel transistor sizes and type).

Myco-Heterophytes and Parasitic Plants in Food Chains.

ERIC Educational Resources Information Center

Hershey, David R.

1999-01-01

Advocates including plants at several trophic levels when studying food chains. Presents background information on parasitic plants, myco-heterophytes (saprophytes), and carnivorous plants. Contains 20 references. (WRM)

Designing Performance Measurement For Supply Chain's Actors And Regulator Using Scale Balanced Scorecard And Data Envelopment Analysis

NASA Astrophysics Data System (ADS)

Kusrini, Elisa; Subagyo; Aini Masruroh, Nur

2016-01-01

This research is a sequel of the author's earlier conducted researches in the fields of designing of integrated performance measurement between supply chain's actors and regulator. In the previous paper, the design of performance measurement is done by combining Balanced Scorecard - Supply Chain Operation Reference - Regulator Contribution model and Data Envelopment Analysis. This model referred as B-S-Rc-DEA model. The combination has the disadvantage that all the performance variables have the same weight. This paper investigates whether by giving weight to performance variables will produce more sensitive performance measurement in detecting performance improvement. Therefore, this paper discusses the development of the model B-S-Rc-DEA by giving weight to its performance'variables. This model referred as Scale B-S-Rc-DEA model. To illustrate the model of development, some samples from small medium enterprises of leather craft industry supply chain in province of Yogyakarta, Indonesia are used in this research. It is found that Scale B-S-Rc-DEA model is more sensitive to detecting performance improvement than B-S- Rc-DEA model.

Share2Quit: Web-Based Peer-Driven Referrals for Smoking Cessation

PubMed Central

2013-01-01

Background Smoking is the number one preventable cause of death in the United States. Effective Web-assisted tobacco interventions are often underutilized and require new and innovative engagement approaches. Web-based peer-driven chain referrals successfully used outside health care have the potential for increasing the reach of Internet interventions. Objective The objective of our study was to describe the protocol for the development and testing of proactive Web-based chain-referral tools for increasing the access to Decide2Quit.org, a Web-assisted tobacco intervention system. Methods We will build and refine proactive chain-referral tools, including email and Facebook referrals. In addition, we will implement respondent-driven sampling (RDS), a controlled chain-referral sampling technique designed to remove inherent biases in chain referrals and obtain a representative sample. We will begin our chain referrals with an initial recruitment of former and current smokers as seeds (initial participants) who will be trained to refer current smokers from their social network using the developed tools. In turn, these newly referred smokers will also be provided the tools to refer other smokers from their social networks. We will model predictors of referral success using sample weights from the RDS to estimate the success of the system in the targeted population. Results This protocol describes the evaluation of proactive Web-based chain-referral tools, which can be used in tobacco interventions to increase the access to hard-to-reach populations, for promoting smoking cessation. Conclusions Share2Quit represents an innovative advancement by capitalizing on naturally occurring technology trends to recruit smokers to Web-assisted tobacco interventions. PMID:24067329

Genetics Home Reference: short-chain acyl-CoA dehydrogenase deficiency

MedlinePlus

... Orphanet: Short chain acyl-CoA dehydrogenase deficiency Screening, Technology and Research in Genetics Patient Support and Advocacy Resources (5 links) Children Living with Inherited Metabolic Disease (CLIMB) Children's Mitochondrial ...

Development of an Assessment Model for Sustainable Supply Chain Management in Batik Industry

NASA Astrophysics Data System (ADS)

Mubiena, G. F.; Ma’ruf, A.

2018-03-01

This research proposes a dynamic assessment model for sustainable supply chain management in batik industry. The proposed model identifies the dynamic relationship between economic aspect, environment aspect and social aspect. The economic aspect refers to the supply chain operation reference model. The environment aspect uses carbon emissions and liquid waste as the attribute assessment, while the social aspect focus on employee’s welfare. Lean manufacturing concept was implemented as an alternative approach to sustainability. The simulation result shows that the average of sustainability score for 5 years increased from 65,3% to 70%. Future experiments will be conducted on design improvements to reach the company target on sustainability score.

Genetics Home Reference: DOLK-congenital disorder of glycosylation

MedlinePlus

... called glycosylation, which attaches groups of sugar molecules (oligosaccharides) to proteins. Glycosylation changes proteins in ways that ... to dolichol phosphate in order to build the oligosaccharide chain. Once the chain is formed, dolichol phosphate ...

Knowing the SCOR: using business metrics to gain measurable improvements.

PubMed

Malin, Jane H

2006-07-01

By using the Supply Chain Operations Reference model, one New York hospital was able to define and measure its supply chains, determine the weak links in its processes, and identify necessary improvements.

Genetics Home Reference: very long-chain acyl-CoA dehydrogenase deficiency

MedlinePlus

... Very long chain acyl-CoA dehydrogenase deficiency Screening, Technology, and Research in Genetics Virginia Department of Health (PDF) Patient Support and Advocacy Resources (4 links) Children's Mitochondrial Disease Network (UK) FOD (Fatty Oxidation Disorders) ...

Genetics Home Reference: long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency

MedlinePlus

... Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency Screening, Technology, and Research in Genetics Virginia Department of Health (PDF) Patient Support and Advocacy Resources (4 links) Children Living with Inherited Metabolic Diseases (CLIMB) Children's Mitochondrial ...

Structural re-alignment in an immunologic surface region of ricin A chain

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

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less

49 CFR 393.7 - Matter incorporated by reference.

Code of Federal Regulations, 2014 CFR

2014-10-01

..., Society of Automotive Engineers (SAE) J581, July 2004, incorporation by reference approved for § 393.24(b... Specification for Strapping, Flat Steel and Seals, American Society for Testing and Materials (ASTM), D3953-97, February 1998, incorporation by reference approved for § 393.104(e). (19) Welded Steel Chain Specifications...

49 CFR 393.7 - Matter incorporated by reference.

Code of Federal Regulations, 2013 CFR

2013-10-01

..., Society of Automotive Engineers (SAE) J581, July 2004, incorporation by reference approved for § 393.24(b... Specification for Strapping, Flat Steel and Seals, American Society for Testing and Materials (ASTM), D3953-97, February 1998, incorporation by reference approved for § 393.104(e). (19) Welded Steel Chain Specifications...

49 CFR 393.7 - Matter incorporated by reference.

Code of Federal Regulations, 2012 CFR

2012-10-01

..., Society of Automotive Engineers (SAE) J581, July 2004, incorporation by reference approved for § 393.24(b... Specification for Strapping, Flat Steel and Seals, American Society for Testing and Materials (ASTM), D3953-97, February 1998, incorporation by reference approved for § 393.104(e). (19) Welded Steel Chain Specifications...

Selection of suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using quantitative real-time polymerase chain reaction.

PubMed

Zornhagen, K W; Kristensen, A T; Hansen, A E; Oxboel, J; Kjaer, A

2015-12-01

Quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) is a sensitive technique for quantifying gene expression. Stably expressed reference genes are necessary for normalization of RT-qPCR data. Only a few articles have been published on reference genes in canine tumours. The objective of this study was to demonstrate how to identify suitable reference genes for normalization of genes of interest in canine soft tissue sarcomas using RT-qPCR. Primer pairs for 17 potential reference genes were designed and tested in archival tumour biopsies from six dogs. The geNorm algorithm was used to analyse the most suitable reference genes. Eight potential reference genes were excluded from this final analysis because of their dissociation curves. β-Glucuronidase (GUSB) and proteasome subunit, beta type, 6 (PSMB6) were most stably expressed with an M value of 0.154 and a CV of 0.053 describing their average stability. We suggest that choice of reference genes should be based on specific testing in every new experimental set-up. © 2014 John Wiley & Sons Ltd.

49 CFR 393.7 - Matter incorporated by reference.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Specification for Strapping, Flat Steel and Seals, American Society for Testing and Materials (ASTM), D3953-97, February 1998, incorporation by reference approved for § 393.104(e). (19) Welded Steel Chain Specifications... Association, WSTDA-T1, 1998, incorporation by reference approved for § 393.104(e). (21) Wire Rope Users Manual...

49 CFR 393.7 - Matter incorporated by reference.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Specification for Strapping, Flat Steel and Seals, American Society for Testing and Materials (ASTM), D3953-97, February 1998, incorporation by reference approved for § 393.104(e). (19) Welded Steel Chain Specifications... Association, WSTDA-T1, 1998, incorporation by reference approved for § 393.104(e). (21) Wire Rope Users Manual...

Supply Chain Management: Are You Maximizing Your Procurement Activity?

ERIC Educational Resources Information Center

Dobbin, James; Jenkins, Mike

2000-01-01

Today's purchasing professionals recognize the need to reduce non-value-added procedures (clerical functions) while emphasizing strategic planning. Results-oriented supply-chain managers need superb communication, negotiation, and leadership skills to achieve long-term value and resist the lowest, first- cost bids. (Contains 13 references.) (MLH)

Equations of state for the fully flexible WCA chains in the fluid and solid phases based on Wertheims-TPT2

NASA Astrophysics Data System (ADS)

Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

2018-03-01

Based on Wertheim's second order thermodynamic perturbation theory (TPT2), equations of state (EOSs) are presented for the fluid and solid phases of tangent, freely jointed spheres. It is considered that the spheres interact with each other through the Weeks-Chandler-Anderson (WCA) potential. The developed TPT2 EOS is the sum of a monomeric reference term and a perturbation contribution due to bonding. MC NVT simulations are performed to determine the structural properties of the reference system in the reduced temperature range of 0.6 ≤ T* ≤ 4.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. Mathematical functions are fitted to the simulation results of the reference system and employed in the framework of Wertheim's theory to develop TPT2 EOSs for the fluid and solid phases. The extended EOSs are compared to the MC NPT simulation results of the compressibility factor and internal energy of the fully flexible chain systems. Simulations are performed for the WCA chain system for chain lengths of up to 15 at T* = 1.0, 1.5, 2.0, 3.0. Across all the reduced temperatures, the agreement between the results of the TPT2 EOS and MC simulations is remarkable. Overall Average Absolute Relative Percent Deviation at T* = 1.0 for the compressibility factor in the entire chain lengths we covered is 0.51 and 0.77 for the solid and fluid phases, respectively. Similar features are observed in the case of residual internal energy.

Equations of state for the fully flexible WCA chains in the fluid and solid phases based on Wertheims-TPT2.

PubMed

Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

2018-03-14

Based on Wertheim's second order thermodynamic perturbation theory (TPT2), equations of state (EOSs) are presented for the fluid and solid phases of tangent, freely jointed spheres. It is considered that the spheres interact with each other through the Weeks-Chandler-Anderson (WCA) potential. The developed TPT2 EOS is the sum of a monomeric reference term and a perturbation contribution due to bonding. MC NVT simulations are performed to determine the structural properties of the reference system in the reduced temperature range of 0.6 ≤ T* ≤ 4.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. Mathematical functions are fitted to the simulation results of the reference system and employed in the framework of Wertheim's theory to develop TPT2 EOSs for the fluid and solid phases. The extended EOSs are compared to the MC NPT simulation results of the compressibility factor and internal energy of the fully flexible chain systems. Simulations are performed for the WCA chain system for chain lengths of up to 15 at T* = 1.0, 1.5, 2.0, 3.0. Across all the reduced temperatures, the agreement between the results of the TPT2 EOS and MC simulations is remarkable. Overall Average Absolute Relative Percent Deviation at T* = 1.0 for the compressibility factor in the entire chain lengths we covered is 0.51 and 0.77 for the solid and fluid phases, respectively. Similar features are observed in the case of residual internal energy.

Evolutionary Game Model Study of Construction Green Supply Chain Management under the Government Intervention

NASA Astrophysics Data System (ADS)

Xing, Yuanzhi; Deng, Xiaoyi

2017-11-01

The paper first has defined the concepts of green supply chain management and evolution game theory, and pointed out the characteristics of green supply chain management in construction. The main participants and key links of the construction green supply chain management are determined by constructing the organization framework. This paper established the evolutionary game model between construction enterprises and recycling enterprises for the green supply chain closed-loop structure. The waste recycling evolutionary stability equilibrium solution is obtained to explore the principle and effective scope of government policy intervention. This paper put forward the relevant countermeasures to the green supply chain management in construction recycling stage from the government point of view. The conclusion has reference value and guidance to the final product construction enterprises, recycling enterprises and the government during green supply chain.

The application of supply chain management principles to emergency management logistics: An empirical study.

PubMed

Peterson, Matthew R; Young, Richard R; Gordon, Gary A

2016-01-01

Key elements of supply chain theory remain relevant to emergency management (EM) logistics activities. The Supply Chain Operations Reference model can also serve as a useful template for the planning, organizing, and execution of EM logistics. Through a series of case studies (developed through intensive survey of organizations and individuals responsible for EM), the authors identified the extent supply chain theory is being adopted and whether the theory was useful for emergency logistics managers. The authors found several drivers that influence the likelihood of an organization to implement elements of supply chain management: the frequency of events, organizational resources, population density, range of events, and severity of the disaster or emergency.

Using National Inventories for Estimating Environmental Impacts of Products from Industrial Sectors: A Case Study of Ethanol and Gasoline

EPA Science Inventory

PurposeIn order to understand the environmental outcomes associated with the life cycle of a product, to compare these outcomes across products, or to design more sustainable supply chains, it is often desirable to estimate results for a reference supply chain representative of t...

Web Supplement to "Teaching Chain-Weight Real GDP Measures."

ERIC Educational Resources Information Center

Cahill, Miles B.

2003-01-01

Describes a Web site that is a companion to the Miles Cahill article, "Teaching Chain-Weight Real GDP Measures." States that the exercises are useful because intermediate level textbooks treat this topic casually. Indicates that the Web site contains the comment tool, an overview of the concepts, and links to article references. (JEH)

From Project Bureaucracy to the Flourishing of Life: Elements for a New Relationship in Financing Adult Education.

ERIC Educational Resources Information Center

Grossi, Francisco Vio

1986-01-01

Presents the context in which the aid chain of adult education operates in Latin America and the Third World. Refers to the characteristics of promotional organizations and international assistance agencies and the way in which the aid chain operates. Suggests ways to overcome major limitations. (CH)

Requirements engineering for cross-sectional information chain models

PubMed Central

Hübner, U; Cruel, E; Gök, M; Garthaus, M; Zimansky, M; Remmers, H; Rienhoff, O

2012-01-01

Despite the wealth of literature on requirements engineering, little is known about engineering very generic, innovative and emerging requirements, such as those for cross-sectional information chains. The IKM health project aims at building information chain reference models for the care of patients with chronic wounds, cancer-related pain and back pain. Our question therefore was how to appropriately capture information and process requirements that are both generally applicable and practically useful. To this end, we started with recommendations from clinical guidelines and put them up for discussion in Delphi surveys and expert interviews. Despite the heterogeneity we encountered in all three methods, it was possible to obtain requirements suitable for building reference models. We evaluated three modelling languages and then chose to write the models in UML (class and activity diagrams). On the basis of the current project results, the pros and cons of our approach are discussed. PMID:24199080

Optimized nested Markov chain Monte Carlo sampling: theory

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

Coe, Joshua D; Shaw, M Sam; Sewell, Thomas D

2009-01-01

Metropolis Monte Carlo sampling of a reference potential is used to build a Markov chain in the isothermal-isobaric ensemble. At the endpoints of the chain, the energy is reevaluated at a different level of approximation (the 'full' energy) and a composite move encompassing all of the intervening steps is accepted on the basis of a modified Metropolis criterion. By manipulating the thermodynamic variables characterizing the reference system we maximize the average acceptance probability of composite moves, lengthening significantly the random walk made between consecutive evaluations of the full energy at a fixed acceptance probability. This provides maximally decorrelated samples ofmore » the full potential, thereby lowering the total number required to build ensemble averages of a given variance. The efficiency of the method is illustrated using model potentials appropriate to molecular fluids at high pressure. Implications for ab initio or density functional theory (DFT) treatment are discussed.« less

Structure and thermodynamics of a simple fluid

NASA Astrophysics Data System (ADS)

Stell, G.; Weis, J. J.

1980-02-01

Monte Carlo results are found for a simple fluid with a pair potential consisting of a hard-sphere core and a Lennard-Jones attractive tail. They are compared with several of the most promising recent theoretical treatments of simple fluids, all of which involve the decomposition of the pair potential into a hard-sphere-core term and an attractive-tail term. This direct comparison avoids the use of a second perturbation scheme associated with softening the core, which would introduce an ambiguity in the significance of the differences found between the theoretical and Monte Carlo results. The study includes the optimized random-phase approximation (ORPA) and exponential (EXP) approximations of Andersen and Chandler, an extension of the latter approximation to nodal order three (the N3 approximation), the linear-plus-square (LIN + SQ) approximation of Høye and Stell, the renormalized hypernetted chain (RHNC) approximation of Lado, and the quadratic (QUAD) approximation suggested by second-order self-consistent Γ ordering, the lowest order of which is identical to the ORPA. As anticipated on the basis of earlier studies, it is found that the EXP approximation yields radial distribution functions and structure factors of excellent overall accuracy in the liquid state, where the RHNC results are also excellent and the EXP, QUAD, and LIN + SQ results prove to be virtually indistinguishable from one another. For all the approximations, however, the thermodynamics from the compressibility relation are poor and the virial-theorem results are not uniformly reliable. Somewhat more surprisingly, it is found that the EXP results yield a negative structure factor S(k) for very small k in the liquid state and poor radial distribution functions at low densities. The RHNC results are nowhere worse than the EXP results and in some states (e.g., at low densities) much better. In contrast, the N3 results are better in some respects than the EXP results but worse in others. The authors briefly comment on the RHNC and EXP approximations applied to the full Lennard-Jones potential, for which the EXP approximation appears somewhat improved in the liquid state as a result of the softening of the potential core.

Effective electrostatic interactions among charged thermo-responsive microgels immersed in a simple electrolyte

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

González-Mozuelos, P.

This work explores the nature and thermodynamic behavior of the effective electrostatic interactions among charged microgels immersed in a simple electrolyte, taking special interest in the effects due to the thermally induced variation of the microgel size while the remaining parameters (microgel charge and concentration, plus the amount of added salt) are kept constant. To this end, the rigorous approach obtained from applying the precise methodology of the dressed ion theory to the proper definition of the effective direct correlation functions, which emerge from tracing-out the degrees of freedom of the microscopic ions, is employed to provide an exact descriptionmore » of the parameters characterizing such interactions: screening length, effective permittivity, and renormalized charges. A model solution with three components is assumed: large permeable anionic spheres for the microgels, plus small charged hard spheres of equal size for the monovalent cations and anions. The two-body correlations among the components of this model suspension, used as the input for the determination of the effective interaction parameters, are here calculated by using the hyper-netted chain approximation. It is then found that at finite microgel concentrations the values of these parameters change as the microgel size increases, even though the ionic strength of the supporting electrolyte and the bare charge of the microgels remain fixed during this process. The variation of the screening length, as well as that of the effective permittivity, is rather small, but still interesting in view of the fact that the corresponding Debye length stays constant. The renormalized charges, in contrast, increase markedly as the microgels swell. The ratio of the renormalized charge to the corresponding analytic result obtained in the context of an extended linear response theory allows us to introduce an effective charge that accounts for the non-linear effects induced by the short-ranged association of microions to the microgels. The behavior of these effective charges as a function of the amount of added salt and the macroion charge, size, and concentration reveals the interplay among all these system parameters.« less

A methodology and supply chain management inspired reference ontology for modeling healthcare teams.

PubMed

Kuziemsky, Craig E; Yazdi, Sara

2011-01-01

Numerous studies and strategic plans are advocating more team based healthcare delivery that is facilitated by information and communication technologies (ICTs). However before we can design ICTs to support teams we need a solid conceptual model of team processes and a methodology for using such a model in healthcare settings. This paper draws upon success in the supply chain management domain to develop a reference ontology of healthcare teams and a methodology for modeling teams to instantiate the ontology in specific settings. This research can help us understand how teams function and how we can design ICTs to support teams.

Detection of a Bacteriophage Gene Encoding a Mu-like Portal Protein in Haemophilus parasuis Reference Strains and Field Isolates by Nested Polymerase Chain Reaction

USDA-ARS?s Scientific Manuscript database

A nested PCR assay was developed to determine the presence of a gene encoding a bacteriophage Mu-like portal protein, gp29, in 15 reference strains and 31 field isolates of Haemophilus parasuis. Specific primers, based on the gene’s sequence, were utilized. A majority of the virulent reference strai...

Comparison of the One- and Bi-Direction Chained Equipercentile Equating

ERIC Educational Resources Information Center

Oh, Hyeonjoo; Moses, Tim

2012-01-01

This study investigated differences between two approaches to chained equipercentile (CE) equating (one- and bi-direction CE equating) in nearly equal groups and relatively unequal groups. In one-direction CE equating, the new form is linked to the anchor in one sample of examinees and the anchor is linked to the reference form in the other…

Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium

USDA-ARS?s Scientific Manuscript database

The rumen is lined on the luminal side by a stratified squamous epithelium that is responsible for not only absorption, but also transport, extensive short-chain fatty acid (SCFA) metabolism and protection. Butyrate has been demonstrated to initiate the differentiation of the tissue following intro...

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.

Influence of alkyl chain length compatibility on microemulsion structure and solubilization

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

Bansal, V.K.; O'Connell, J.P.; Shah, D.O.

1980-06-01

The water solubilization capacity of water/oil microemulsions is studied as a function of alkyl chain length of oil (C/sub 8/ to C/sub 16/), surfactant (C/sub 14/ and C/sub 18/ fatty acid soaps), and alcohol (C/sub 4/ to C/sub 7/). Sodium stearate and sodium myristate were used as surfactants. For n-butanol microemulsions the maximum amount of water solubilized in the microemulsion decreased continuously with increasing oil chain length; for n-heptanol it increased continuously. For n-pentanol and n-hexanol systems, water solubilization reached a maximum when the oil chain length plus alcohol chain length was equal to that of the surfactant. The electricmore » resistance and dielectric constant of the microemulsions also are measured as a function of alkyl chain length of the oil. 48 references.« less

Field guide to summit area and upper east rift zone, Kilauea Volcano, Hawaii

NASA Technical Reports Server (NTRS)

1974-01-01

The field trip is divided into two sections: (1) Crater Rim Road; and (2) Chain of Craters Road. Most bibliographic references are omitted from the text, but a selected list of references to recent Hawaiian volcanic activity and to special studies is included.

Validation of Reference Genes in mRNA Expression Analysis Applied to the Study of Asthma.

PubMed

Segundo-Val, Ignacio San; Sanz-Lozano, Catalina S

2016-01-01

The quantitative Polymerase Chain Reaction is the most used technique for the study of gene expression. To correct putative experimental errors of this technique is necessary normalizing the expression results of the gene of interest with the obtained for reference genes. Here, we describe an example of the process to select reference genes. In this particular case, we select reference genes for expression studies in the peripheral blood mononuclear cells of asthmatic patients.

An analytical equation of state for describing isotropic-nematic phase equilibria of Lennard-Jones chain fluids with variable degree of molecular flexibility

NASA Astrophysics Data System (ADS)

van Westen, Thijs; Oyarzún, Bernardo; Vlugt, Thijs J. H.; Gross, Joachim

2015-06-01

We develop an equation of state (EoS) for describing isotropic-nematic (IN) phase equilibria of Lennard-Jones (LJ) chain fluids. The EoS is developed by applying a second order Barker-Henderson perturbation theory to a reference fluid of hard chain molecules. The chain molecules consist of tangentially bonded spherical segments and are allowed to be fully flexible, partially flexible (rod-coil), or rigid linear. The hard-chain reference contribution to the EoS is obtained from a Vega-Lago rescaled Onsager theory. For the description of the (attractive) dispersion interactions between molecules, we adopt a segment-segment approach. We show that the perturbation contribution for describing these interactions can be divided into an "isotropic" part, which depends only implicitly on orientational ordering of molecules (through density), and an "anisotropic" part, for which an explicit dependence on orientational ordering is included (through an expansion in the nematic order parameter). The perturbation theory is used to study the effect of chain length, molecular flexibility, and attractive interactions on IN phase equilibria of pure LJ chain fluids. Theoretical results for the IN phase equilibrium of rigid linear LJ 10-mers are compared to results obtained from Monte Carlo simulations in the isobaric-isothermal (NPT) ensemble, and an expanded formulation of the Gibbs-ensemble. Our results show that the anisotropic contribution to the dispersion attractions is irrelevant for LJ chain fluids. Using the isotropic (density-dependent) contribution only (i.e., using a zeroth order expansion of the attractive Helmholtz energy contribution in the nematic order parameter), excellent agreement between theory and simulations is observed. These results suggest that an EoS contribution for describing the attractive part of the dispersion interactions in real LCs can be obtained from conventional theoretical approaches designed for isotropic fluids, such as a Perturbed-Chain Statistical Associating Fluid Theory approach.

Evaluation of reference gene suitability for quantitative expression analysis by quantitative polymerase chain reaction in the mandibular condyle of sheep.

PubMed

Jiang, Xin; Xue, Yang; Zhou, Hongzhi; Li, Shouhong; Zhang, Zongmin; Hou, Rui; Ding, Yuxiang; Hu, Kaijin

2015-10-01

Reference genes are commonly used as a reliable approach to normalize the results of quantitative polymerase chain reaction (qPCR), and to reduce errors in the relative quantification of gene expression. Suitable reference genes belonging to numerous functional classes have been identified for various types of species and tissue. However, little is currently known regarding the most suitable reference genes for bone, specifically for the sheep mandibular condyle. Sheep are important for the study of human bone diseases, particularly for temporomandibular diseases. The present study aimed to identify a set of reference genes suitable for the normalization of qPCR data from the mandibular condyle of sheep. A total of 12 reference genes belonging to various functional classes were selected, and the expression stability of the reference genes was determined in both the normal and fractured area of the sheep mandibular condyle. RefFinder, which integrates the following currently available computational algorithms: geNorm, NormFinder, BestKeeper, and the comparative ΔCt method, was used to compare and rank the candidate reference genes. The results obtained from the four methods demonstrated a similar trend: RPL19, ACTB, and PGK1 were the most stably expressed reference genes in the sheep mandibular condyle. As determined by RefFinder comprehensive analysis, the results of the present study suggested that RPL19 is the most suitable reference gene for studies associated with the sheep mandibular condyle. In addition, ACTB and PGK1 may be considered suitable alternatives.

The Analysis of Orders of Perishable Goods in Relation to the Bullwhip Effect in the Logistic Supply Chain of the Food Industry: a Case Study

NASA Astrophysics Data System (ADS)

Chocholáč, Jan; Průša, Petr

2016-12-01

The bullwhip effect generally refers to the phenomenon where order variability increases as the orders move upstream in the supply chain. It is serious problem for every member of the supply chain. This effect begins at customers and passes through the chain to producers, which are at the end of the logistic chain. Especially food supply chains are affected by this issue. These chains are unique for problems of expiration of goods (particularly perishable goods), variable demand, orders with quantity discounts and effort to maximize the customer satisfaction. This paper will present the problem of the bullwhip effect in the real supply chain in the food industry. This supply chain consists of approximately 350 stores, four central warehouses and more than 1000 suppliers, but the case study will examine 87 stores, one central warehouse and one supplier in 2015. The aim of this paper is the analysis of the order variability between the various links in this chain and confirmation of the bullwhip effect in this chain. The subject of the analysis will be perishable goods.

Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula)

USDA-ARS?s Scientific Manuscript database

Quantitative real-time polymerase chain reaction (qRT-PCR) is the most important tool in measuring levels of gene expression due to its accuracy, specificity, and sensitivity. However, the accuracy of qRT-PCR analysis strongly depends on transcript normalization using stably expressed reference gene...

Identification and evaluation of reliable reference genes for quantitative real-time PCR analysis in tea plant (Camellia sinensis (L.) O. Kuntze)

USDA-ARS?s Scientific Manuscript database

Quantitative real-time polymerase chain reaction (qRT-PCR) is a commonly used technique for measuring gene expression levels due to its simplicity, specificity, and sensitivity. Reliable reference selection for the accurate quantification of gene expression under various experimental conditions is a...

Wheat-specific gene, ribosomal protein l21, used as the endogenous reference gene for qualitative and real-time quantitative polymerase chain reaction detection of transgenes.

PubMed

Liu, Yi-Ke; Li, He-Ping; Huang, Tao; Cheng, Wei; Gao, Chun-Sheng; Zuo, Dong-Yun; Zhao, Zheng-Xi; Liao, Yu-Cai

2014-10-29

Wheat-specific ribosomal protein L21 (RPL21) is an endogenous reference gene suitable for genetically modified (GM) wheat identification. This taxon-specific RPL21 sequence displayed high homogeneity in different wheat varieties. Southern blots revealed 1 or 3 copies, and sequence analyses showed one amplicon in common wheat. Combined analyses with sequences from common wheat (AABBDD) and three diploid ancestral species, Triticum urartu (AA), Aegilops speltoides (BB), and Aegilops tauschii (DD), demonstrated the presence of this amplicon in the AA genome. Using conventional qualitative polymerase chain reaction (PCR), the limit of detection was 2 copies of wheat haploid genome per reaction. In the quantitative real-time PCR assay, limits of detection and quantification were about 2 and 8 haploid genome copies, respectively, the latter of which is 2.5-4-fold lower than other reported wheat endogenous reference genes. Construct-specific PCR assays were developed using RPL21 as an endogenous reference gene, and as little as 0.5% of GM wheat contents containing Arabidopsis NPR1 were properly quantified.

Serum free light chain reference values: a critical approach.

PubMed

Altinier, Sara; Seguso, Mara; Zaninotto, Martina; Varagnolo, Mariacristina; Adami, Fausto; Angeli, Paolo; Plebani, Mario

2013-05-01

The clinical usefulness of serum free light chain (FLC) measurement in the management of patients with plasma cell proliferative disorders has been reported in several papers, and most clinical studies use the reference ranges declared by the manufacturer. The aim of the present study was to evaluate the reproducibility of FLCs immunoassay and to validate the reference range, before introducing it in routine setting. Internal quality control materials and a pool of fresh serum samples were used to evaluate imprecision; 162 fresh sera from healthy blood donors were analyzed to evaluate the reference range for FLCs. In order to verify the κ/λ FLC ratio, 43 sera from patients with polyclonal hypergammaglobulinemia were tested. The FLC immunoassay was performed using a nephelometer with the Freelite reagents. The imprecision studies performed using a serum pool tested with two different lots of reagents showed a mean CV of 16.09% for κFLC and of 16.72% for λFLC. Lower CV%s and different mean values were found by calculating the results from each specific lot separately, while different results were obtained using the control materials provided by the manufacturer. In reference subjects, the 2.5-97.5th percentiles were found to be 4.52-22.33 and 4.84-21.88mg/L for κFLC and λFLC, respectively. The range for κ/λ ratio (0.65-2.36) was validated with the values obtained from subjects with polyclonal hypergammaglobulinemia. In retesting 15 samples from blood donor subjects with a different lot of reagents, mean bias percentages of 17.60 for κFLC and 15.26 for λFLC were obtained. These findings confirm the lot-to-lot variability of the FLC assays also in the measurement of polyclonal light chains, as well as the need to carefully validate the reference values. Published by Elsevier Inc.

Network Polymers Formed Under Nonideal Conditions.

DTIC Science & Technology

1986-12-01

the system or the limited ability of the statistical model to account for stochastic correlations. The viscosity of the reacting system was measured as...based on competing reactions (ring, chain) and employs equilibrium chain statistics . The work thus far has been limited to single cycle growth on an...polymerizations, because a large number of differential equations must be solved. The Makovian approach (sometimes referred to as the statistical or

Evaluation and selection of internal reference genes from two- and six-row U.S. malting barley varieties throughout micromalting for use in RT-qPCR

USDA-ARS?s Scientific Manuscript database

Reverse Transcription quantitative Polymerase Chain Reaction (qRT-PCR) is a popular method for measuring transcript abundance. The most commonly used method of interpretation is relative quantification and thus necessitates the use of normalization controls (i.e. reference genes) to standardize tran...

Selection of internal reference genes for normalization of quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis in the canine brain and other organs.

PubMed

Park, Sang-Je; Huh, Jae-Won; Kim, Young-Hyun; Lee, Sang-Rae; Kim, Sang-Hyun; Kim, Sun-Uk; Kim, Heui-Soo; Kim, Min Kyu; Chang, Kyu-Tae

2013-05-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive technique for quantifying gene expression. To analyze qRT-PCR data accurately, suitable reference genes that show consistent expression patterns across different tissues and experimental conditions should be selected. The objective of this study was to obtain the most stable reference genes in dogs, using samples from 13 different brain tissues and 10 other organs. 16 well-known candidate reference genes were analyzed by the geNorm, NormFinder, and BestKeeper programs. Brain tissues were derived from several different anatomical regions, including the forebrain, cerebrum, diencephalon, hindbrain, and metencephalon, and grouped accordingly. Combination of the three different analyses clearly indicated that the ideal reference genes are ribosomal protien S5 (RPS5) in whole brain, RPL8 and RPS5 in whole body tissues, RPS5 and RPS19 in the forebrain and cerebrum, RPL32 and RPS19 in the diencephalon, GAPDH and RPS19 in the hindbrain, and MRPS7 and RPL13A in the metencephalon. These genes were identified as ideal for the normalization of qRT-PCR results in the respective tissues. These findings indicate more suitable and stable reference genes for future studies of canine gene expression.

A de novo transcriptome and valid reference genes for quantitative real-time PCR in Colaphellus bowringi.

PubMed

Tan, Qian-Qian; Zhu, Li; Li, Yi; Liu, Wen; Ma, Wei-Hua; Lei, Chao-Liang; Wang, Xiao-Ping

2015-01-01

The cabbage beetle Colaphellus bowringi Baly is a serious insect pest of crucifers and undergoes reproductive diapause in soil. An understanding of the molecular mechanisms of diapause regulation, insecticide resistance, and other physiological processes is helpful for developing new management strategies for this beetle. However, the lack of genomic information and valid reference genes limits knowledge on the molecular bases of these physiological processes in this species. Using Illumina sequencing, we obtained more than 57 million sequence reads derived from C. bowringi, which were assembled into 39,390 unique sequences. A Clusters of Orthologous Groups classification was obtained for 9,048 of these sequences, covering 25 categories, and 16,951 were assigned to 255 Kyoto Encyclopedia of Genes and Genomes pathways. Eleven candidate reference gene sequences from the transcriptome were then identified through reverse transcriptase polymerase chain reaction. Among these candidate genes, EF1α, ACT1, and RPL19 proved to be the most stable reference genes for different reverse transcriptase quantitative polymerase chain reaction experiments in C. bowringi. Conversely, aTUB and GAPDH were the least stable reference genes. The abundant putative C. bowringi transcript sequences reported enrich the genomic resources of this beetle. Importantly, the larger number of gene sequences and valid reference genes provide a valuable platform for future gene expression studies, especially with regard to exploring the molecular mechanisms of different physiological processes in this species.

Biophysical characterization and structure of the Fab fragment from the NIST reference antibody, RM 8671.

PubMed

Karageorgos, Ioannis; Gallagher, Elyssia S; Galvin, Connor; Gallagher, D Travis; Hudgens, Jeffrey W

2017-11-01

Monoclonal antibody pharmaceuticals are the fastest-growing class of therapeutics, with a wide range of clinical applications. To assure their safety, these protein drugs must demonstrate highly consistent purity and stability. Key to these objectives is higher order structure measurements validated by calibration to reference materials. We describe preparation, characterization, and crystal structure of the Fab fragment prepared from the NIST Reference Antibody RM 8671 (NISTmAb). NISTmAb is a humanized IgG1κ antibody, produced in murine cell culture and purified by standard biopharmaceutical production methods, developed at the National Institute of Standards and Technology (NIST) to serve as a reference material. The Fab fragment was derived from NISTmAb through papain cleavage followed by protein A based purification. The purified Fab fragment was characterized by SDS-PAGE, capillary gel electrophoresis, multi-angle light scattering, size exclusion chromatography, mass spectrometry, and x-ray crystallography. The crystal structure at 0.2 nm resolution includes four independent Fab molecules with complete light chains and heavy chains through Cys 223, enabling assessment of conformational variability and providing a well-characterized reference structure for research and engineering applications. This nonproprietary, publically available reference material of known higher-order structure can support metrology in biopharmaceutical applications, and it is a suitable platform for validation of molecular modeling studies. Published by Elsevier Ltd.

Selection and Validation of Reference Genes for Quantitative Real-Time Polymerase Chain Reaction Studies in Mossy Maze Polypore, Cerrena unicolor (Higher Basidiomycetes).

PubMed

Yang, Jie; Lin, Qi; Lin, Juan; Ye, Xiuyun

2016-01-01

With its ability to produce ligninolytic enzymes such as laccases, white-rot basidiomycete Cerrena unicolor, a medicinal mushroom, has great potential in biotechnology. Elucidation of the expression profiles of genes encoding ligninolytic enzymes are important for increasing their production. Quantitative real-time polymerase chain reaction (qPCR) is a powerful tool to study transcriptional regulation of genes of interest. To ensure accuracy and reliability of qPCR analysis of C. unicolor, expression levels of seven candidate reference genes were studied at different growth phases, under various induction conditions, and with a range of carbon/nitrogen ratios and carbon and nitrogen sources. The stability of the genes were analyzed with five statistical approaches, namely geNorm, NormFinder, BestKeeper, the ΔCt method, and RefFinder. Our results indicated that the selection of reference genes varied with sample sets. A combination of four reference genes (Cyt-c, ATP6, TEF1, and β-tubulin) were recommended for normalizing gene expression at different growth phases. GAPDH and Cyt-c were the appropriate reference genes under different induction conditions. ATP6 and TEF1 were most stable in fermentation media with various carbon/nitrogen ratios. In the fermentation media with various carbon or nitrogen sources, 18S rRNA and GAPDH were the references of choice. The present study represents the first validation analysis of reference genes in C. unicolor and serves as a foundation for its qPCR analysis.

Copy number ratios determined by two digital polymerase chain reaction systems in genetically modified grains

NASA Astrophysics Data System (ADS)

Pérez Urquiza, M.; Acatzi Silva, A. I.

2014-02-01

Three certified reference materials produced from powdered seeds to measure the copy number ratio sequences of p35S/hmgA in maize containing MON 810 event, p35S/Le1 in soybeans containing GTS 40-3-2 event and DREB1A/acc1 in wheat were produced according to the ISO Guides 34 and 35. In this paper, we report digital polymerase chain reaction (dPCR) protocols, performance parameters and results of copy number ratio content of genetically modified organisms (GMOs) in these materials using two new dPCR systems to detect and quantify molecular deoxyribonucleic acid: the BioMark® (Fluidigm) and the OpenArray® (Life Technologies) systems. These technologies were implemented at the National Institute of Metrology in Mexico (CENAM) and in the Reference Center for GMO Detection from the Ministry of Agriculture (CNRDOGM), respectively. The main advantage of this technique against the more-used quantitative polymerase chain reaction (qPCR) is that it generates an absolute number of target molecules in the sample, without reference to standards or an endogenous control, which is very useful when not much information is available for new developments or there are no standard reference materials in the market as in the wheat case presented, or when it was not possible to test the purity of seeds as in the maize case presented here. Both systems reported enhanced productivity, increased reliability and reduced instrument footprint. In this paper, the performance parameters and uncertainty of measurement obtained with both systems are presented and compared.

Lipid Metabolism during Infection and Endotoxemia

DTIC Science & Technology

1981-01-01

containing 8- and 10-carbon fatty acids almost exclusively) have been used in certain therapeutic diets . In contrast to the long-chain triglycerides...increased utilization of ketone bodies. The major substrates for hepatic ketogenesis are long-chain fatty acids. The term ’ ketogenic capacity’ refers to the...bodies is influenced not only by substrate availability and enzyme activities, but also more directly by the dis- posal of acetyl-CoA through ketogenic

Evidence Study Guide.

DTIC Science & Technology

1987-04-01

involving novel scientific evidence, e.g., the drug-induced or hypnosis -induced interview of a witness. Although the rules on experts contain no reference...under the Fed.R.Evid. Among the evidence which Nil.R.Evid. 803(6) makes admissible are forensic laboratory reports and chain of custody documents. The...34 inclusion of forensic laboratory reports and chain of custody documents in this Mil.R.Evid. is in conflict with the legislative history of

Managing risks in the fisheries supply chain using House of Risk Framework (HOR) and Interpretive Structural Modeling (ISM)

NASA Astrophysics Data System (ADS)

Nguyen, T. L. T.; Tran, T. T.; Huynh, T. P.; Ho, T. K. D.; Le, A. T.; Do, T. K. H.

2018-04-01

One of the sectors which contributes importantly to the development of Vietnam economy is fishery industry. However, during recent year, it has been witnessed many difficulties on managing the performance of the fishery supply chain operations as a whole. In this paper, a framework for supply chain risk management (SCRM) is proposed. Initially, all the activities are mapped by using Supply Chain Operations Reference (SCOR) model. Next, the risk ranking is analyzed in House of Risk. Furthermore, interpretive structural modeling (ISM) is used to identify inter-relationships among supply chain risks and to visualize the risks according to their levels. For illustration, the model has been tested in several case studies with fishery companies in Can Tho, Mekong Delta. This study identifies 22 risk events and 20 risk agents through the supply chain. Also, the risk priority could be used for further House of Risk with proactive actions in future studies.

Antibody repertoire development in camelids.

PubMed

De Genst, Erwin; Saerens, Dirk; Muyldermans, Serge; Conrath, Katja

2006-01-01

The humoral immune response of the Camelidae is unique as these animals are the only known mammals that seem to possess functional homodimeric heavy-chain antibodies besides the classical heteromeric antibodies composed of heavy (H) and light (L) chains. By definition, the heavy-chain antibodies lack the L-chain, and it was noticed that their H-chain is devoid of the typical first constant domain (CH1) and contains a dedicated variable domain, referred to as VHH. The VHH exon is assembled from separate V-D-J gene segments. The recombined VHH region is subjected to somatic hypermutations; however, the timing and actual mechanism of the class switch from mu to the dedicated gamma-isotype remains elusive. Interestingly, antigen-specific VHHs are easily retrieved after panning of a phage-displayed rearranged V-gene pool cloned from an immunised camelid. These single-domain antigen binding entities possess a number of biophysical properties that offer particular advantages in various medical and biotechnological applications.

SCOR based key success factors in cooking oil supply chain buyers perspective in Padang City

NASA Astrophysics Data System (ADS)

Zahara, Fatimah; Hadiguna, Rika Ampuh

2017-11-01

Supply chain of cooking oil is a network of companies from palm oil as raw material to retailers which work to create the value and deliver products into the end consumers. This paper is aimed to study key success factors based on consumer's perspective as the last stage in the supply chain. Consumers who are examined in this study are restaurants management or owners. Restaurant is the biggest consumption of cooking oil. The factors is studied based on Supply Chain Operation Reference (SCOR) version 10.0. Factors used are formulated based on the third-level metrics of SCOR Model. Factors are analyzed using factors analysis. This study found factors which become key success factors in managing supply chain of cooking oil encompass reliability, responsiveness and agility. Key success factors can be applied by governments as policy making and cooking oil companies as formulation of the distribution strategies.

Altering surface fluctuations by blending tethered and untethered chains

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

Lee, J. K.; Akgun, B.; Jiang, Z.

"Partially tethering" a thin film of a polymer melt by covalently attaching to the substrate a fraction of the chains in an unentangled melt dramatically increases the relaxation time of the surface height fluctuations. This phenomenon is observed even when the film thickness, h, is 20 times the unperturbed chain radius, R g,tethered, of the tethered chains, indicating that partial tethering is more influential than any physical attraction with the substrate. Furthermore, a partially tethered layer of a low average molecular weight of 5k showed much slower surface fluctuations than did a reference layer of pure untethered chains of muchmore » greater molecular weight (48k), so the partial tethering effect is stronger than the effects of entanglement and increase in glass transition temperature, Tg, with molecular weight. Partial tethering offers a means of tailoring these fluctuations which influence wetting, adhesion, and tribology of the surface.« less

Altering surface fluctuations by blending tethered and untethered chains

DOE PAGES

Lee, J. K.; Akgun, B.; Jiang, Z.; ...

2017-10-16

"Partially tethering" a thin film of a polymer melt by covalently attaching to the substrate a fraction of the chains in an unentangled melt dramatically increases the relaxation time of the surface height fluctuations. This phenomenon is observed even when the film thickness, h, is 20 times the unperturbed chain radius, R g,tethered, of the tethered chains, indicating that partial tethering is more influential than any physical attraction with the substrate. Furthermore, a partially tethered layer of a low average molecular weight of 5k showed much slower surface fluctuations than did a reference layer of pure untethered chains of muchmore » greater molecular weight (48k), so the partial tethering effect is stronger than the effects of entanglement and increase in glass transition temperature, Tg, with molecular weight. Partial tethering offers a means of tailoring these fluctuations which influence wetting, adhesion, and tribology of the surface.« less

LPTF frequency synthesis chain: Results and improvement for the near future

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

Touahri, D.; Zondy, J.J.; Acef, O.

1994-12-31

We have measured the frequency of the He-Ne/12 laser starting from the Cs referenced CO{sub 2}/OsO{sub 4} laboratory standard. As the laser diode stabilized on the two-photon transition in Rb seems to be a suitable reference for spectroscopic studies. (H, He ... ) and a promising standard, we are modifying our chain in order to measure frequencies around 780 nm and specially the Rb one.

Copper accumulation and transport in a marine food chain composed of Platymonas subcordiformis, brachionus plicatilis and Penaeus monodon

NASA Astrophysics Data System (ADS)

Cai, A.-Gen; Chen, Wei-Qi; Li, Wen-Quan

1997-09-01

Accumulation, transport and toxicity of Cu in the food chain consisting of Platymonas subcordiformis, Brachionus plicatilis and Penaeus monodon were studied. Effects of Cu on the growth of organisms in the food chain were investigated and the inhibiting effect concentration (EC50) of Cu was then determined according to the dynamics of the relative number of cells or total individuals of organisms, expressed in percentages with reference to the controlled system, under different culture conditions. On the basis of the variations in accumulation and percentages of accumulation of Cu in the biological phase, the relationship between the accumulation of Cu in organisms and its toxicity was analyzed and the main approach for determining the transport of Cu in the food chain was then discussed.

Using SCOR as a Supply Chain Management Framework for Government Agency Contract Requirements

NASA Technical Reports Server (NTRS)

Paxton, Joseph; Tucker, Brian

2010-01-01

This paper will present a model that uses the Supply-Chain Operations Reference (SCOR) model as a foundation for a framework to illustrate the information needed throughout a product lifecycle to support a healthy supply chain management function and the subsequent contract requirements to enable it. It will also show where in the supply chain the information must be extracted. The ongoing case study used to exemplify the model is NASA's (National Aeronautics and Space Administration) Ares I program for human spaceflight. Effective supply chain management and contract requirements are ongoing opportunities for continuous improvement within government agencies, specifically development of systems for human spaceflight operations. Multiple reports from the Government Accountability Office (GAO) reinforce this importance. The SCOR model is a framework for describing a supply chain with process building blocks and business activities. It provides a set of metrics for measuring supply chain performance and best practices for continuously improving. This paper expands the application of the SCOR to also provide the framework for defining information needed from different levels of the supply chain and at different phases of the lifecycle. These needs can be incorporated into contracts to enable more effective supply chain management. Depending on the phase of the lifecycle, effective supply chain management will require involvement from different levels of the organization and different levels of the supply chain.

Markov chains and semi-Markov models in time-to-event analysis.

PubMed

Abner, Erin L; Charnigo, Richard J; Kryscio, Richard J

2013-10-25

A variety of statistical methods are available to investigators for analysis of time-to-event data, often referred to as survival analysis. Kaplan-Meier estimation and Cox proportional hazards regression are commonly employed tools but are not appropriate for all studies, particularly in the presence of competing risks and when multiple or recurrent outcomes are of interest. Markov chain models can accommodate censored data, competing risks (informative censoring), multiple outcomes, recurrent outcomes, frailty, and non-constant survival probabilities. Markov chain models, though often overlooked by investigators in time-to-event analysis, have long been used in clinical studies and have widespread application in other fields.

Markov chains and semi-Markov models in time-to-event analysis

PubMed Central

Abner, Erin L.; Charnigo, Richard J.; Kryscio, Richard J.

2014-01-01

A variety of statistical methods are available to investigators for analysis of time-to-event data, often referred to as survival analysis. Kaplan-Meier estimation and Cox proportional hazards regression are commonly employed tools but are not appropriate for all studies, particularly in the presence of competing risks and when multiple or recurrent outcomes are of interest. Markov chain models can accommodate censored data, competing risks (informative censoring), multiple outcomes, recurrent outcomes, frailty, and non-constant survival probabilities. Markov chain models, though often overlooked by investigators in time-to-event analysis, have long been used in clinical studies and have widespread application in other fields. PMID:24818062

Subunit-Specific Labeling of Ubiquitin Chains by Using Sortase: Insights into the Selectivity of Deubiquitinases.

PubMed

Crowe, Sean O; Pham, Grace H; Ziegler, Jacob C; Deol, Kirandeep K; Guenette, Robert G; Ge, Ying; Strieter, Eric R

2016-08-17

Information embedded in different ubiquitin chains is transduced by proteins with ubiquitin-binding domains (UBDs) and erased by a set of hydrolytic enzymes referred to as deubiquitinases (DUBs). Understanding the selectivity of UBDs and DUBs is necessary for decoding the functions of different ubiquitin chains. Critical to these efforts is the access to chemically defined ubiquitin chains bearing site-specific fluorescent labels. One approach toward constructing such molecules involves peptide ligation by sortase (SrtA), a bacterial transpeptidase responsible for covalently attaching cell surface proteins to the cell wall. Here, we demonstrate the utility of SrtA in modifying individual subunits of ubiquitin chains. Using ubiquitin derivatives in which an N-terminal glycine is unveiled after protease-mediated digestion, we synthesized ubiquitin dimers, trimers, and tetramers with different isopeptide linkages. SrtA was then used in combination with fluorescent depsipeptide substrates to effect the modification of each subunit in a chain. By constructing branched ubiquitin chains with individual subunits tagged with a fluorophore, we provide evidence that the ubiquitin-specific protease USP15 prefers ubiquitin trimers but has little preference for a particular isopeptide linkage. Our results emphasize the importance of subunit-specific labeling of ubiquitin chains when studying how DUBs process these chains. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

50 CFR 218.4 - Mitigation.

Code of Federal Regulations, 2010 CFR

2010-10-01

... activities. (ii) The Navy shall follow internal chain of command reporting procedures as promulgated through... noted) of the specified associated reference points: (1) South and East of Block Island (37 km (20 NM...

50 CFR 218.4 - Mitigation.

Code of Federal Regulations, 2012 CFR

2012-10-01

... activities. (ii) The Navy shall follow internal chain of command reporting procedures as promulgated through... noted) of the specified associated reference points: (1) South and East of Block Island (37 km (20 NM...

AED INFORMATION SERVICE. SERIES C: BIBLIOGRAPHIES. SECTION 02: RADIATION EFFECTS ON FOOD (INCL. RADIOACTIVE CONTAMINATION)

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

Lueck, H. comp.

Eleven hundred and fifty-eight references are presented to the world literature on radiation effects on food. References to related biological and chemical studies and studies on radiation dosimetry are included. Emphasis is placed on radiation processing of foods and food products to increase storage life and the effects of fallout fission products on radioactivity in food chains. (C.H.)

Accelerating the Kill Chain via Future Unmanned Aircraft

DTIC Science & Technology

2007-04-01

Controller JTRS Joint Tactical Radio System Lasercom Laser communications LDHD Low Density High Demand LEO Low Earth Orbit LGB Laser Guided Bomb...published the Unmanned Aircraft Systems Roadmap 2005 that included the terms Unmanned Aircraft System (UAS) and Unmanned Aircraft (UA). This...comprehensive publication used the term Unmanned Aircraft Systems when referring to the entire system and the term Unmanned Aircraft when referring only to the

Overcharging and charge reversal in the electrical double layer around the point of zero charge.

PubMed

Guerrero-García, G Iván; González-Tovar, Enrique; Chávez-Páez, Martín; Lozada-Cassou, Marcelo

2010-02-07

The ionic adsorption around a weakly charged spherical colloid, immersed in size-asymmetric 1:1 and 2:2 salts, is studied. We use the primitive model (PM) of an electrolyte to perform Monte Carlo simulations as well as theoretical calculations by means of the hypernetted chain/mean spherical approximation (HNC/MSA) and the unequal-radius modified Gouy-Chapman (URMGC) integral equations. Structural quantities such as the radial distribution functions, the integrated charge, and the mean electrostatic potential are reported. Our Monte Carlo "experiments" evidence that near the point of zero charge, the smallest ionic species is preferentially adsorbed onto the macroparticle, independently of the sign of the charge carried by this tiniest electrolytic component, giving rise to the appearance of the phenomena of charge reversal (CR) and overcharging (OC). Accordingly, colloidal CR, due to an excessive attachment of counterions, is observed when the macroion is slightly charged and the coions are larger than the counterions. In the opposite situation, i.e., if the counterions are larger than the coions, the central macroion acquires additional like-charge (coions) and hence becomes "overcharged," a feature theoretically predicted in the past [F. Jiménez-Angeles and M. Lozada-Cassou, J. Phys. Chem. B 108, 7286 (2004)]. In other words, here we present the first simulation data on OC in the PM electrical double layer, showing that close to the point of zero charge, this novel effect surges as a consequence of the ionic size asymmetry. We also find that the HNC/MSA theory captures well the CR and OC phenomena exhibited by the computer experiments, especially as the macroion's charge increases. On the contrary, even if URMGC also displays CR and OC, its predictions do not compare favorably with the Monte Carlo data, evidencing that the inclusion of hard-core correlations in Monte Carlo and HNC/MSA enhances and extends those effects. We explain our findings in terms of the energy-entropy balance. In the field of electrophoresis, it has been generally agreed that the charge of a colloid in motion is partially decreased by counterion adsorption. Depending on the location of the macroion's slipping surface, the OC results of this paper could imply an increase in the expected electrophoretic mobility. These observations aware about the interpretation of electrokinetic measurements using the standard Poisson-Boltzmann approximation beyond its validity region.

Structure des fluides de bâtonnets polaires et polarisables dans l'approximation des chaînes hypertressées avec amplification du potentiel répulsif. Un modèle simple d'acétonitrile liquide.

NASA Astrophysics Data System (ADS)

Salamito, B.; Fries, P. H.

1991-07-01

We study fluids of rigid rods which are generated by a distribution of line sites and which carry a polarizable electric point dipole at their centre. We examine the difficulties for solving the integral equations, which result from truncating the rotational invariant expansion of the usual intermolecular rapidly varying shape potentials. In order to overcome these convergence problems, soft shape potentials are used in addition to an approximation HNCAR, of the hypernetted chain (HNC) type, which Amplifies these soft Repulsive effects. The polarization due to all the molecules is treated at a self-consistent mean field level. This formalism is applied to a model of liquid acetonitrile at 291K. The Kirkwood factors, the dielectric constant, and the cross sections of neutron or X-rays diffraction studies are in good agreement with experiment. This justifies the theoretical molecular pair distribution, from which the local molecular order is carefully analyzed. On étudie des fluides de bâtonnets rigides engendrés par une distribution de sites alignés et portant en leur centre un dipôle électrique ponctuel polarisable. On examine les difficultés de résolution des équations intégrales liées à la troncature du développement en invariants rotationnels des potentiels de forme intermoléculaires usuels à variation rapide. Pour contourner ces problèmes de convergence on utilise des potentiels de forme molle combinés à une approximation HNCAR, du type des chaînes hypertressées (HNC), qui Amplifie ces effets Répulsifs mous. On traite la polarisation due à l'ensemble des molécules par une approximation auto-cohérente de champ moyen. On applique ce formalisme à un modèle d'acétonitrile liquide à 291K. Les facteurs de Kirkwood, la constante diélectrique et les sections efficaces de diffusion des neutrons ou des rayons X calculés sont en bon accord avec l'expérience. Ceci justifie la distribution théorique de paires de molécules à partir de laquelle on analyse en détail l'ordre moléculaire local.

Genetics Home Reference: deoxyguanosine kinase deficiency

MedlinePlus

... the mitochondrial respiratory chain in patients with hepatic involvement. Mol Genet Metab. 2005 Dec;86(4):462-5. Epub 2005 Nov 2. ... What is direct-to-consumer genetic testing? What are genome editing and CRISPR- ...

Genetics Home Reference: short/branched chain acyl-CoA dehydrogenase deficiency

MedlinePlus

... PDF) Orphanet: 2-methylbutyryl-CoA dehydrogenase deficiency Screening, Technology, and Research in Genetics Patient Support and Advocacy Resources (2 links) Children Living with Inherited Metabolic Diseases (CLIMB) Organic Acidemia ...

Genetics Home Reference: 3-hydroxyacyl-CoA dehydrogenase deficiency

MedlinePlus

... short chain 3-hydroxylacyl-CoA dehydrogenase deficiency Screening, Technology and Research in Genetics (STAR-G) Patient Support and Advocacy Resources (3 links) Children Living with Inherited Metabolic Diseases (CLIMB) FOD (Fatty ...

Collaborative ring trial of the papaya endogenous reference gene and its polymerase chain reaction assays for genetically modified organism analysis.

PubMed

Wei, Jiaojun; Li, Feiwu; Guo, Jinchao; Li, Xiang; Xu, Junfeng; Wu, Gang; Zhang, Dabing; Yang, Litao

2013-11-27

The papaya (Carica papaya L.) Chymopapain (CHY) gene has been reported as a suitable endogenous reference gene for genetically modified (GM) papaya detection in previous studies. Herein, we further validated the use of the CHY gene and its qualitative and quantitative polymerase chain reaction (PCR) assays through an interlaboratory collaborative ring trial. A total of 12 laboratories working on detection of genetically modified organisms participated in the ring trial and returned test results. Statistical analysis of the returned results confirmed the species specificity, low heterogeneity, and single-copy number of the CHY gene among different papaya varieties. The limit of detection of the CHY qualitative PCR assay was 0.1%, while the limit of quantification of the quantitative PCR assay was ∼25 copies of haploid papaya genome with acceptable PCR efficiency and linearity. The differences between the tested and true values of papaya content in 10 blind samples ranged from 0.84 to 6.58%. These results indicated that the CHY gene was suitable as an endogenous reference gene for the identification and quantification of GM papaya.

The emerging complexity of ubiquitin architecture.

PubMed

Ohtake, Fumiaki; Tsuchiya, Hikaru

2017-02-01

Ubiquitylation is an essential post-translational modification (PTM) of proteins with diverse cellular functions. Polyubiquitin chains with different topologies have different cellular roles, and are referred to as a 'ubiquitin code'. Recent studies have begun to reveal that more complex ubiquitin architectures function as important signals in several biological pathways. These include PTMs of ubiquitin itself, such as acetylated ubiquitin and phospho-ubiquitin. Moreover, important roles for heterogeneous polyubiquitin chains, such as mixed or branched chains, have been reported, which significantly increase the diversity of the ubiquitin code. In this review, we describe mass spectrometry-based methods to characterize the ubiquitin signal. We also describe recent advances in our understanding of complex ubiquitin architectures, including our own findings concerning ubiquitin acetylation and branching within polyubiquitin chains. © The Authors 2016. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Geometric modelling of the contact point between the bushing and sprocket in chain drives

NASA Astrophysics Data System (ADS)

Saulescu, R.; Velicu, R.; Lates, M.

2017-02-01

An important problem of the bush chains dynamics is represented by the calculus of the normal and transversal forces on all the contacts; these forces are producing vibrations in the chain and due to this, the chain is affected by the wear. One aspect of that dynamics is referring directly on the sprockets geometry and on the bushing and sprocket contact. The paper presents a calculus method for the contact angle between the bushing and the sprocket; this angle is a variable one depending on the bushing’s number being in contact (i) and on the specific elongation of the chain (x) due to the functioning of it. Based on the presented calculus model, a comparative analysis is proposed for these factors by using sprockets with different teeth numbers and different specific elongations of the chain. The results of the numerical simulations allow the dissemination of recommendations regarding the contact angle’s evolution, from the beginning to the end of the contact and regarding the influence of the chain’s specific elongations on the out of use of it.

The Kinetic Chain Revisited: New Concepts on Throwing Mechanics and Injury.

PubMed

Chu, Samuel K; Jayabalan, Prakash; Kibler, W Ben; Press, Joel

2016-03-01

The overhead throwing motion is a complex activity that is achieved through activation of the kinetic chain. The kinetic chain refers to the linkage of multiple segments of the body that allows for transfer of forces and motion. The lower extremities and core provide a base of support, generating energy that is transferred eventually through the throwing arm and hand, resulting in release of the ball. The kinetic chain requires optimal anatomy, physiology, and mechanics and is involved in all 6 phases of overhead throwing: windup, stride, arm cocking, acceleration, deceleration, and follow-through. Breaks or deficits in the kinetic chain can lead to injury or decreased performance. Through an understanding of the mechanics and pathomechanics seen in each phase of throwing, the clinician can better evaluate and screen for potential kinetic chain deficits in the overhead throwing athlete. The purpose of this article is to review the biomechanics of the overhead throwing motion, the role of the kinetic chain in throwing, and the clinical evaluation and management of abnormal throwing mechanics and related injuries. Copyright © 2016 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

[The study of medical supplies automation replenishment algorithm in hospital on medical supplies supplying chain].

PubMed

Sheng, Xi

2012-07-01

The thesis aims to study the automation replenishment algorithm in hospital on medical supplies supplying chain. The mathematical model and algorithm of medical supplies automation replenishment are designed through referring to practical data form hospital on the basis of applying inventory theory, greedy algorithm and partition algorithm. The automation replenishment algorithm is proved to realize automatic calculation of the medical supplies distribution amount and optimize medical supplies distribution scheme. A conclusion could be arrived that the model and algorithm of inventory theory, if applied in medical supplies circulation field, could provide theoretical and technological support for realizing medical supplies automation replenishment of hospital on medical supplies supplying chain.

Canadian High Arctic Ionospheric Network (CHAIN)

NASA Astrophysics Data System (ADS)

Jayachandran, P. T.; Langley, R. B.; MacDougall, J. W.; Mushini, S. C.; Pokhotelov, D.; Hamza, A. M.; Mann, I. R.; Milling, D. K.; Kale, Z. C.; Chadwick, R.; Kelly, T.; Danskin, D. W.; Carrano, C. S.

2009-02-01

Polar cap ionospheric measurements are important for the complete understanding of the various processes in the solar wind-magnetosphere-ionosphere system as well as for space weather applications. Currently, the polar cap region is lacking high temporal and spatial resolution ionospheric measurements because of the orbit limitations of space-based measurements and the sparse network providing ground-based measurements. Canada has a unique advantage in remedying this shortcoming because it has the most accessible landmass in the high Arctic regions, and the Canadian High Arctic Ionospheric Network (CHAIN) is designed to take advantage of Canadian geographic vantage points for a better understanding of the Sun-Earth system. CHAIN is a distributed array of ground-based radio instruments in the Canadian high Arctic. The instrument components of CHAIN are 10 high data rate Global Positioning System ionospheric scintillation and total electron content monitors and six Canadian Advanced Digital Ionosondes. Most of these instruments have been sited within the polar cap region except for two GPS reference stations at lower latitudes. This paper briefly overviews the scientific capabilities, instrument components, and deployment status of CHAIN. This paper also reports a GPS signal scintillation episode associated with a magnetospheric impulse event. More details of the CHAIN project and data can be found at http://chain.physics.unb.ca/chain.

Evaluation of reference genes for quantitative real-time RT-PCR analysis of gene expression in Nile tilapia (Oreochromis niloticus).

PubMed

Yang, Chang Geng; Wang, Xian Li; Tian, Juan; Liu, Wei; Wu, Fan; Jiang, Ming; Wen, Hua

2013-09-15

Quantitative real-time reverse-transcriptase polymerase chain reaction (RT-qPCR) has been used frequently to study gene expression related to fish immunology. In such studies, a stable reference gene should be selected to correct the expression of the target gene. In this study, seven candidate reference genes (glyceraldehyde-3-phosphate dehydrogenase (GADPH), ubiquitin-conjugating enzyme (UBCE), 18S ribosomal RNA (18S rRNA), beta-2-microglobulin (B2M), elongation factor 1 alpha (EF1A), tubulin alpha chain-like (TUBA) and beta actin (ACTB)), were selected to analyze their stability and normalization in seven tissues (liver, spleen, kidney, brain, heart, muscle and intestine) of Nile tilapia (Oreochromis niloticus) challenged with Streptococcus agalactiae or Streptococcus iniae, respectively. The results showed that all the candidate reference genes exhibited tissue-dependent transcriptional variations. With PBS injection as a control, UBCE was the most stable and suitable single reference gene in the intestine, liver, brain, kidney, and spleen after S. iniae infection, and in the liver, kidney, and spleen after S. agalactiae infection. EF1A was the most suitable in heart and muscle after S. iniae or S. agalactiae infection. GADPH was the most suitable gene in intestine and brain after S. agalactiae infection. In normal conditions, UBCE and 18S rRNA were the most stably expressed genes across the various tissues. These results showed that for RT-qPCR analysis of tilapia, selecting two or more reference genes may be more suitable for cross-tissue analysis of gene expression. Copyright © 2013 Elsevier B.V. All rights reserved.

Automatic Near-Real-Time Image Processing Chain for Very High Resolution Optical Satellite Data

NASA Astrophysics Data System (ADS)

Ostir, K.; Cotar, K.; Marsetic, A.; Pehani, P.; Perse, M.; Zaksek, K.; Zaletelj, J.; Rodic, T.

2015-04-01

In response to the increasing need for automatic and fast satellite image processing SPACE-SI has developed and implemented a fully automatic image processing chain STORM that performs all processing steps from sensor-corrected optical images (level 1) to web-delivered map-ready images and products without operator's intervention. Initial development was tailored to high resolution RapidEye images, and all crucial and most challenging parts of the planned full processing chain were developed: module for automatic image orthorectification based on a physical sensor model and supported by the algorithm for automatic detection of ground control points (GCPs); atmospheric correction module, topographic corrections module that combines physical approach with Minnaert method and utilizing anisotropic illumination model; and modules for high level products generation. Various parts of the chain were implemented also for WorldView-2, THEOS, Pleiades, SPOT 6, Landsat 5-8, and PROBA-V. Support of full-frame sensor currently in development by SPACE-SI is in plan. The proposed paper focuses on the adaptation of the STORM processing chain to very high resolution multispectral images. The development concentrated on the sub-module for automatic detection of GCPs. The initially implemented two-step algorithm that worked only with rasterized vector roads and delivered GCPs with sub-pixel accuracy for the RapidEye images, was improved with the introduction of a third step: super-fine positioning of each GCP based on a reference raster chip. The added step exploits the high spatial resolution of the reference raster to improve the final matching results and to achieve pixel accuracy also on very high resolution optical satellite data.

Multiple Myeloma and Its Precursor Disease Among Firefighters Exposed to the World Trade Center Disaster.

PubMed

Landgren, Ola; Zeig-Owens, Rachel; Giricz, Orsolya; Goldfarb, David; Murata, Kaznouri; Thoren, Katie; Ramanathan, Lakshmi; Hultcrantz, Malin; Dogan, Ahmet; Nwankwo, George; Steidl, Ulrich; Pradhan, Kith; Hall, Charles B; Cohen, Hillel W; Jaber, Nadia; Schwartz, Theresa; Crowley, Laura; Crane, Michael; Irby, Shani; Webber, Mayris P; Verma, Amit; Prezant, David J

2018-06-01

The World Trade Center (WTC) attacks on September 11, 2001, created an unprecedented environmental exposure to known and suspected carcinogens suggested to increase the risk of multiple myeloma. Multiple myeloma is consistently preceded by the precursor states of monoclonal gammopathy of undetermined significance (MGUS) and light-chain MGUS, detectable in peripheral blood. To characterize WTC-exposed firefighters with a diagnosis of multiple myeloma and to conduct a screening study for MGUS and light-chain MGUS. Case series of multiple myeloma in firefighters diagnosed between September 11, 2001, and July 1, 2017, together with a seroprevalence study of MGUS in serum samples collected from Fire Department of the City of New York (FDNY) firefighters between December 2013 and October 2015. Participants included all WTC-exposed FDNY white, male firefighters with a confirmed physician diagnosis of multiple myeloma (n = 16) and WTC-exposed FDNY white male firefighters older than 50 years with available serum samples (n = 781). WTC exposure defined as rescue and/or recovery work at the WTC site between September 11, 2001, and July 25, 2002. Multiple myeloma case information, and age-adjusted and age-specific prevalence rates for overall MGUS (ie, MGUS and light-chain MGUS), MGUS, and light-chain MGUS. Sixteen WTC-exposed white male firefighters received a diagnosis of multiple myeloma after September 11, 2001; median age at diagnosis was 57 years (interquartile range, 50-68 years). Serum/urine monoclonal protein isotype/free light-chain data were available for 14 cases; 7 (50%) had light-chain multiple myeloma. In a subset of 7 patients, myeloma cells were assessed for CD20 expression; 5 (71%) were CD20 positive. In the screening study, we assayed peripheral blood from 781 WTC-exposed firefighters. The age-standardized prevalence rate of MGUS and light-chain MGUS combined was 7.63 per 100 persons (95% CI, 5.45-9.81), 1.8-fold higher than rates from the Olmsted County, Minnesota, white male reference population (relative rate, 1.76; 95% CI, 1.34-2.29). The age-standardized prevalence rate of light-chain MGUS was more than 3-fold higher than in the same reference population (relative rate, 3.13; 95% CI, 1.99-4.93). Environmental exposure to the WTC disaster site is associated with myeloma precursor disease (MGUS and light-chain MGUS) and may be a risk factor for the development of multiple myeloma at an earlier age, particularly the light-chain subtype.

Selection of internal reference genes for normalization of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis in the rumen epithelium.

PubMed

Die, Jose V; Baldwin, Ransom L; Rowland, Lisa J; Li, Robert; Oh, Sunghee; Li, Congjun; Connor, Erin E; Ranilla, Maria-Jose

2017-01-01

The rumen is lined on the luminal side by a stratified squamous epithelium that is responsible for not only absorption, but also transport, extensive short-chain fatty acid (SCFA) metabolism and protection. Butyrate has been demonstrated to initiate the differentiation of the tissue following introduction of solid feed to the weaning neonate as well as affecting the metabolism of other nutrients and absorption of nutrients in in vitro experiments. The objective of the present study was to validate expression stability of eight putative reference genes bovine rumen, considering the intrinsic heterogeneity of bovine rumen with regard to different luminal characteristics due to direct infusion of butyrate to double the intra-ruminal content of the rumen liquor. Our focus was on identifying stable reference genes which are suitable to normalize real-time RT-qPCR experiments from rumen samples collected from clinical assays, irrespective of localization within the organ and the across physiological state. The most stably expressed genes included: ACTB, UXT, DBNDD2, RPS9, DDX54 and HMBS. Their high stability values suggest these reference genes will facilitate better evaluation of variation of across an array of conditions including: localization within the rumen, differences among cattle fed an array of rations, as well as response to development in the weaning animal. Moreover, we anticipate these reference genes may be useful for expression studies in other ruminants.

A Human Factors Analysis of USAF Remotely Piloted Aircraft Mishaps

DTIC Science & Technology

2013-06-01

conditions or unsafe acts, where their respective removal would prevent a chain reaction from propagating, thus preventing the accident . This model...Force Col. Anthony Tvaryanas stated that “If you 19 really wanted to make a dent in preventing RPA accidents , the DoD needs to look at how they do...REFERENCES Greenwood, M. & Woods, H.M. (1919). The incidence of industrial accidents upon individuals with special reference to multiple accidents . (British

Genetics Home Reference: peroxisomal acyl-CoA oxidase deficiency

MedlinePlus

... of certain fat molecules called very long-chain fatty acids (VLCFAs). Specifically, it is involved in the first step of a process called the peroxisomal fatty acid beta-oxidation pathway. This process shortens the VLCFA ...

Analysis of Food Contaminants, Residues, and Chemical Constituents of Concern

NASA Astrophysics Data System (ADS)

Ismail, Baraem; Reuhs, Bradley L.; Nielsen, S. Suzanne

The food chain that starts with farmers and ends with consumers can be complex, involving multiple stages of production and distribution (planting, harvesting, breeding, transporting, storing, importing, processing, packaging, distributing to retail markets, and shelf storing) (Fig. 18.1). Various practices can be employed at each stage in the food chain, which may include pesticide treatment, agricultural bioengineering, veterinary drug administration, environmental and storage conditions, processing applications, economic gain practices, use of food additives, choice of packaging material, etc. Each of these practices can play a major role in food quality and safety, due to the possibility of contamination with or introduction (intentionally and nonintentionally) of hazardous substances or constituents. Legislation and regulation to ensure food quality and safety are in place and continue to develop to protect the stakeholders, namely farmers, consumers, and industry. [Refer to reference (1) for information on regulations of food contaminants and residues.

Molprobity's ultimate rotamer-library distributions for model validation.

PubMed

Hintze, Bradley J; Lewis, Steven M; Richardson, Jane S; Richardson, David C

2016-09-01

Here we describe the updated MolProbity rotamer-library distributions derived from an order-of-magnitude larger and more stringently quality-filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to model validation as seen by users. To include only side-chains with satisfactory justification for their given conformation, we added residue-specific filters for electron-density value and model-to-density fit. The combined new protocol retains a million residues of data, while cleaning up false-positive noise in the multi- χ datapoint distributions. It enables unambiguous characterization of conformational clusters nearly 1000-fold less frequent than the most common ones. We describe examples of local interactions that favor these rare conformations, including the role of authentic covalent bond-angle deviations in enabling presumably strained side-chain conformations. Further, along with favored and outlier, an allowed category (0.3-2.0% occurrence in reference data) has been added, analogous to Ramachandran validation categories. The new rotamer distributions are used for current rotamer validation in MolProbity and PHENIX, and for rotamer choice in PHENIX model-building and refinement. The multi-dimensional χ distributions and Top8000 reference dataset are freely available on GitHub. These rotamers are termed "ultimate" because data sampling and quality are now fully adequate for this task, and also because we believe the future of conformational validation should integrate side-chain with backbone criteria. Proteins 2016; 84:1177-1189. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Supply Chain Engineering and the Use of a Supporting Knowledge Management Application

NASA Astrophysics Data System (ADS)

Laakmann, Frank

The future competition in markets will happen between logistics networks and no longer between enterprises. A new approach for supporting the engineering of logistics networks is developed by this research as a part of the Collaborative Research Centre (SFB) 559: "Modeling of Large Networks in Logistics" at the University of Dortmund together with the Fraunhofer-Institute of Material Flow and Logistics founded by Deutsche Forschungsgemeinschaft (DFG). Based on a reference model for logistics processes, the process chain model, a guideline for logistics engineers is developed to manage the different types of design tasks of logistics networks. The technical background of this solution is a collaborative knowledge management application. This paper will introduce how new Internet-based technologies support supply chain design projects.

Genetics Home Reference: medium-chain acyl-CoA dehydrogenase deficiency

MedlinePlus

... body's fat tissues. Fatty acids are a major source of energy for the heart and muscles. During periods of fasting, fatty acids are also an important energy source for the liver and other tissues. Mutations in ...

Fibrinogen Lincoln: a new truncated alpha chain variant with delayed clotting.

PubMed

Ridgway, H J; Brennan, S O; Gibbons, S; George, P M

1996-04-01

A patient referred for preoperative investigation of prolonged bleeding and easy bruising was found to have increased thrombin and reptilase times; however, the thrombin catalysed release of fibrinopeptides A and B was normal. Analysis of five other family members, spanning three generations, indicated that three had a similar defect and suggested autosomal dominant inheritance. Non-reducing SDS-PAGE of purified fibrinogen from affected individuals showed that the 340 kD form of their fibrinogen ran as a doublet. SSCP (single-stranded conformational polymorphism) analysis of exon 5 of the A alpha gene, which encodes the C-terminal half of the chain, confirmed the presence of a mutation. Cycle sequencing of PCR amplified DNA revealed a 13 base pair deletion (nt 4758-4770), resulting in a frame-shift at Ala 475, which translates as four new amino acids before terminating at a new stop codon (-476His-Cys-Leu-Ala-Stop). The presence of a circulating truncated A alpha chain was confirmed when SDS-PAGE gels were probed with an alpha chain specific antisera; which showed that the variant A alpha chain comigrated with gamma chains. The truncation results in a variant A alpha chain with a deletion of 131 amino acids (480-610), and four new amino acids at the C-terminal.

Proximal tubulopathies associated with monoclonal light chains: the spectrum of clinicopathologic manifestations and molecular pathogenesis.

PubMed

Herrera, Guillermo A

2014-10-01

Lesions associated with monoclonal light and heavy chains display a variety of glomerular, tubular interstitial, and vascular manifestations. While some of the entities are well recognized, including light and heavy chain deposition diseases, AL (light chain) and AH (heavy chain) amyloidosis, and light chain ("myeloma") cast nephropathy, other lesions centered on proximal tubules are much less accurately identified, properly diagnosed, and adequately understood in terms of pathogenesis and molecular mechanisms involved. These proximal tubule-centered lesions are typically associated with monoclonal light chains and have not been reported in patients with circulating monoclonal heavy chains. To determine the incidence of proximal tubulopathies in a series of patients with monoclonal light chain-related renal lesions and characterize them with an emphasis on clinical correlations and elucidation of molecular mechanisms involved in their pathogenesis. A study of 5410 renal biopsies with careful evaluation of light microscopic, immunofluorescence, and electron microscopic findings was conducted to identify these monoclonal light/heavy chain-related lesions. In selected cases, ultrastructural immunolabeling was performed to better illustrate and understand molecular mechanisms involved or to resolve specific diagnostic difficulties. In all, 2.5% of the biopsies were diagnosed as demonstrating renal pathology associated with monoclonal light or heavy chains. Of these, approximately 46% were classified as proximal tubule-centered lesions, also referred to as monoclonal light chain-associated proximal tubulopathies. These proximal tubulopathies were divided into 4 groups defined by characteristic immunomorphologic manifestations associated with specific clinical settings. These are important lesions whose recognition in the different clinical settings is extremely important for patients' clinical management, therapeutic purposes, and prognosis. These entities have been segregated into 4 distinct variants, conceptualized morphologically and clinically. Specific mechanisms involved in their pathogenesis are proposed.

Dynamic Simulation Research on Chain Drive Mechanism of Corn Seeder Based on ADAMS

NASA Astrophysics Data System (ADS)

Wang, Y. B.; Jia, H. P.

2017-12-01

In order to reduce the damage to the chain and improve the seeding quality of the seeding machine, the corn seeder has the characteristics of the seeding quality and some technical indexes in the work of the corn seeding machine. The dynamic analysis of the chain drive mechanism is carried out by using the dynamic virtual prototype. In this paper, the speed of the corn planter is 5km/h, and the speed of the simulated knuckle is 0.1~0.9s. The velocity is 0.12m/s, which is equal to the chain speed when the seeder is running normally. Of the dynamic simulation of the movement and the actual situation is basically consistent with the apparent speed of the drive wheel has changed the acceleration and additional dynamic load, the chain drive has a very serious damage, and the maximum load value of 47.28N, in order to reduce the damage to the chain, As far as possible so that the sowing machine in the work to maintain a reasonable uniform speed, to avoid a greater acceleration, the corn sowing machine drive the design of a certain reference.

The distribution of conformational disorder in the high-temperature phases of the crystalline n-alkanes

NASA Astrophysics Data System (ADS)

Maroncelli, M.; Strauss, H. L.; Snyder, R. G.

1985-03-01

The distributions of conformational defects that exist in the high-temperature phase II (also referred to as the hexagonal or rotator phase) of the crystalline n-alkanes C21 and C29 have been measured by an infrared CD2-substitution technique and have been accounted for in terms of a lattice model that provides freedom for longitudinal displacement of the chains. The defects consist almost entirely of gtg' kinks distributed nonuniformly along the chain. The uneven distribution is indicated in the variation in the concentration of gauche bonds measured at various sites along the chain. The highest concentration is at the chain ends, and the concentrations at interior sites decrease exponentially in going toward the middle. To explain the distribution we used a modification of a lattice model that had been successfully applied to the lipid bilayer. Comparison of observed distributions with those computed from the model indicates that the factors that determine the shape of the distribution are quite different in the n-alkane and bilayer cases. For the bilayer, the dominant factor is the variation in the lateral density of chains; for the n-alkane, the dominant factor is associated with longitudinal displacement of the chains.

Typed Linear Chain Conditional Random Fields and Their Application to Intrusion Detection

NASA Astrophysics Data System (ADS)

Elfers, Carsten; Horstmann, Mirko; Sohr, Karsten; Herzog, Otthein

Intrusion detection in computer networks faces the problem of a large number of both false alarms and unrecognized attacks. To improve the precision of detection, various machine learning techniques have been proposed. However, one critical issue is that the amount of reference data that contains serious intrusions is very sparse. In this paper we present an inference process with linear chain conditional random fields that aims to solve this problem by using domain knowledge about the alerts of different intrusion sensors represented in an ontology.

[Mitochondrial disease due to the deficit of Q-cytochrome C oxidoreductase coenzyme in the respiratory chain. Report of a new case].

PubMed

Roldán, S; Lluch, M D; Navarro Quesada, F J; Hevia, A

1995-01-01

Reference has been made in the literature of the variability in the clinical presentation of deficiency of complex III of the respiratory chain, identifying up to the moment, four groups, the first of which is characterized by hipotonia and wearness starting at variable ages. We report a new case of mitochondrial myopathy due to deficiency of this complex and included within this first group, and consider the importance of defining the clinical and histochemical characteristics of this polymorphous entity.

Optical Frequency Synthesizer for Precision Spectroscopy

NASA Astrophysics Data System (ADS)

Holzwarth, R.; Udem, Th.; Hänsch, T. W.; Knight, J. C.; Wadsworth, W. J.; Russell, P. St. J.

2000-09-01

We have used the frequency comb generated by a femtosecond mode-locked laser and broadened to more than an optical octave in a photonic crystal fiber to realize a frequency chain that links a 10 MHz radio frequency reference phase-coherently in one step to the optical region. By comparison with a similar frequency chain we set an upper limit for the uncertainty of this new approach to 5.1×10-16. This opens the door for measurement and synthesis of virtually any optical frequency and is ready to revolutionize frequency metrology.

Description of polymerase chain reaction and sequencing DNA Mycobacterium tuberculosis from specimen sputum of tuberculosis patients in Medan

NASA Astrophysics Data System (ADS)

Lily; Siregar, Y.; Ilyas, S.

2018-03-01

This study purposed to describe the product Polymerase Chain Reaction (PCR) and sequencing of DNA Mycobacterium (M.) tuberculosis from sputum of tuberculosis (TB) patients in Medan. Sputum was collected from patients that diagnosed with pulmonary TB by a physician. Specimen processed by PCR method of Li et al. and sequencing at Macrogen Laboratory. All of 12 product PCR were showed brightness bands at 126 base pair (bp). These results indicated similarity to the study of Li et al. Sequencing analysis showed the presence of a mutation and non-mutation groups of M. tuberculosis. The reference and outcome berange of the mutation and non-mutation of M. tuberculosis were 56-107, 59-85, 60-120 and 63-94, respectively. The percentage bp difference between the outcome and references for mutation and non-mutation were 3.448-6.569and 3.278-7.428%, respectively. In conclusion, the successful amplification of PCR products in a 1.5% agarose gel electrophoresis where all 12 sputa contained rpoB-positive M. tuberculosis and 0.644% difference was found between the outcome with reference bp of the mutation and non-mutation M. tuberculosis groups.

The Canadian High Arctic Ionospheric Network (CHAIN)

NASA Astrophysics Data System (ADS)

Jayachandran, P. T.; Langley, R. B.; MacDougall, J. W.; Mushini, S. C.; Pokhotelov, D.; Chadwick, R.; Kelly, T.

2009-05-01

Polar cap ionospheric measurements are important for the complete understanding of the various processes in the solar wind - magnetosphere - ionosphere (SW-M-I) system as well as for space weather applications. Currently the polar cap region is lacking high temporal and spatial resolution ionospheric measurements because of the orbit limitations of space-based measurements and the sparse network providing ground- based measurements. Canada has a unique advantage in remedying this shortcoming because it has the most accessible landmass in the high Arctic regions and the Canadian High Arctic Ionospheric Network (CHAIN) is designed to take advantage of Canadian geographic vantage points for a better understanding of the Sun-Earth system. CHAIN is a distributed array of ground-based radio instruments in the Canadian high Arctic. The instruments components of CHAIN are ten high data-rate Global Positioning System ionospheric scintillation and total electron content monitors and six Canadian Advanced Digital Ionosondes. Most of these instruments have been sited within the polar cap region except for two GPS reference stations at lower latitudes. This paper briefly overviews the scientific capabilities, instrument components, and deployment status of CHAIN.

Solubilization of cyclohexane in aqueous solutions of sodium. cap alpha. -alkyl alkanoates

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

Sagitani, H.; Suzuki, T.; Nagai, M.

1982-01-01

The effect of branched alkyl chain length and the position of the COONa group on the solubilizing power of n-alkane sodium carboxylates was studied. The lipophilic property and the amount of solubilized cyclohexane increased with the branched chain length of branched soaps, and with the change of the position of the -COONa group from 3 to 7 in the alkyl chain of pentadecane -3, -5, and -7 sodium carboxylates. Alpha-branched soaps having proper branched alkyl chains were better solubilizers for cyclohexane than straight chain compounds. The amount of cyclohexane solublized by C/sub 10/ H/sub 21/ CH(C/sub 6/H/sub 13/) COONa wasmore » about three times greater than the amount solubilized by C/sub 17/ H/sub 35/ COONa. There was a marked increase in the solubilization of cyclohexane replacing ..cap alpha..-branched fatty acid soaps with optimum amount of cosurfactants such as C/sub 8/H/sub 17/ (OCH/sub 2/CH/sub 2/)/sub 2/OH. Namely, solubilization increased markedly at the optimum hydrophile-lipophile balance of mixed surfactant. 21 references.« less

Preparing Schools for Terrorist Attacks.

ERIC Educational Resources Information Center

School Safety, 1991

1991-01-01

Outlines 21 actions, both immediate and over the long term, that administrators can take to protect students and schools from terrorist activities. Includes establishing a chain of command, a command post, a crisis response team, a communications staff, and inservice training. (four references) (MLF)

LORAN-C data reduction at the US Naval Observatory

NASA Technical Reports Server (NTRS)

Chadsey, Harold

1992-01-01

As part of its mission and in cooperation with the U.S. Coast Guard, the U.S. Naval Observatory (USNO) monitors and reports the timing of the LORAN-C chains. The procedures for monitoring and processing the reported values have evolved with advances in monitoring equipment, computer interfaces and PCs. This paper discusses the current standardized procedures used by USNO to sort the raw data according to Group Repetition Interval (GRI) rate, to fit and smooth the data points, and, for chains remotely monitored, to tie the values to the USNO Master Clock. The results of these procedures are the LORAN time of transmission values, as references to UTC(USNO) (Universal Coordinated Time) for all LORAN chains. This information is available to users via USNO publications and the USNO Automated Data Service (ADS).

Environmental and sustainability ethics in supply chain management.

PubMed

Beamon, Benita M

2005-04-01

Environmentally Conscious Supply Chain Management (ECSCM refers to the control exerted over all immediate and eventual environmental effects of products and processes associated with converting raw materials into final products. While much work has been done in this area, the focus has traditionally been on either: product recovery (recycling, remanufacturing, or re-use) or the product design function only (e.g., design for environment). Environmental considerations in manufacturing are often viewed as separate from traditional, value-added considerations. However, the case can be made that professional engineers have an ethical responsibility to consider the immediate and eventual environmental impacts of products and processes that they design and/or manage. This paper describes ECSCM as a component of engineering ethics, and highlights the major issues associated with ethical decision-making in supply chain management.

Higher-order automatic differentiation of mathematical functions

NASA Astrophysics Data System (ADS)

Charpentier, Isabelle; Dal Cappello, Claude

2015-04-01

Functions of mathematical physics such as the Bessel functions, the Chebyshev polynomials, the Gauss hypergeometric function and so forth, have practical applications in many scientific domains. On the one hand, differentiation formulas provided in reference books apply to real or complex variables. These do not account for the chain rule. On the other hand, based on the chain rule, the automatic differentiation has become a natural tool in numerical modeling. Nevertheless automatic differentiation tools do not deal with the numerous mathematical functions. This paper describes formulas and provides codes for the higher-order automatic differentiation of mathematical functions. The first method is based on Faà di Bruno's formula that generalizes the chain rule. The second one makes use of the second order differential equation they satisfy. Both methods are exemplified with the aforementioned functions.

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

PubMed

Rueda, Oscar M; Diaz-Uriarte, Ramon

2007-10-16

Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nucleotide polymorphism arrays. One of the methods compared is our non-homogenous Hidden Markov Model approach. Our approach uses Markov Chain Monte Carlo for inference, but Yu et al. ran the sampler for a severely insufficient number of iterations for a Markov Chain Monte Carlo-based method. Moreover, they did not use the appropriate reference level for the non-altered state. We rerun the analysis in Yu et al. using appropriate settings for both the Markov Chain Monte Carlo iterations and the reference level. Additionally, to show how easy it is to obtain answers to additional specific questions, we have added a new analysis targeted specifically to the detection of breakpoints. The reanalysis shows that the performance of our method is comparable to that of the other methods analyzed. In addition, we can provide probabilities of a given spot being a breakpoint, something unique among the methods examined. Markov Chain Monte Carlo methods require using a sufficient number of iterations before they can be assumed to yield samples from the distribution of interest. Running our method with too small a number of iterations cannot be representative of its performance. Moreover, our analysis shows how our original approach can be easily adapted to answer specific additional questions (e.g., identify edges).

Detection of Genetically Modified Food: Has Your Food Been Genetically Modified?

ERIC Educational Resources Information Center

Brandner, Diana L.

2002-01-01

Explains the benefits and risks of genetically-modified foods and describes methods for genetically modifying food. Presents a laboratory experiment using a polymerase chain reaction (PCR) test to detect foreign DNA in genetically-modified food. (Contains 18 references.) (YDS)

The Real World and Virtual Worlds.

ERIC Educational Resources Information Center

Glaser, Stan

1997-01-01

Discusses some of the limitations of virtual reality (VR) with reference to socio-technical systems, i.e., the interaction of people with technology. Points to a significant opportunity for VR technology to be used in strategic partnership marketing and supply chain management. (Author/LRW)

Objects of Desire.

ERIC Educational Resources Information Center

Zielinski, Dave

2000-01-01

Describes learning objects, also known as granules, chunks, or information nuggets, and likens them to help screens. Discusses concerns about how they can go wrong: (1) faulty pretest questions; (2) missing links in the learning object chain; (3) poor frames of reference; and (4) lack of customization. (JOW)

L-carnitine and cancer cachexia. I. L-carnitine distribution and metabolic disorders in cancer cachexia.

PubMed

Szefel, Jarosław; Kruszewski, Wiesław Janusz; Ciesielski, Maciej; Szajewski, Mariusz; Kawecki, Krzysztof; Aleksandrowicz-Wrona, Ewa; Jankun, Jerzy; Lysiak-Szydłowska, Wiesława

2012-07-01

Cancer cachexia (CC), a progressive loss of body mass, is associated with decreased energy production. Abnormally low levels of L-carnitine (LC) in skeletal muscle means that mitochondrial β-oxidation of long-chain fatty acids (LCFA) does not occur efficiently in patients with CC. We assessed the influence of CC on LC distribution and the effects of parenteral lipid emulsions on plasma LC levels and urinary excretion. Fifty patients with CC were randomly assigned to total parenteral nutrition (TPN) with long-chain triglycerides (LCTs), or LCTs plus medium-chain triglycerides (MCTs) as 50/50. Patients were further separated into those with body-mass index (BMI) ≤ 19 kg/m(2) and BMI >19 kg/m(2). Plasma concentrations of total LC (TC) and free LC (FC) and their urinary excretion were measured, along with skeletal muscle LC levels. On average, plasma FC and TC were higher than reference values in all patients. Patients with BMI ≤ 19 kg/m(2) had lower plasma FC and TC than those with BMI >19 kg/m(2). Skeletal muscle FC in the BMI ≤ 19 kg/m(2) group was lower than reference value, but within the normal range in others. LC and FC urinary excretion was higher than reference values. Plasma LC and its urinary excretion were higher in patients administered pure LCTs relative to those given MCTs/LCTs. A decrease in skeletal muscle LC in cancer patients with CC (BMI ≤ 19 kg/m(2)) correlates with an increase in its plasma levels and increased renal excretion. A diet of MCTs/LCTs reduces LC release from muscle to plasma and urine more effectively than LCTs.

Quantifying Short-Chain Chlorinated Paraffin Congener Groups.

PubMed

Yuan, Bo; Bogdal, Christian; Berger, Urs; MacLeod, Matthew; Gebbink, Wouter A; Alsberg, Tomas; de Wit, Cynthia A

2017-09-19

Accurate quantification of short-chain chlorinated paraffins (SCCPs) poses an exceptional challenge to analytical chemists. SCCPs are complex mixtures of chlorinated alkanes with variable chain length and chlorination level; congeners with a fixed chain length (n) and number of chlorines (m) are referred to as a "congener group" C n Cl m . Recently, we resolved individual C n Cl m by mathematically deconvolving soft ionization high-resolution mass spectra of SCCP mixtures. Here we extend the method to quantifying C n Cl m by introducing C n Cl m specific response factors (RFs) that are calculated from 17 SCCP chain-length standards with a single carbon chain length and variable chlorination level. The signal pattern of each standard is measured on APCI-QTOF-MS. RFs of each C n Cl m are obtained by pairwise optimization of the normal distribution's fit to the signal patterns of the 17 chain-length standards. The method was verified by quantifying SCCP technical mixtures and spiked environmental samples with accuracies of 82-123% and 76-109%, respectively. The absolute differences between calculated and manufacturer-reported chlorination degrees were -0.9 to 1.0%Cl for SCCP mixtures of 49-71%Cl. The quantification method has been replicated with ECNI magnetic sector MS and ECNI-Q-Orbitrap-MS. C n Cl m concentrations determined with the three instruments were highly correlated (R 2 > 0.90) with each other.

Glycosaminoglycan Chain of Dentin Sialoprotein Proteoglycan

PubMed Central

Zhu, Q.; Sun, Y.; Prasad, M.; Wang, X.; Yamoah, A.K.; Li, Y.; Feng, J.; Qin, C.

2010-01-01

Dentin sialophosphoprotein (DSPP) is processed into dentin sialoprotein (DSP) and dentin phosphoprotein. A molecular variant of rat DSP, referred to as “HMW-DSP”, has been speculated to be a proteoglycan form of DSP. To determine if HMW-DSP is the proteoglycan form of DSP and to identify the glycosaminoglycan side-chain attachment site(s), we further characterized HMW-DSP. Chondroitinase ABC treatment reduced the migration rate for portions of rat HMW-DSP to the level of DSP. Disaccharide analysis showed that rat HMW-DSP contains glycosaminoglycan chains made of chondroitin-4-sulfate and has an average of 31-32 disaccharides/mol. These observations confirmed that HMW-DSP is the proteoglycan form of DSP (renamed “DSP-PG”). Edman degradation and mass spectrometric analyses of tryptic peptides from rat DSP-PG, along with substitution analyses of candidate Ser residues in mouse DSPP, confirmed that 2 glycosaminoglycan chains are attached to Ser241 and Ser253 in the rat, or Ser242 and Ser254 in the mouse DSPP sequence. PMID:20400719

Glycosaminoglycan chain of dentin sialoprotein proteoglycan.

PubMed

Zhu, Q; Sun, Y; Prasad, M; Wang, X; Yamoah, A K; Li, Y; Feng, J; Qin, C

2010-08-01

Dentin sialophosphoprotein (DSPP) is processed into dentin sialoprotein (DSP) and dentin phosphoprotein. A molecular variant of rat DSP, referred to as "HMW-DSP", has been speculated to be a proteoglycan form of DSP. To determine if HMW-DSP is the proteoglycan form of DSP and to identify the glycosaminoglycan side-chain attachment site(s), we further characterized HMW-DSP. Chondroitinase ABC treatment reduced the migration rate for portions of rat HMW-DSP to the level of DSP. Disaccharide analysis showed that rat HMW-DSP contains glycosaminoglycan chains made of chondroitin-4-sulfate and has an average of 31-32 disaccharides/mol. These observations confirmed that HMW-DSP is the proteoglycan form of DSP (renamed "DSP-PG"). Edman degradation and mass spectrometric analyses of tryptic peptides from rat DSP-PG, along with substitution analyses of candidate Ser residues in mouse DSPP, confirmed that 2 glycosaminoglycan chains are attached to Ser(241) and Ser(253) in the rat, or Ser(242) and Ser(254) in the mouse DSPP sequence.

Analysis of Business Process at PT XYZ by Using SCOR Thread Diagram

NASA Astrophysics Data System (ADS)

Sembiring, M. T.; Rambe, H. C.

2017-03-01

Supply Chain Operations Reference (SCOR) is a standard supply chain performance evaluation model which is proposed by Supply Chain Council (SCC). SCOR makes companies can analyse and evaluate their supply chain performance. SCOR has Thread Diagram which describes business process simply and systematically to help the analysis of company’s business process. This research takes place in PT XYZ that is involved in Crude Palm Oil (CPO) industry. PT XYZ used to be the market leader of CPO industry but nowadays they have a trouble to compete with new competitors. The purpose of this study is to provide the input for PT XYZ business process improvement to enhance the competitiveness of the company with the others. The result obtained shows that there are two performance metrics that are not reached. The analysis of business process shows the lack of control role of PT XYZ to supplier and customer side which is going to be the suggestion of improvement.

Waste biomass toward hydrogen fuel supply chain management for electricity: Malaysia perspective

NASA Astrophysics Data System (ADS)

Zakaria, Izatul Husna; Ibrahim, Jafni Azhan; Othman, Abdul Aziz

2016-08-01

Green energy is becoming an important aspect of every country in the world toward energy security by reducing dependence on fossil fuel import and enhancing better life quality by living in the healthy environment. This conceptual paper is an approach toward determining physical flow's characteristic of waste wood biomass in high scale plantation toward producing gas fuel for electricity using gasification technique. The scope of this study is supply chain management of syngas fuel from wood waste biomass using direct gasification conversion technology. Literature review on energy security, Malaysia's energy mix, Biomass SCM and technology. This paper uses the theoretical framework of a model of transportation (Lumsden, 2006) and the function of the terminal (Hulten, 1997) for research purpose. To incorporate biomass unique properties, Biomass Element Life Cycle Analysis (BELCA) which is a novel technique develop to understand the behaviour of biomass supply. Theoretical framework used to answer the research questions are Supply Chain Operations Reference (SCOR) framework and Sustainable strategy development in supply chain management framework

Cloud Computing Value Chains: Understanding Businesses and Value Creation in the Cloud

NASA Astrophysics Data System (ADS)

Mohammed, Ashraf Bany; Altmann, Jörn; Hwang, Junseok

Based on the promising developments in Cloud Computing technologies in recent years, commercial computing resource services (e.g. Amazon EC2) or software-as-a-service offerings (e.g. Salesforce. com) came into existence. However, the relatively weak business exploitation, participation, and adoption of other Cloud Computing services remain the main challenges. The vague value structures seem to be hindering business adoption and the creation of sustainable business models around its technology. Using an extensive analyze of existing Cloud business models, Cloud services, stakeholder relations, market configurations and value structures, this Chapter develops a reference model for value chains in the Cloud. Although this model is theoretically based on porter's value chain theory, the proposed Cloud value chain model is upgraded to fit the diversity of business service scenarios in the Cloud computing markets. Using this model, different service scenarios are explained. Our findings suggest new services, business opportunities, and policy practices for realizing more adoption and value creation paths in the Cloud.

Biological and surface-active properties of double-chain cationic amino acid-based surfactants.

PubMed

Greber, Katarzyna E; Dawgul, Małgorzata; Kamysz, Wojciech; Sawicki, Wiesław; Łukasiak, Jerzy

2014-08-01

Cationic amino acid-based surfactants were synthesized via solid phase peptide synthesis and terminal acylation of their α and ε positions with saturated fatty acids. Five new lipopeptides, N-α-acyl-N-ε-acyl lysine analogues, were obtained. Minimum inhibitory concentration and minimum bactericidal (fungicidal) concentration were determined on reference strains of bacteria and fungi to evaluate the antimicrobial activity of the lipopeptides. Toxicity to eukaryotic cells was examined via determination of the haemolytic activities. The surface-active properties of these compounds were evaluated by measuring the surface tension and formation of micelles as a function of concentration in aqueous solution. The cationic surfactants demonstrated diverse antibacterial activities dependent on the length of the fatty acid chain. Gram-negative bacteria and fungi showed a higher resistance than Gram-positive bacterial strains. It was found that the haemolytic activities were also chain length-dependent values. The surface-active properties showed a linear correlation between the alkyl chain length and the critical micelle concentration.

Children's Books in Translation: Facts and Beliefs

ERIC Educational Resources Information Center

Orvig, Mary

1972-01-01

The distribution channels of children's books and the part played by translations within children's literature of different countries are neglected fields of research. Translation is the strongest link in an international chain which is constantly in need of amplification and reinforcement. (34 references) (Author/NH)

3D Printing: How Much Will It Improve the DoD Supply Chain of the Future

DTIC Science & Technology

2014-06-01

Defense AT&L: May–June 2014 6 3D Printing How Much Will It Improve the DoD Supply Chain of the Future? Robin Brown Jim Davis Mark Dobson...so? DoD Enters the 3D Printing Arena First let’s set the stage by defining 3D printing . To put it sim- ply, 3D printing is a manufacturing process in...where the object is built up from scratch, which is why 3D printing is also referred to as “additive manufacturing.” This process is the opposite of the

Stratus Ocean Reference Station (20 deg S, 85 deg W) Mooring Recovery and Deployment Cruise, R/V Ronald H. Brown Cruise 06-07, October 9-October 27, 2006

DTIC Science & Technology

2007-02-01

SUNWAVE as a viable alternative to organotin, copper , and other more toxic coatings. The Table III.D.3 below shows methods used for coating the buoy hull...trasdu 1.8 m (2 each) Tsunameter S almm chain (3.5 m) Swivel ss , u-d ct, of-aoic 25 mm nylon G.l as ball acoustic flotation teiemetry 1 22 mm nylon...e - Size(s) Manufacturer .... .......... Chain ,Wire Rope- Hardware Flotation Type (G.8.s, Spheres,_etc) Si ze Quantijty Color No. of Flotation

To what extent are microplastics from the open ocean weathered?

PubMed

Ter Halle, Alexandra; Ladirat, Lucie; Martignac, Marion; Mingotaud, Anne Françoise; Boyron, Olivier; Perez, Emile

2017-08-01

It is necessary to better characterize plastic marine debris in order to understand its fate in the environment and interaction with organisms, the most common type of debris being made of polyethylene (PE) and polypropylene (PP). In this work, plastic debris was collected in the North Atlantic sub-tropical gyre during the Expedition 7th Continent sea campaign and consisted mainly in PE. While the mechanisms of PE photodegradation and biodegradation in controlled laboratory conditions are well known, plastic weathering in the environment is not well understood. This is a difficult task to examine because debris comes from a variety of manufactured objects, the original compositions and properties of which vary considerably. A statistical approach was therefore used to compare four sample sets: reference PE, manufactured objects, mesoplastics (5-20 mm) and microplastics (0.3-5 mm). Infrared spectroscopy showed that the surface of all debris presented a higher oxidation state than the reference samples. Differential scanning calorimetry analysis revealed that the microplastics were more crystalline contrarily to the mesoplastics which were similar to references samples. Size exclusion chromatography showed that the molar mass decreased from the references to meso- and microplastics, revealing a clear degradation of the polymer chains. It was thus concluded that the morphology of marine microplastic was much altered and that an unambiguous shortening of the polymer chains took place even for this supposedly robust and inert polymer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of real-time PCR method for the detection and the quantification of a new endogenous reference gene in sugar beet "Beta vulgaris L.": GMO application.

PubMed

Chaouachi, Maher; Alaya, Akram; Ali, Imen Ben Haj; Hafsa, Ahmed Ben; Nabi, Nesrine; Bérard, Aurélie; Romaniuk, Marcel; Skhiri, Fethia; Saïd, Khaled

2013-01-01

KEY MESSAGE : Here, we describe a new developed quantitative real-time PCR method for the detection and quantification of a new specific endogenous reference gene used in GMO analysis. The key requirement of this study was the identification of a new reference gene used for the differentiation of the four genomic sections of the sugar beet (Beta vulgaris L.) (Beta, Corrollinae, Nanae and Procumbentes) suitable for quantification of genetically modified sugar beet. A specific qualitative polymerase chain reaction (PCR) assay was designed to detect the sugar beet amplifying a region of the adenylate transporter (ant) gene only from the species of the genomic section I of the genus Beta (cultivated and wild relatives) and showing negative PCR results for 7 species of the 3 other sections, 8 related species and 20 non-sugar beet plants. The sensitivity of the assay was 15 haploid genome copies (HGC). A quantitative real-time polymerase chain reaction (QRT-PCR) assay was also performed, having high linearity (R (2) > 0.994) over sugar beet standard concentrations ranging from 20,000 to 10 HGC of the sugar beet DNA per PCR. The QRT-PCR assay described in this study was specific and more sensitive for sugar beet quantification compared to the validated test previously reported in the European Reference Laboratory. This assay is suitable for GMO quantification in routine analysis from a wide variety of matrices.

[Detection of large deletions in X linked Alport syndrome using competitive multiplex fluorescence polymerase chain reaction].

PubMed

Wang, F; Zhang, Y Q; Ding, J; Yu, L X

2017-10-18

To evaluate the ability of multiplex competitive fluorescence polymerase chain reaction in detection of large deletion and duplication genotypes of X-linked Alport syndrome. Clinical diagnosis of X-linked Alport syndrome was based on either abnormal staining of type IV collagen α5 chain in the epidermal basement membrane alone or with abnormal staining of type IV collagen α5 chain in the glomerular basement membrane and Bowman's capsule/ultrastructural changes in the glomerular basement membrane typical of Alport syndrome. A total of 20 unrelated Chinese patients (13 males and 7 females) clinically diagnosed as X-linked Alport syndrome were included in the study. Their genotypes were unknown. Control subjects included a male patient with other renal disease and two patients who had large deletions in COL4A5 gene detected by multiplex ligation-dependent probe amplification. Genomic DNA was isolated from peripheral blood leukocytes in all the participants. Multiplex competitive fluorescence polymerase chain reaction was used to coamplify 53 exons of COL4A5 gene and four reference genes in a single reaction. When a deletion removed exon 1 of COL4A5 gene was identified, the same method was used to coamplify the first 4 exons of COL4A5 and COL4A6 genes, a promoter shared by COL4A5 and COL4A6 genes, and three reference genes in a single reaction. Any copy number loss suggested by this method was verified by electrophoresis of corresponding polymerase chain reaction amplified products or DNA sequencing to exclude possible DNA variations in the primer regions. Genotypes of two positive controls identified by multiplex competitive fluorescence polymerase chain reaction were consistent with those detected by multiplex ligation-dependent probe amplification. Deletions were identified in 6 of the 20 patients, including two large deletions removing the 5' part of both COL4A5 and COL4A6 genes with the breakpoint located in the second intron of COL4A6, two large deletions removing more than 30 exons of COL4A5 gene, one large deletion removing at least 1 exon of COL4A5 gene, and one small deletion involving 13 bps. No duplication was found. Our results show that multiplex competitive fluorescence polymerase chain reaction is a good alternative to classical techniques for large deletion genotyping in X-linked Alport syndrome.

Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

PubMed Central

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

2011-01-01

One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0.8 – 1.5 Å from the reference structures determined by traditional NMR approaches. PMID:21706248

Entanglement Length in Miscible Blends of cis-Polyisoprene and Poly(ptert-butylstyrene)

NASA Astrophysics Data System (ADS)

Watanabe, Hiroshi; Matsumiya, Yumi

In miscible polymer blends, the entanglement length is common for the components, but its changes with the composition w remain unclear. For this problem, this study analyzed viscoelastic data for miscible blends of cis-polyisoprene (PI) and poly(ptert-butylstyrene) (PtBS), considering the basic feature that the local relaxation is determined only by wPI. On the basis of this feature, a series of unentangled low- M PI/PtBS blends having various M and a given wPI were utilized as references for well-entangled high- M PI/PtBS blends having the same wPI, and the modulus data of the references were subtracted from the high- M blend data. For an optimally chosen reference, the storage modulus Ge'of the high- M blends obtained after the subtraction exhibited a clear entanglement plateau GN and the corresponding Ge' ' decreased in proportion to 1/ ω at high frequencies ω. Thus, the onset of entanglement relaxation was detected. The GN values were well described by a linear mixing rule of the entanglement length with the number fraction of Kuhn segments of the components being utilized as the averaging weight. This result, not explained by a mean-field picture of entanglement, is discussed in relation to local packing of bulky PtBS chains and skinny PI chains.

Beyond the double banana: improved recognition of temporal lobe seizures in long-term EEG.

PubMed

Rosenzweig, Ivana; Fogarasi, András; Johnsen, Birger; Alving, Jørgen; Fabricius, Martin Ejler; Scherg, Michael; Neufeld, Miri Y; Pressler, Ronit; Kjaer, Troels W; van Emde Boas, Walter; Beniczky, Sándor

2014-02-01

To investigate whether extending the 10-20 array with 6 electrodes in the inferior temporal chain and constructing computed montages increases the diagnostic value of ictal EEG activity originating in the temporal lobe. In addition, the accuracy of computer-assisted spectral source analysis was investigated. Forty EEG samples were reviewed by 7 EEG experts in various montages (longitudinal and transversal bipolar, common average, source derivation, source montage, current source density, and reference-free montages) using 2 electrode arrays (10-20 and the extended one). Spectral source analysis used source montage to calculate density spectral array, defining the earliest oscillatory onset. From this, phase maps were calculated for localization. The reference standard was the decision of the multidisciplinary epilepsy surgery team on the seizure onset zone. Clinical performance was compared with the double banana (longitudinal bipolar montage, 10-20 array). Adding the inferior temporal electrode chain, computed montages (reference free, common average, and source derivation), and voltage maps significantly increased the sensitivity. Phase maps had the highest sensitivity and identified ictal activity at earlier time-point than visual inspection. There was no significant difference concerning specificity. The findings advocate for the use of these digital EEG technology-derived analysis methods in clinical practice.

Extraction and determination of chondroitin sulfate from fish processing byproducts

USDA-ARS?s Scientific Manuscript database

Chondroitin sulfate (CS) refers to a group of sulfated glycosaminoglycan containing a chain of alternating N-acetylgalactosamine and glucuronic acid sugars. It is a major component of the extracellular matrix of cartilage and attached to proteins. CS is usually an over the counter dietary supplement...

The accelerator facility of the Heidelberg Ion-Beam Therapy Centre (HIT)

NASA Astrophysics Data System (ADS)

Peters, Andreas

The following sections are included: * Introduction * Beam parameters * General layout of the HIT facility * The accelerator chain in detail * Operational aspects of a particle therapy facility * 24/7 accelerator operation at 335 days per year * Safety and regulatory aspects * Status and perspectives * References

Air Force Commodity Councils: A Template for Future Implementation Comparing Successful and Failed Approaches

DTIC Science & Technology

2007-12-01

Northwest QantasLink 67 References Mankiw , N. Gregory, Essentials of Economics , Chapter 13 Weinstein, David E; Yafeh...Purchasing, Transaction Cost Analysis, Transaction Cost Economics , Air Force, Supply Chain Management, Procurement, Transformation 16. PRICE CODE 17...SOURCING .............................................................................7 C. TRANSACTION COST ECONOMICS

Alternative Fuels Data Center

Science.gov Websites

% alcohol, natural gas, propane, coal-derived liquid fuels, hydrogen, electricity, pure biodiesel, renewable . Biodiesel is defined as mono-alkyl esters of long chain fatty acids derived from vegetable oils or animal fats that meets current ASTM biodiesel standards. (Reference Wyoming Statutes 39-17-301

EMI Array for Cued UXO Discrimination

DTIC Science & Technology

2011-02-07

that comprise a chain of former volcanoes extending from the southwest portion of the site to the coast. Due to its proximity to the tectonic ...interaction of the North American and Pacific crustal plates, the area is seismically active. Additional details are available in Reference 11. 4.2.3

Frankfurt Medical Department Activity (FMEDDAC) OB/GYN Clinic Study

DTIC Science & Technology

1993-08-01

ideas took hold and flourished in post-World War II Japan ( Arikan , 1990). The Japanese institutionalized the following chain FMEDDAC OB-GYN 8 reaction...be required for most organizations. FMEDDAC OB-GYN 69 References Arikan , V.L. (1991). Total quality management - Applications to nursing service

Lineage-restricted retention of a primitive immunoglobulin heavy chain isotype within the Dipnoi reveals an evolutionary paradox

PubMed Central

Ota, Tatsuya; Rast, Jonathan P.; Litman, Gary W.; Amemiya, Chris T.

2003-01-01

The lineage leading to lungfishes is one of the few major jawed vertebrate groups in which Ig heavy chain isotype structure has not been investigated at the genetic level. In this study, we have characterized three different Ig heavy chain isotypes of the African lungfish, Protopterus aethiopicus, including an IgM-type heavy chain and short and long forms of non-IgM heavy chains. Northern blot analysis as well as patterns of VH utilization suggest that the IgM and non-IgM isotypes are likely encoded in separate loci. The two non-IgM isotypes identified in Protopterus share structural features with the short and long forms of IgX/W/NARC (referred to hereafter as IgW), which were previously considered to be restricted to the cartilaginous fish. It seems that the IgW isotype has a far broader phylogenetic distribution than considered originally and raises questions with regard to the origin and evolutionary divergence of IgM and IgW. Moreover, its absence in other gnathostome lineages implies paradoxically that the IgW-type genes were lost from teleost and tetrapod lineages. PMID:12606718

Reference intervals and diagnostic ranges for serum free κ and free λ immunoglobulin light chains vary by instrument platform: Implications for classification of patient results in a multi-center study.

PubMed

Cotten, Steven W; Shajani-Yi, Zahra; Cervinski, Mark A; Voorhees, Timothy; Tuchman, Sascha A; Korpi-Steiner, Nichole

2018-06-06

Serum free light chain (FLC) immunoglobulins are key biomarkers that aid in the diagnosis, prognosis and assessment of treatment response in patients with plasma cell disorders (PCD). Here we investigated the transference of manufacturer's reported κFLC, λFLC and κ to λ FLC reference intervals (RI) and established de novo FLC RI and diagnostic ranges on four instruments at three academic medical centers. In addition, we also compared the classification of patient FLC results using manufacturer's versus established RIs and diagnostic ranges. CLSI EP28-A3C protocol was applied to investigate transference and establishment of FLC reference intervals on the cobas (Roche), Immage (Beckman), Optilite and SPA Plus (Binding Site). Serum κ FLC and λ FLC were measured in reference sera (N = 126) with estimation of central 95% RIs and FLC ratio diagnostic range (total range). Frequencies (%) in patient FLC results (N > 380 per institution) classified above, below or within manufacturer's versus established FLC RI were compared. Three of four instrument platforms did not exhibit acceptable transference of manufacturer's reported κFLC RI. The manufacturer's reported FLC total diagnostic range did not encompass all values observed in reference sera for any of the four platforms evaluated. Established FLC ratio diagnostic ranges reduced the frequency of patient results classified above range for three of four platforms evaluated. Transference of manufacturer's reported FLC RIs may be inappropriate for select instrument platforms. De novo establishment of FLC RIs specific to instrument platform is highly recommended in order to assure correct patient result classification. Copyright © 2017. Published by Elsevier Inc.

Phase locking of a 2.7 THz quantum cascade laser to a microwave reference.

PubMed

Khosropanah, P; Baryshev, A; Zhang, W; Jellema, W; Hovenier, J N; Gao, J R; Klapwijk, T M; Paveliev, D G; Williams, B S; Kumar, S; Hu, Q; Reno, J L; Klein, B; Hesler, J L

2009-10-01

We demonstrate the phase locking of a 2.7 THz metal-metal waveguide quantum cascade laser (QCL) to an external microwave signal. The reference is the 15th harmonic, generated by a semiconductor superlattice nonlinear device, of a signal at 182 GHz, which itself is generated by a multiplier chain (x12) from a microwave synthesizer at approximately 15 GHz. Both laser and reference radiations are coupled into a bolometer mixer, resulting in a beat signal, which is fed into a phase-lock loop. The spectral analysis of the beat signal confirms that the QCL is phase locked. This result opens the possibility to extend heterodyne interferometers into the far-infrared range.

Phase Locking of a 2.7 THz Quantum Cascade Laser to a Microwave Reference

NASA Technical Reports Server (NTRS)

Khosropanah, P.; Baryshev, A.; Zhang, W.; Jellema, W.; Hovenier, J. N.; Gao, J. R.; Klapwijk, T. M.; Paveliev, D. G.; Williams, B. S.; Hu, Q.;

Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS)☟

PubMed Central

Xin, Dongyue; Ko, Eunhwa; Perez, Lisa M.; Ioerger, Thomas R.; Burgess, Kevin

2013-01-01

Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, “minimalist helical mimics”. It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i+4, i+7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i+3, i+7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds;(iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain “triads” in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the “side-chain correspondences” (eg i, i+4, i+7 or i, i+3, i+4) of those overlays, and the energy of this state relative to the minimum located. This protocol was tested on some of the most widely cited minimalist α-helical mimics (1 – 8 in the text). The data obtained indicates several of these compounds preferentially exist in conformations that resemble other secondary structures as well as α-helices, and many of the α-helical conformations have unexpected side-chain correspondences. These observations imply the featured minimalist mimics have more scope for disrupting PPI interfaces than previously anticipated. Finally, the same simulation method was used to match preferred conformations of minimalist mimics with actual protein/peptide structures at interfaces providing quantitative comparisons of predicted fits of the test mimics at protein-protein interaction sites. PMID:24121516

Evaluating minimalist mimics by exploring key orientations on secondary structures (EKOS).

PubMed

Xin, Dongyue; Ko, Eunhwa; Perez, Lisa M; Ioerger, Thomas R; Burgess, Kevin

2013-11-28

Peptide mimics that display amino acid side-chains on semi-rigid scaffolds (not peptide polyamides) can be referred to as minimalist mimics. Accessible conformations of these scaffolds may overlay with secondary structures giving, for example, "minimalist helical mimics". It is difficult for researchers who want to apply minimalist mimics to decide which one to use because there is no widely accepted protocol for calibrating how closely these compounds mimic secondary structures. Moreover, it is also difficult for potential practitioners to evaluate which ideal minimalist helical mimics are preferred for a particular set of side-chains. For instance, what mimic presents i, i + 4, i + 7 side-chains in orientations that best resemble an ideal α-helix, and is a different mimic required for a i, i + 3, i + 7 helical combination? This article describes a protocol for fitting each member of an array of accessible scaffold conformations on secondary structures. The protocol involves: (i) use quenched molecular dynamics (QMD) to generate an ensemble consisting of hundreds of accessible, low energy conformers of the mimics; (ii) representation of each of these as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; (iii) similar representation of each combination of three side-chains in each ideal secondary structure as a set of Cα and Cβ coordinates corresponding to three amino acid side-chains displayed by the scaffolds; and, (iv) overlay Cα and Cβ coordinates of all the conformers on all the sets of side-chain "triads" in the ideal secondary structures and express the goodness of fit in terms of root mean squared deviation (RMSD, Å) for each overlay. We refer to this process as Exploring Key Orientations on Secondary structures (EKOS). Application of this procedure reveals the relative bias of a scaffold to overlay on different secondary structures, the "side-chain correspondences" (e.g. i, i + 4, i + 7 or i, i + 3, i + 4) of those overlays, and the energy of this state relative to the minimum located. This protocol was tested on some of the most widely cited minimalist α-helical mimics (1-8 in the text). The data obtained indicates several of these compounds preferentially exist in conformations that resemble other secondary structures as well as α-helices, and many of the α-helical conformations have unexpected side-chain correspondences. These observations imply the featured minimalist mimics have more scope for disrupting PPI interfaces than previously anticipated. Finally, the same simulation method was used to match preferred conformations of minimalist mimics with actual protein/peptide structures at interfaces providing quantitative comparisons of predicted fits of the test mimics at protein-protein interaction sites.

Identification of reference genes for RT-qPCR analysis in peach genotypes with contrasting chilling requirements.

PubMed

Marini, N; Bevilacqua, C B; Büttow, M V; Raseira, M C B; Bonow, S

2017-05-25

Selecting and validating reference genes are the first steps in studying gene expression by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). The present study aimed to evaluate the stability of five reference genes for the purpose of normalization when studying gene expression in various cultivars of Prunus persica with different chilling requirements. Flower bud tissues of nine peach genotypes from Embrapa's peach breeding program with different chilling requirements were used, and five candidate reference genes based on the RT-qPCR that were useful for studying the relative quantitative gene expression and stability were evaluated using geNorm, NormFinder, and bestKeeper software packages. The results indicated that among the genes tested, the most stable genes to be used as reference genes are Act and UBQ10. This study is the first survey of the stability of reference genes in peaches under chilling stress and provides guidelines for more accurate RT-qPCR results.

Emergency management logistics must become emergency supply chain management.

PubMed

Young, Richard R; Peterson, Matthew R

2014-01-01

Much has been written about how emergency management (EM) needs to look to the future regarding issues of resource management (monetary, human, and material). Constraints on budgets are ongoing and the staffing of emergency response activities is often difficult because volunteers have little to no training. The management of material resources has also been a challenge because 1) the categories of material vary by the type of emergency, 2) the necessary quantities of material are often not located near the ultimate point of need, and 3) the transportation assets are rarely available in the form and quantity required to allow timely and effective response. The logistics and resource management functions of EM (what we refer to as EM logistics) have been largely reactive, with little to no pre-event planning for potential demand. We applied the Supply Chain Operational Reference (SCOR) model to EM logistics in an effort to transform it to an integrated and scalable system of physical, information, and financial flows into which are woven the functions of sourcing, making, delivering, and returning, with an overarching planning function that transcends the organizational boundaries of participants. The result is emergency supply chain management, which embraces many more participants who share in a larger quantity of more useful information about the resources that need to be deployed when responding to and recovering from emergency events.

Event-Driven Process Chains (EPC)

NASA Astrophysics Data System (ADS)

Mendling, Jan

This chapter provides a comprehensive overview of Event-driven Process Chains (EPCs) and introduces a novel definition of EPC semantics. EPCs became popular in the 1990s as a conceptual business process modeling language in the context of reference modeling. Reference modeling refers to the documentation of generic business operations in a model such as service processes in the telecommunications sector, for example. It is claimed that reference models can be reused and adapted as best-practice recommendations in individual companies (see [230, 168, 229, 131, 400, 401, 446, 127, 362, 126]). The roots of reference modeling can be traced back to the Kölner Integrationsmodell (KIM) [146, 147] that was developed in the 1960s and 1970s. In the 1990s, the Institute of Information Systems (IWi) in Saarbrücken worked on a project with SAP to define a suitable business process modeling language to document the processes of the SAP R/3 enterprise resource planning system. There were two results from this joint effort: the definition of EPCs [210] and the documentation of the SAP system in the SAP Reference Model (see [92, 211]). The extensive database of this reference model contains almost 10,000 sub-models: 604 of them non-trivial EPC business process models. The SAP Reference model had a huge impact with several researchers referring to it in their publications (see [473, 235, 127, 362, 281, 427, 415]) as well as motivating the creation of EPC reference models in further domains including computer integrated manufacturing [377, 379], logistics [229] or retail [52]. The wide-spread application of EPCs in business process modeling theory and practice is supported by their coverage in seminal text books for business process management and information systems in general (see [378, 380, 49, 384, 167, 240]). EPCs are frequently used in practice due to a high user acceptance [376] and extensive tool support. Some examples of tools that support EPCs are ARIS Toolset by IDS Scheer AG, AENEIS by ATOSS Software AG, ADONIS by BOC GmbH, Visio by Microsoft Corp., Nautilus by Gedilan Consulting GmbH, and Bonapart by Pikos GmbH. In order to facilitate the interchange of EPC business process models between these tools, there is a tool neutral interchange format called EPC Markup Language (EPML) [283, 285, 286, 287, 289, 290, 291].

Global stocks of selected mineral-based commodities

USGS Publications Warehouse

Wilburn, David R.; Bleiwas, Donald I.; Karl, Nick A.

2016-12-05

IntroductionThe U.S. Geological Survey, National Minerals Information Center, analyzes mineral and metal supply chains by identifying and describing major components of mineral and material flows from ore extraction, through intermediate forms, to a final product. This report focuses on an important component of the world’s supply chain: the amounts and global distribution of major consumer, producer, and exchange stocks of selected mineral commodities. In this report, the term “stock” is used instead of “inventory” and refers to accumulations of mined ore, intermediate products, and refined mineral-based commodities that are in a form that meets the agreed-upon specifications of a buyer or processor of intermediate products. These may include certain ores such as bauxite, concentrates, smelter products, and refined metals. Materials sometimes referred to as inventory for accounting purposes, such as ore contained in a deposit or in a leach pile, or materials that need to be further processed before they can be shipped to a consumer, are not considered. Stocks may be held (owned) by consumers, governments, investors, producers, and traders. They may serve as (1) a means to achieve economic, social, and strategic goals through government policies; (2) a secure source of supply to meet demand and to mitigate potential shortages in the supply chain; (3) a hedge to mitigate price volatility; and (4) vehicles for speculative investment.The paucity and uneven reliability of data for stocks of ores and concentrates and for material held by producers, consumers, and merchants hinder the accurate estimating of the size and distribution of this portion of the supply chain for certain commodities. This paper reviews the more visible stocks held in commodity exchange warehouses distributed throughout the world.

Genomic DNA-based absolute quantification of gene expression in Vitis

USDA-ARS?s Scientific Manuscript database

Many studies in which gene expression is quantified by polymerase chain reaction represent the expression of a gene of interest (GOI) relative to that of a reference gene (RG). Relative expression is founded on the assumptions that RG expression is stable across samples, treatments, organs, etc., an...

Development and Preliminary Evaluation of a Positive Health Scale

ERIC Educational Resources Information Center

Becker, Craig; Dolbier, Christyn L.; Durham, Thomas W.; Glascoff, Mary A.; Adams, Troy B.

2008-01-01

Background: Health educators have long advocated health promotion, yet their health measurement techniques have a pathogenic focus. Pathogenesis refers to the origin of a disease and the chain of events (precursors) leading to that disease. Traditional health measurement tools with this focus therefore measure health by assessing for the absence…

Stateline: Critical Mass

ERIC Educational Resources Information Center

Christie, Kathy

2005-01-01

In Physics "critical mass" refers to the minimum amount of fissionable material required to sustain a chain reaction. The adoption of state education policy isn't often equated with this concept, but occasionally solutions and ideas seem to gather around a common problem. If the solution at hand is simple, easily understood, and…

Introducing an M-Commerce Course into the Business Management Curriculum: Experiences and Recommendations

ERIC Educational Resources Information Center

Nandi, Santosh; Nandi, Madhavi L.

2015-01-01

Mobility has become an important extension to the business strategies of present-day organizations. Thus, organizations are increasingly seeking managers with knowledge of value chain related to mobile-oriented business activities, usually referred to as mobile commerce (m-commerce). Accordingly, business management schools are interesting in…

Effect of platform, reference material, and quantification model on enumeration of Enterococcus by quantitative PCR methods

EPA Science Inventory

Quantitative polymerase chain reaction (qPCR) is increasingly being used for the quantitative detection of fecal indicator bacteria in beach water. QPCR allows for same-day health warnings, and its application is being considered as an optionn for recreational water quality testi...

The Separation and Identification of Straight Chain Hydrocarbons: An Experiment Using Gas-Liquid Chromatography.

ERIC Educational Resources Information Center

Benson, G. A.

1982-01-01

An experiment using gas-liquid chromatography is discussed, introducing the student to concept of dead volume and its measurement, idea and use of an internal reference compound, and to linear relationship existing between measurements of a separation on two different stationary phases. (Author/SK)

Drug Supply Chain Security Act

THOMAS, 113th Congress

Sen. Bennet, Michael F. [D-CO

2013-05-15

Senate - 05/15/2013 Read twice and referred to the Committee on Health, Education, Labor, and Pensions. (All Actions) Notes: For further action, see H.R.3204, which became Public Law 113-54 on 11/27/2013. Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model.

PubMed

Tomar, Dheeraj S; Weber, Valéry; Pettitt, B Montgomery; Asthagiri, D

2014-04-17

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute-solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration and the conflation of background contributions with energetics attributed to the side chain limit the ability of a single scaling factor, such as the fractional solvent exposure of the group in the protein, to map the component energetic contributions of the model-compound data to their value in the protein. But ignoring the origin of cancellations in the underlying components the group-transfer model may appear to provide a reasonable estimate of the free energy for a given error tolerance.

Gene Expression Profile Analysis is Directly Affected by the Selected Reference Gene: The Case of Leaf-Cutting Atta Sexdens

PubMed Central

Máximo, Wesley P. F.; Zanetti, Ronald; Paiva, Luciano V.

2018-01-01

Although several ant species are important targets for the development of molecular control strategies, only a few studies focus on identifying and validating reference genes for quantitative reverse transcription polymerase chain reaction (RT-qPCR) data normalization. We provide here an extensive study to identify and validate suitable reference genes for gene expression analysis in the ant Atta sexdens, a threatening agricultural pest in South America. The optimal number of reference genes varies according to each sample and the result generated by RefFinder differed about which is the most suitable reference gene. Results suggest that the RPS16, NADH and SDHB genes were the best reference genes in the sample pool according to stability values. The SNF7 gene expression pattern was stable in all evaluated sample set. In contrast, when using less stable reference genes for normalization a large variability in SNF7 gene expression was recorded. There is no universal reference gene suitable for all conditions under analysis, since these genes can also participate in different cellular functions, thus requiring a systematic validation of possible reference genes for each specific condition. The choice of reference genes on SNF7 gene normalization confirmed that unstable reference genes might drastically change the expression profile analysis of target candidate genes. PMID:29419794

Lean production in improving supply chain performance through hybrid model SCOR 11.0 - system dynamics

NASA Astrophysics Data System (ADS)

Saleh, Chairul; Fatcha Mubiena, Ghaida; Immawan, Taufiq; Hassan, Azmi

2016-02-01

Supply Chain Operation Reference (SCOR) is a method to measure supply chain serving the business process framework, performance indicators and unique technologies to support communication and collaboration among supply chain partners. The objective of this paper is to measure Supply Chain Management performance by using SCOR version 11.0 for production typology of MTS-MTO in Indonesian Batik Industry. This research combines SCOR's model and System Dynamics in order to predict the complex activities on batik industry. The hybrid SCOR-SD could identify the interaction among five attributes with the associated variables simultaneously. The results are obtained after the performance of lean production application is increased and the targets are achieved, even exceeding the target. For reliability attributes that associated with perfect order fulfilment started from 2015 to 2019 respectively are calculated as 80.06%, 103.53%, 105.58%, 93.76%, and 72.17%. Responsiveness attributes associated with the order fulfilment cycle time, respectively 122.45%, 149.10%, 159.26%, 131.53%, and 119.36%. Attributes associated with the total cost of service charge respectively 93.46%, 93.53%, 93.45%, 93.49, and 93.49%. Attributes associated with cash management assets to cash cycle time in a row were 160%, 153%, 146.3%, 150%, and 126.7%. The latter attribute is agility attributes associated with supply chain flexibility upside respectively 100%, 87.2%, 100%, 82%, and 82%.

Retail sector distribution chains for malaria treatment in the developing world: a review of the literature.

PubMed

Patouillard, Edith; Hanson, Kara G; Goodman, Catherine A

2010-02-11

In many low-income countries, the retail sector plays an important role in the treatment of malaria and is increasingly being considered as a channel for improving medicine availability. Retailers are the last link in a distribution chain and their supply sources are likely to have an important influence on the availability, quality and price of malaria treatment. This article presents the findings of a systematic literature review on the retail sector distribution chain for malaria treatment in low and middle-income countries. Publication databases were searched using key terms relevant to the distribution chain serving all types of anti-malarial retailers. Organizations involved in malaria treatment and distribution chain related activities were contacted to identify unpublished studies. A total of 32 references distributed across 12 developing countries were identified. The distribution chain had a pyramid shape with numerous suppliers at the bottom and fewer at the top. The chain supplying rural and less-formal outlets was made of more levels than that serving urban and more formal outlets. Wholesale markets tended to be relatively concentrated, especially at the top of the chain where few importers accounted for most of the anti-malarial volumes sold. Wholesale price mark-ups varied across chain levels, ranging from 27% to 99% at the top of the chain, 8% at intermediate level (one study only) and 2% to 67% at the level supplying retailers directly. Retail mark-ups tended to be higher, and varied across outlet types, ranging from 3% to 566% in pharmacies, 29% to 669% in drug shops and 100% to 233% in general shops. Information on pricing determinants was very limited. Evidence on the distribution chain for retail sector malaria treatment was mainly descriptive and lacked representative data on a national scale. These are important limitations in the advent of the Affordable Medicine Facility for Malaria, which aims to increase consumer access to artemisinin-based combination therapy (ACT), through a subsidy introduced at the top of the distribution chain. This review calls for rigorous distribution chain analysis, notably on the factors that influence ACT availability and prices in order to contribute to efforts towards improved access to effective malaria treatment.

Oscillatory Dynamics of One-Dimensional Homogeneous Granular Chains

NASA Astrophysics Data System (ADS)

Starosvetsky, Yuli; Jayaprakash, K. R.; Hasan, Md. Arif; Vakakis, Alexander F.

The acoustics of the homogeneous granular chains has been studied extensively both numerically and experimentally in the references cited in the previous chapters. This chapter focuses on the oscillatory behavior of finite dimensional homogeneous granular chains. It is well known that normal vibration modes are the building blocks of the vibrations of linear systems due to the applicability of the principle of superposition. One the other hand, nonlinear theory is deprived of such a general superposition principle (although special cases of nonlinear superpositions do exist), but nonlinear normal modes ‒ NNMs still play an important role in the forced and resonance dynamics of these systems. In their basic definition [1], NNMs were defined as time-periodic nonlinear oscillations of discrete or continuous dynamical systems where all coordinates (degrees-of-freedom) oscillate in-unison with the same frequency; further extensions of this definition have been considered to account for NNMs of systems with internal resonances [2]...

Progress in the field of physiologically active lanosterol compounds

NASA Astrophysics Data System (ADS)

Reshetova, I. G.; Tkhaper, R. K.; Kamernitskii, Alexey V.

1992-08-01

This review correlates the studies (up to 1991) on the isolation, structural determination, biological activity, and synthesis of physiologically active polyoxidised lanosterol derivatives of vegetable (inotodiol, ganoderic acids) and animal (seychellogenin) origin. The cytotoxic, cardiovascular, and other forms of activity of compounds of this type are of considerable interest in relation to their medical use. It is noted that the functionalised side chain (in an open form or containing lactones, lactols, etc.) is generally responsible for the activity exhibited by lanosterol derivatives. Two basic approaches to the derivation of these structures are defined: either by complete reconstruction of the side chain of lanosterol (degradation and rebuilding with oxygen-containing residues) or by progressive functionalisation of the Δ24-side chain of lanosterol. The synthesis of the known anticancer compound "inotodiol", seychellogenins, ganoderic acids, and other compounds are described. The bibliography includes 105 references.

Non-conserved magnetization operator and 'fire-and-ice' ground states in the Ising-Heisenberg diamond chain

NASA Astrophysics Data System (ADS)

Torrico, Jordana; Ohanyan, Vadim; Rojas, Onofre

2018-05-01

We consider the diamond chain with S = 1/2 XYZ vertical dimers which interact with the intermediate sites via the interaction of the Ising type. We also suppose all four spins form the diamond-shaped plaquette to have different g-factors. The non-uniform g-factors within the quantum spin dimer as well as the XY-anisotropy of the exchange interaction lead to the non-conserving magnetization for the chain. We analyze the effects of non-conserving magnetization as well as the effects of the appearance of negative g-factors among the spins from the unit cell. A number of unusual frustrated states for ferromagnetic couplings and g-factors with non-uniform signs are found out. These frustrated states generalize the "half-fire-half-ice" state introduced in reference Yin et al. (2015). The corresponding zero-temperature ground state phase diagrams are presented.

Sustainability in Supply Chain Management: Aggregate Planning from Sustainability Perspective.

PubMed

Türkay, Metin; Saraçoğlu, Öztürk; Arslan, Mehmet Can

2016-01-01

Supply chain management that considers the flow of raw materials, products and information has become a focal issue in modern manufacturing and service systems. Supply chain management requires effective use of assets and information that has far reaching implications beyond satisfaction of customer demand, flow of goods, services or capital. Aggregate planning, a fundamental decision model in supply chain management, refers to the determination of production, inventory, capacity and labor usage levels in the medium term. Traditionally standard mathematical programming formulation is used to devise the aggregate plan so as to minimize the total cost of operations. However, this formulation is purely an economic model that does not include sustainability considerations. In this study, we revise the standard aggregate planning formulation to account for additional environmental and social criteria to incorporate triple bottom line consideration of sustainability. We show how these additional criteria can be appended to traditional cost accounting in order to address sustainability in aggregate planning. We analyze the revised models and interpret the results on a case study from real life that would be insightful for decision makers.

Expected distributions of root-mean-square positional deviations in proteins.

PubMed

Pitera, Jed W

2014-06-19

The atom positional root-mean-square deviation (RMSD) is a standard tool for comparing the similarity of two molecular structures. It is used to characterize the quality of biomolecular simulations, to cluster conformations, and as a reaction coordinate for conformational changes. This work presents an approximate analytic form for the expected distribution of RMSD values for a protein or polymer fluctuating about a stable native structure. The mean and maximum of the expected distribution are independent of chain length for long chains and linearly proportional to the average atom positional root-mean-square fluctuations (RMSF). To approximate the RMSD distribution for random-coil or unfolded ensembles, numerical distributions of RMSD were generated for ensembles of self-avoiding and non-self-avoiding random walks. In both cases, for all reference structures tested for chains more than three monomers long, the distributions have a maximum distant from the origin with a power-law dependence on chain length. The purely entropic nature of this result implies that care must be taken when interpreting stable high-RMSD regions of the free-energy landscape as "intermediates" or well-defined stable states.

Synthesis and antimalarial activity study of some new Mannich bases of 7-chloro-4-aminoquinoline.

PubMed

Roy, Susanta; Chetia, Dipak; Rudrapal, Mithun; Prakash, Anil

2013-05-01

New derivatives of 7-chloro-4-aminoquinoline Mannich base were prepared by selectively modifying the aliphatic diethyl amino function of isoquine with different aliphatic/aromatic heterocyclic primary amino moieties at Mannich side chain. The synthesized compounds were characterized by their analytical and spectral data, and screened for in-vitro antimalarial activity against a chloroquine-sensitive 3D7 strain of Plasmodium falciparum. All the compounds showed in-vitro antimalarial activity at the tested dose; which, however, was considerably less than that of the standard reference drug, chloroquine. Among synthesized compounds, compounds with cyclohexyl (2f), methyl (2c) substitutions showed better activity than compounds substituted with n-octyl (2a), propyl (2b), 3-aminopropyl (2d) and furan-2- ylmethyl (2e) moieties at aminomethyl side chain. The results clearly demonstrate that the compound substituted with saturated cycloalkyl moiety (cyclohexyl) exhibited to some extent increased activity as compared to the compound containing heterocyclic moiety (furan-2-ylmethyl), and compounds with short chain alkyl substitutions (methyl, propyl) were found to be more active than that of compounds with long chain alkyl substitution (n-octyl).

Multi-scale modeling of diffusion-controlled reactions in polymers: renormalisation of reactivity parameters.

PubMed

Everaers, Ralf; Rosa, Angelo

2012-01-07

The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-controlled reactions in polymers developed by Wilemski, Fixman, and Doi to discuss the renormalisation of the reactivity parameters in polymer models with varying spatial resolution. In particular, we show that the adjustments are independent of chain length. As a consequence, it is possible to match reactions times between descriptions with different resolution for relatively short reference chains and to use the coarse-grained model to make quantitative predictions for longer chains. We illustrate our results by a detailed discussion of the classical problem of chain cyclization in the Rouse model, which offers the simplest example of a multi-scale descriptions, if we consider differently discretized Rouse models for the same physical system. Moreover, we are able to explore different combinations of compact and non-compact diffusion in the local and large-scale dynamics by varying the embedding dimension.

Sustainability in Supply Chain Management: Aggregate Planning from Sustainability Perspective

PubMed Central

Türkay, Metin; Saraçoğlu, Öztürk; Arslan, Mehmet Can

2016-01-01

Supply chain management that considers the flow of raw materials, products and information has become a focal issue in modern manufacturing and service systems. Supply chain management requires effective use of assets and information that has far reaching implications beyond satisfaction of customer demand, flow of goods, services or capital. Aggregate planning, a fundamental decision model in supply chain management, refers to the determination of production, inventory, capacity and labor usage levels in the medium term. Traditionally standard mathematical programming formulation is used to devise the aggregate plan so as to minimize the total cost of operations. However, this formulation is purely an economic model that does not include sustainability considerations. In this study, we revise the standard aggregate planning formulation to account for additional environmental and social criteria to incorporate triple bottom line consideration of sustainability. We show how these additional criteria can be appended to traditional cost accounting in order to address sustainability in aggregate planning. We analyze the revised models and interpret the results on a case study from real life that would be insightful for decision makers. PMID:26807848

Phase-locking of a 2.7-THz Quantum Cascade Laser to a Microwave Reference

NASA Astrophysics Data System (ADS)

Baryshev, A. M.; Khosropanah, P.; Zhang, W.; Jellema, W.; Hovenier, J. N.; Gao, J. R.; Klapwijk, T. M.; Paveliev, D. G.; William, B. S.; Kumar, S.; Hu, Q.; Reno, J. L.; Klein, B.; Hesler, J. L.

2009-04-01

We demonstrate phase-locking of a 2.7-THz metal-metal waveguide quantum cascade laser (QCL) to an external microwave signal. The reference is the 15th harmonic, generated by a semiconductor superlattice nonlinear device, of a signal at 182 GHz, which itself is generated by a multiplier-chain (x2x3x2) from a microwave synthesizer at 15 GHz. Both laser and reference radiations are coupled into a hot electron bolometer mixer, resulting in a beat signal, which is fed into a phase-lock loop. Spectral analysis of the beat signal (see fig. 1) confirms that the QCL is phase locked. This result opens the possibility to extend heterodyne interferometers into the far-infrared range.

Identification and validation of reference genes for qRT-PCR studies of the obligate aphid pathogenic fungus Pandora neoaphidis during different developmental stages.

PubMed

Zhang, Shutao; Chen, Chun; Xie, Tingna; Ye, Sudan

2017-01-01

The selection of stable reference genes is a critical step for the accurate quantification of gene expression. To identify and validate the reference genes in Pandora neoaphidis-an obligate aphid pathogenic fungus-the expression of 13classical candidate reference genes were evaluated by quantitative real-time reverse transcriptase polymerase chain reaction(qPCR) at four developmental stages (conidia, conidia with germ tubes, short hyphae and elongated hyphae). Four statistical algorithms, including geNorm, NormFinder, BestKeeper and Delta Ct method were used to rank putative reference genes according to their expression stability and indicate the best reference gene or combination of reference genes for accurate normalization. The analysis of comprehensive ranking revealed that ACT1and 18Swas the most stably expressed genes throughout the developmental stages. To further validate the suitability of the reference genes identified in this study, the expression of cell division control protein 25 (CDC25) and Chitinase 1(CHI1) genes were used to further confirm the validated candidate reference genes. Our study presented the first systematic study of reference gene(s) selection for P. neoaphidis study and provided guidelines to obtain more accurate qPCR results for future developmental efforts.

Discussing Laddering Application by the Means-End Chain Theory

ERIC Educational Resources Information Center

Veludo-de-Oliveira, Tania Modesto; Ikeda, Ana Akemi; Campomar, Marcos Cortez

2006-01-01

This article aims at analyzing laddering as a technique of qualitative research, emphasizing the procedures for data collection, analysis and interpretation, and its main limitations as well. "Laddering refers to an in-depth, one-on-one interviewing technique used to develop an understanding of how consumers translate the attributes of products…

Detection of Neorickettsia risticii, the agent of Potomac horse fever, in a Gypsy Vanner stallion from Manitoba.

PubMed

Durán, María Carolina; Marqués, Fernando J

2016-03-01

A horse with colitis from Manitoba referred to the Veterinary Medical Centre, Western College of Veterinary Medicine, was diagnosed with Potomac horse fever (PHF). Polymerase chain reaction analysis of the feces confirmed Neorickettsia risticii infection. This is the first reported case of PHF in Manitoba.

The Impact of Values on a Principal's Daily Activities.

ERIC Educational Resources Information Center

Moorhead, Roslyn; Nediger, William

1991-01-01

A two-year study of four effective secondary school principals suggests that a principal's actions can be represented by a value-based model (or Markov chain) in which beliefs and values lead to goals, activities, and outcomes. Findings show that no one value set brings about more effective leadership than another. (27 references) (MLH)

A Model for Logistics Systems Engineering Management Education in Europe.

ERIC Educational Resources Information Center

Naim, M.; Lalwani, C.; Fortuin, L.; Schmidt, T.; Taylor, J.; Aronsson, H.

2000-01-01

Presents the need for a systems and process perspective of logistics, and develops a template for a logistics education course. The template addresses functional, process, and supply chain needs and was developed by a number of university partners with core skills in different traditional disciplines. (Contains 31 references.) (Author/WRM)

Does Delaying Judgments of Learning Really Improve the Efficacy of Study Decisions? Not So Much

ERIC Educational Resources Information Center

Kimball, Daniel R.; Smith, Troy A.; Muntean, William J.

2012-01-01

A widely held assumption in metamemory is that better, more accurate metamemory monitoring leads to better, more efficacious restudy decisions, reflected in better memory performance--we refer to this causal chain as the "restudy selectivity hypothesis". In 3 sets of experiments, we tested this hypothesis by factorially manipulating…

Evaluation of reference genes for expression studies in ash (Fraxinus spp.)

Treesearch

Loren Rivera-Vega; Praveen Mamidala; Jennifer L. Koch; Mary E. Mason; Omprakash Mittapalli

2012-01-01

Ash (Fraxinus spp.) is a dominant tree species in North America, in both managed and natural landscapes. However, due to the rapid invasion by the emerald ash borer (Agrilus planipennis), an exotic invasive insect pest, millions of North American ash trees have been killed. Real-time quantitative polymerase chain reaction (RTq-PCR...

Barriers, Springboards and Benchmarks: China Conceptualizes the Pacific Island Chains

DTIC Science & Technology

2016-03-04

the South China Sea during World War II, severing Japanese SLOCs and thus Japan’s sup- ply of oil and raw materials.”59 Chinese sources refer to Guam...Training for joint operations in an informatized battle- field), Renmin haijun, 7 April 2009. 65 Jiefangjun bao, 12 June 1980, 1, cited in Muller

78 FR 51192 - Secure Supply Chain Pilot Program

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-20

... (PDF) and using the Electronic Common Technical Document (eCTD) format and the Electronic Submissions.... The PDF file name should contain ``3676'' as part of the file name, and the eCTD leaf title should.... For further information regarding eCTD, please refer to the Web site at http://www.fda.gov/Drugs...

Quantitative fucK gene polymerase chain reaction on sputum and nasopharyngeal secretions to detect Haemophilus influenzae pneumonia.

PubMed

Abdeldaim, Guma M K; Strålin, Kristoffer; Olcén, Per; Blomberg, Jonas; Mölling, Paula; Herrmann, Björn

2013-06-01

A quantitative polymerase chain reaction (PCR) for the fucK gene was developed for specific detection of Haemophilus influenzae. The method was tested on sputum and nasopharyngeal aspirate (NPA) from 78 patients with community-acquired pneumonia (CAP). With a reference standard of sputum culture and/or serology against the patient's own nasopharyngeal isolate, H. influenzae etiology was detected in 20 patients. Compared with the reference standard, fucK PCR (using the detection limit 10(5) DNA copies/mL) on sputum and NPA showed a sensitivity of 95.0% (19/20) in both cases, and specificities of 87.9% (51/58) and 89.5% (52/58), respectively. In a receiver operating characteristic curve analysis, sputum fucK PCR was found to be significantly superior to sputum P6 PCR for detection of H. influenzae CAP. NPA fucK PCR was positive in 3 of 54 adult controls without respiratory symptoms. In conclusion, quantitative fucK real-time PCR provides a sensitive and specific identification of H. influenzae in respiratory secretions. Copyright © 2013 Elsevier Inc. All rights reserved.

Using Reference Quantitative Polymerase Chain Reaction to Assess the Clinical Performance of the Paracheck-Pf® Rapid Diagnostic Test in a Field Setting in Uganda.

PubMed

Mitran, Catherine J; Mbonye, Anthony K; Hawkes, Michael; Yanow, Stephanie K

2018-06-04

Malaria rapid diagnostic tests (RDTs) are widely used in clinical and surveillance settings. However, the performance of most RDTs has not been characterized at parasite densities below detection by microscopy. We present findings from Uganda, where RDT results from 491 participants with suspected malaria were correlated with quantitative polymerase chain reaction (qPCR)-defined parasitemia. Compared with qPCR, the sensitivity and specificity of the RDT for Plasmodium falciparum mono-infections were 76% (95% confidence interval [CI]: 68-83%) and 95% (95% CI: 92-97%), respectively. The sensitivity of the RDT at parasite densities between 0.2 and 200 parasites/μL was surprisingly high (87%, 95% CI: 74-94%). The high sensitivity of the RDT is likely because of histidine-rich protein 2 from submicroscopic infections, gametocytes, or sequestered parasites. These findings underscore the importance of evaluating different RDTs in field studies against qPCR reference testing to better define the sensitivity and specificity, particularly at low parasite densities.

Successful treatment of nephrotic syndrome induced by lambda light chain deposition disease using lenalidomide: A case report and review of the literature
.

PubMed

Mima, Akira; Nagahara, Dai; Tansho, Kosuke

2018-06-01

Light chain deposition disease (LCDD) is a monoclonal immunoglobulin deposition disease (MIDD) that is characterized by the deposition of monoclonal light chains in multiple organs, including the kidney. It is a rare disorder caused by an underlying monoclonal plasma cell dyscrasia. LCDD with renal involvement causes proteinuria, which sometimes can lead to nephrotic syndrome. The monoclonal light chains are mostly in the κ form. Treatment of LCDD is the same as that for multiple myeloma (MM); however, some conventional anticancer drugs show substantial toxicity and therefore cannot be administered to older patients or those with renal impairment. An 80-year-old woman was referred to our department with severe nephrotic syndrome (13.6 g/gCr) and anemia. A renal biopsy showed mesangial proliferation and mesangial matrix expansion, and immunohistochemistry showed positive staining for λ chains along the glomerular basement membrane, but was negative for κ chains or amyloid deposition. A bone marrow biopsy revealed 64% plasma cells. Immunoglobulin G (IgG)-λ type M protein was detected, and the levels of free λ chain was significantly increased. We concluded that her nephrotic syndrome was caused by LCDD, which resulted from IgG-λ MM. The induction of a BCD (bortezomib, cyclophosphamide, and dexamethasone) treatment regimen did not lead to a hematological response or decrease in proteinuria. The administration of combination therapy of lenalidomide and prednisolone led to the successful reduction of proteinuria and hematuria. We presented a very rare case report describing the successful treatment of LCDD (λ chain)-induced nephrotic syndrome with lenalidomide.
.

Macromolecular 'size' and 'hardness' drives structure in solvent-swollen blends of linear, cyclic, and star polymers.

PubMed

Gartner, Thomas E; Jayaraman, Arthi

2018-01-17

In this paper, we apply molecular simulation and liquid state theory to uncover the structure and thermodynamics of homopolymer blends of the same chemistry and varying chain architecture in the presence of explicit solvent species. We use hybrid Monte Carlo (MC)/molecular dynamics (MD) simulations in the Gibbs ensemble to study the swelling of ∼12 000 g mol -1 linear, cyclic, and 4-arm star polystyrene chains in toluene. Our simulations show that the macroscopic swelling response is indistinguishable between the various architectures and matches published experimental data for the solvent annealing of linear polystyrene by toluene vapor. We then use standard MD simulations in the NPT ensemble along with polymer reference interaction site model (PRISM) theory to calculate effective polymer-solvent and polymer-polymer Flory-Huggins interaction parameters (χ eff ) in these systems. As seen in the macroscopic swelling results, there are no significant differences in the polymer-solvent and polymer-polymer χ eff between the various architectures. Despite similar macroscopic swelling and effective interaction parameters between various architectures, the pair correlation function between chain centers-of-mass indicates stronger correlations between cyclic or star chains in the linear-cyclic blends and linear-star blends, compared to linear chain-linear chain correlations. Furthermore, we note striking similarities in the chain-level correlations and the radius of gyration of cyclic and 4-arm star architectures of identical molecular weight. Our results indicate that the cyclic and star chains are 'smaller' and 'harder' than their linear counterparts, and through comparison with MD simulations of blends of soft spheres with varying hardness and size we suggest that these macromolecular characteristics are the source of the stronger cyclic-cyclic and star-star correlations.

General polytropic self-gravitating cylinder free-fall and accreting mass string with a chain of collapsed objects

NASA Astrophysics Data System (ADS)

Lou, Yu-Qing; Hu, Xu-Yao

2016-06-01

We present a theoretical model framework for general polytropic (GP) hydrodynamic cylinder under self-gravity of infinite length with axial uniformity and axisymmetry. For self-similar dynamic solutions, we derive valuable integrals, analytic asymptotic solutions, sonic critical curves, shock conditions, and global numerical solutions with or without expansion shocks. Among others, we investigate various dynamic solutions featured with central free-fall asymptotic behaviours, corresponding to a collapsed mass string with a sustained dynamic accretion from a surrounding mass reservoir. Depending on the allowed ranges of a scaling index a < -1, such cylindrical dynamic mass accretion rate could be steady, increasing with time and decreasing with time. Physically, such a collapsed mass string or filament would break up into a sequence of sub-clumps and segments as induced by gravitational Jeans instabilities. Depending on the scales involved, such sub-clumps would evolve into collapsed objects or gravitationally bound systems. In diverse astrophysical and cosmological contexts, such a scenario can be adapted on various temporal, spatial and mass scales to form a chain of collapsed clumps and/or compact objects. Examples include the formation of chains of proto-stars, brown dwarfs and gaseous planets along molecular filaments; the formation of luminous massive stars along magnetized spiral arms and circum-nuclear starburst rings in barred spiral galaxies; the formation of chains of compact stellar objects such as white dwarfs, neutron stars, and black holes along a highly condensed mass string. On cosmological scales, one can perceive the formation of chains of galaxies, chains of galaxy clusters or even chains of supermassive and hypermassive black holes in the Universe including the early Universe. All these chains referred to above include possible binaries.

Softening of the stiffness of bottle-brush polymers by mutual interaction

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

Bolisetty, S.; Airaud, C.; Rosenfeldt, S.

2007-04-15

We study bottle-brush macromolecules in a good solvent by small-angle neutron scattering (SANS), static light scattering (SLS), and dynamic light scattering (DLS). These polymers consist of a linear backbone to which long side chains are chemically grafted. The backbone contains about 1600 monomer units (weight average) and every second monomer unit carries side chains with approximately 60 monomer units. The SLS and SANS data extrapolated to infinite dilution lead to the form factor of the polymer that can be described in terms of a wormlike chain with a contour length of 380 nm and a persistence length of 17.5 nm.more » An analysis of the DLS data confirms these model parameters. The scattering intensities taken at finite concentration can be modeled using the polymer reference interaction site model. It reveals a softening of the bottle-brush polymers caused by their mutual interaction. We demonstrate that the persistence decreases from 17.5 nm down to 5 nm upon increasing the concentration from dilute solution to the highest concentration (40.59 g/l) under consideration. The observed softening of the chains is comparable to the theoretically predicted decrease of the electrostatic persistence length of linear polyelectrolyte chains at finite concentrations.« less

Conditional Solvation Thermodynamics of Isoleucine in Model Peptides and the Limitations of the Group-Transfer Model

PubMed Central

2015-01-01

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute–solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration and the conflation of background contributions with energetics attributed to the side chain limit the ability of a single scaling factor, such as the fractional solvent exposure of the group in the protein, to map the component energetic contributions of the model-compound data to their value in the protein. But ignoring the origin of cancellations in the underlying components the group-transfer model may appear to provide a reasonable estimate of the free energy for a given error tolerance. PMID:24650057

Leading a supply chain turnaround.

PubMed

Slone, Reuben E

2004-10-01

Just five years ago, salespeople at Whirlpool were in the habit of referring to their supply chain organization as the "sales disablers." Now the company excels at getting products to the right place at the right time--while managing to keep inventories low. How did that happen? In this first-person account, Reuben Slone, Whirlpool's vice president of Global Supply Chain, describes how he and his colleagues devised the right supply chain strategy, sold it internally, and implemented it. Slone insisted that the right focal point for the strategy was the satisfaction of consumers at the end of the supply chain. Most supply chain initiatives do the opposite: They start with the realities of a company's manufacturing base and proceed from there. Through a series of interviews with trade customers large and small, his team identified 27 different capabilities that drove industry perceptions of Whirlpool's performance. Knowing it was infeasible to aim for world-class performance across all of them, Slone weighed the costs of excelling at each and found the combination of initiatives that would provide overall competitive advantage. A highly disciplined project management office and broad training in project management were key to keeping work on budget and on benefit. Slone set an intense pace--three "releases" of new capabilities every month--that the group maintains to this day. Lest this seem like a technology story, however, Slone insists it is just as much a "talent renaissance." People are proud today to be part of Whirlpool's supply chain organization, and its new generation of talent will give the company a competitive advantage for years to come.

Habitat and environment of islands: primary and supplemental island sets

USGS Publications Warehouse

Matalas, Nicholas C.; Grossling, Bernardo F.

2002-01-01

The original intent of the study was to develop a first-order synopsis of island hydrology with an integrated geologic basis on a global scale. As the study progressed, the aim was broadened to provide a framework for subsequent assessments on large regional or global scales of island resources and impacts on those resources that are derived from global changes. Fundamental to the study was the development of a comprehensive framework?a wide range of parameters that describe a set of 'saltwater' islands sufficiently large to Characterize the spatial distribution of the world?s islands; Account for all major archipelagos; Account for almost all oceanically isolated islands, and Account collectively for a very large proportion of the total area of the world?s islands whereby additional islands would only marginally contribute to the representativeness and accountability of the island set. The comprehensive framework, which is referred to as the ?Primary Island Set,? is built on 122 parameters that describe 1,000 islands. To complement the investigations based on the Primary Island Set, two supplemental island sets, Set A?Other Islands (not in the Primary Island Set) and Set B?Lagoonal Atolls, are included in the study. The Primary Island Set, together with the Supplemental Island Sets A and B, provides a framework that can be used in various scientific disciplines for their island-based studies on broad regional or global scales. The study uses an informal, coherent, geophysical organization of the islands that belong to the three island sets. The organization is in the form of a global island chain, which is a particular sequential ordering of the islands referred to as the 'Alisida.' The Alisida was developed through a trial-and-error procedure by seeking to strike a balance between 'minimizing the length of the global chain' and 'maximizing the chain?s geophysical coherence.' The fact that an objective function cannot be minimized and maximized simultaneously indicates that the Alisida is not unique. Global island chains other than the Alisida may better serve disciplines other than those of hydrology and geology.

Reverse transcription quantitative real-time polymerase chain reaction reference genes in the spared nerve injury model of neuropathic pain: validation and literature search.

PubMed

Piller, Nicolas; Decosterd, Isabelle; Suter, Marc R

2013-07-10

The reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used, highly sensitive laboratory technique to rapidly and easily detect, identify and quantify gene expression. Reliable RT-qPCR data necessitates accurate normalization with validated control genes (reference genes) whose expression is constant in all studied conditions. This stability has to be demonstrated.We performed a literature search for studies using quantitative or semi-quantitative PCR in the rat spared nerve injury (SNI) model of neuropathic pain to verify whether any reference genes had previously been validated. We then analyzed the stability over time of 7 commonly used reference genes in the nervous system - specifically in the spinal cord dorsal horn and the dorsal root ganglion (DRG). These were: Actin beta (Actb), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal proteins 18S (18S), L13a (RPL13a) and L29 (RPL29), hypoxanthine phosphoribosyltransferase 1 (HPRT1) and hydroxymethylbilane synthase (HMBS). We compared the candidate genes and established a stability ranking using the geNorm algorithm. Finally, we assessed the number of reference genes necessary for accurate normalization in this neuropathic pain model. We found GAPDH, HMBS, Actb, HPRT1 and 18S cited as reference genes in literature on studies using the SNI model. Only HPRT1 and 18S had been once previously demonstrated as stable in RT-qPCR arrays. All the genes tested in this study, using the geNorm algorithm, presented gene stability values (M-value) acceptable enough for them to qualify as potential reference genes in both DRG and spinal cord. Using the coefficient of variation, 18S failed the 50% cut-off with a value of 61% in the DRG. The two most stable genes in the dorsal horn were RPL29 and RPL13a; in the DRG they were HPRT1 and Actb. Using a 0.15 cut-off for pairwise variations we found that any pair of stable reference gene was sufficient for the normalization process. In the rat SNI model, we validated and ranked Actb, RPL29, RPL13a, HMBS, GAPDH, HPRT1 and 18S as good reference genes in the spinal cord. In the DRG, 18S did not fulfill stability criteria. The combination of any two stable reference genes was sufficient to provide an accurate normalization.

Conceptual Model of Supply Chain Structure Mapping - A Case of Subsidized LPG Commodity in Yogyakarta

NASA Astrophysics Data System (ADS)

Sulistio, Joko; Thoif, Afifuddin; Fitri Alindira, Aulia

2016-01-01

— In 2007, the government launched a conversion program of kerosene to LPG by issuing a Presidential Regulation No. 104/2007 on Supply, Distribution and Pricing LPG 3 Kg. Article 2 on the regulation says that setting the supply, distribution, and pricing of LPG 3 Kg include planning an annual sales volume of enterprises, the reference price and the retail price and conditions of export and import of LPG 3 Kg in order to reduce subsidies Kerosene especially to divert the use of kerosene according to government policy. In principle, the purpose of this policy is to reduce energy subsidies on commodities, especially Kerosene. Although the government claimed the conversion program is success, there are few problems arising from conversion program. In 2014, many scarcity and high price of LPG 3 Kg were reported. In this case, Pertamina was given full authority to manage all supply chain and distribution. Because the root of the problem of scarcity that occurred in the supply chain system has not been explained, the proposed solutions will also be partial and not comprehensive. Thus, this research will build a structural map of the causes of supply chain system LPG 3 Kg, as well as providing a comprehensive picture of system dynamics of LPG 3 Kg supply chain system which applied in Indonesia. And the result is expected as in form of Causal Loop Diagram of supply chain system.

Comparison of several classical density functional theories for the adsorption of flexible chain molecules into cylindrical nanopores.

PubMed

Hlushak, S P; Cummings, P T; McCabe, C

2013-12-21

Adsorption of flexible oligomers into narrow cylindrical pores has been studied by means of several versions of classical density functional theory (CDFT) and Monte Carlo simulation. The adsorption process is interesting to study due to the competition between the entropic depletion of oligomers from the pores and the wall-oligomer attraction. It is also challenging to describe using current CDFTs, which tend to overestimate the amount of the adsorbed fluid. From a comparison of several different CDFT approaches, we find that this is due to the assumption of ideal or freely jointed chain conformations. Moreover, it is demonstrated that it is impossible to obtain a reasonable description of the adsorption isotherms without taking into account accurate contact values in the distribution functions describing the structure of the reference monomer fluid. At low densities, more accurate result are obtained in comparison with Monte Carlo simulation data when accurate contact values are incorporated into the theory rather than the more commonly used hard-sphere contact value. However, even the CDFT with accurate contact values still overestimates the amount of the adsorbed fluid due to the ideal or freely jointed chain approximation, used for the description of chain conformations in most CDFT approaches. We find that significant improvement can achieved by employing self-consistent field theory, which samples self-avoiding chain conformations and decreases the number of possible chain conformations, and, consequently, the amount of the adsorbed fluid.

Coordination geometry of lead carboxylates - spectroscopic and crystallographic evidence.

PubMed

Catalano, Jaclyn; Murphy, Anna; Yao, Yao; Yap, Glenn P A; Zumbulyadis, Nicholas; Centeno, Silvia A; Dybowski, Cecil

2015-02-07

Despite their versatility, only a few single-crystal X-ray structures of lead carboxylates exist, due to difficulties with solubility. In particular, the structures of long-chain metal carboxylates have not been reported. The lone electron pair in Pb(ii) can be stereochemically active or inactive, leading to two types of coordination geometries commonly referred to as hemidirected and holodirected structures, respectively. We report (13)C and (207)Pb solid-state NMR and infrared spectra for a series of lead carboxylates, ranging from lead hexanoate (C6) to lead hexadecanoate (C18). The lead carboxylates based on consistent NMR parameters can be divided in two groups, shorter-chain (C6, C7, and C8) and longer-chain (C9, C10, C11, C12, C14, C16, and C18) carboxylates. This dichotomy suggests two modes of packing in these solids, one for the short-chain lead carboxylates and one for long-chain lead carboxylates. The consistency of the (13)C and (207)Pb NMR parameters, as well as the IR data, in each group suggests that each motif represents a structure characteristic of each subgroup. We also report the single-crystal X-ray diffraction structure of lead nonanoate (C9), the first single-crystal structure to have been reported for the longer-chain subgroup. Taken together the evidence suggests that the coordination geometry of C6-C8 lead carboxylates is hemidirected, and that of C9-C14, C16 and C18 lead carboxylates is holodirected.

Frequency measurement of the 5 S{1}/{2}(F = 3)-5 D{5}/{2}(F = 5) two-photon transition in rubidium

NASA Astrophysics Data System (ADS)

Touahri, D.; Acef, O.; Clairon, A.; Zondy, J.-J.; Felder, R.; Hilico, L.; de Beauvoir, B.; Biraben, F.; Nez, F.

1997-02-01

We have measured the frequencies of three diode lasers stabilized on the 5 S{1}/{2}(F = 3)-5 D{5}/{2}(F = 5) two-photon transition in rubidium at λ = 778.1 nm, with an uncertainty of 1 kHz, using BNM-LPTF frequency synthesis chain starting from a {CO 2}/{OsO 4} reference laser at 10.3 μm. We show that this frequency chain is able to reach the 10 -13 resolution level. After a discussion of the systematic effects that may shift the resonance, the transition frequency is found to be ν = 385 285 142 378.280 ± 2 kHz.

A Spectral Analysis of Discrete-Time Quantum Walks Related to the Birth and Death Chains

NASA Astrophysics Data System (ADS)

Ho, Choon-Lin; Ide, Yusuke; Konno, Norio; Segawa, Etsuo; Takumi, Kentaro

2018-04-01

In this paper, we consider a spectral analysis of discrete time quantum walks on the path. For isospectral coin cases, we show that the time averaged distribution and stationary distributions of the quantum walks are described by the pair of eigenvalues of the coins as well as the eigenvalues and eigenvectors of the corresponding random walks which are usually referred as the birth and death chains. As an example of the results, we derive the time averaged distribution of so-called Szegedy's walk which is related to the Ehrenfest model. It is represented by Krawtchouk polynomials which is the eigenvectors of the model and includes the arcsine law.

Front propagation in a vortex lattice: dependence on boundary conditions and vortex depth.

PubMed

Beauvier, E; Bodea, S; Pocheau, A

2016-11-04

We experimentally address the propagation of reaction-diffusion fronts in vortex lattices by combining, in a Hele-Shaw cell and at low Reynolds number, forced electroconvective flows and an autocatalytic reaction in solution. We consider both vortex chains and vortex arrays, the former referring to mixed free/rigid boundary conditions for vortices and the latter to free boundary conditions. Varying the depth of the fluid layer, we observe no variation of the mean front velocities for vortex arrays and a noticeable variation for vortex chains. This questions the two-dimensional character of front propagation in low Reynolds number vortex lattices, as well as the mechanisms of this dependence.

Phase separation of comb polymer nanocomposite melts.

PubMed

Xu, Qinzhi; Feng, Yancong; Chen, Lan

2016-02-07

In this work, the spinodal phase demixing of branched comb polymer nanocomposite (PNC) melts is systematically investigated using the polymer reference interaction site model (PRISM) theory. To verify the reliability of the present method in characterizing the phase behavior of comb PNCs, the intermolecular correlation functions of the system for nonzero particle volume fractions are compared with our molecular dynamics simulation data. After verifying the model and discussing the structure of the comb PNCs in the dilute nanoparticle limit, the interference among the side chain number, side chain length, nanoparticle-monomer size ratio and attractive interactions between the comb polymer and nanoparticles in spinodal demixing curves is analyzed and discussed in detail. The results predict two kinds of distinct phase separation behaviors. One is called classic fluid phase boundary, which is mediated by the entropic depletion attraction and contact aggregation of nanoparticles at relatively low nanoparticle-monomer attraction strength. The second demixing transition occurs at relatively high attraction strength and involves the formation of an equilibrium physical network phase with local bridging of nanoparticles. The phase boundaries are found to be sensitive to the side chain number, side chain length, nanoparticle-monomer size ratio and attractive interactions. As the side chain length is fixed, the side chain number has a large effect on the phase behavior of comb PNCs; with increasing side chain number, the miscibility window first widens and then shrinks. When the side chain number is lower than a threshold value, the phase boundaries undergo a process from enlarging the miscibility window to narrowing as side chain length increases. Once the side chain number overtakes this threshold value, the phase boundary shifts towards less miscibility. With increasing nanoparticle-monomer size ratio, a crossover of particle size occurs, above which the phase separation is consistent with that of chain PNCs. The miscibility window for this condition gradually narrows while the other parameters of the PNCs system are held constant. These results indicate that the present PRISM theory can give molecular-level details of the underlying mechanisms of the comb PNCs. It is hoped that the results can be used to provide useful guidance for the future design control of novel, thermodynamically stable comb PNCs.

Effect of chain extension on rheology and tensile properties of PHB and PHB-PLA blends

NASA Astrophysics Data System (ADS)

Bousfield, Glenn

Poly(3-hydroxybutyrate), referred to as PHB, is a bacterially-synthesized and biodegradable polymer which is being considered as a substitute for non-biodegradable bulk polymers like polypropylene. PHB is naturally extremely isotactic and naturally has a very high degree of crystallinity, resulting in a stiff but brittle material. The stability of PHB crystals also means that the melting point of the polymer is approximately 170°C, high with respect to similar polymers. For instance, the melting point of poly(4-hydroxybutyrate) is only 53°C (Saito, Nakamura, Hiramitsu, & Doi, 1996). Above 170°C, PHB is subject to a thermomechanical degradation mechanism, meaning that the polymer cannot be melted without degrading. One possible solution to the problem of degradation is to add a chain extender to the molten polymer to increase average molecular weight to counteract the molecular weight lost to degradation. In this work, a variety of chain extenders (JoncrylRTM ADR 4368-C, pyromellitic dianhydride, hexamethylene diisocyanate, polycarbodiimide) were compounded with a random copolymer of 98 mol% 3-hydroxybutyrate and 2 mol% 3-hydroxyvalerate (referred to as PHB) in concentrations ranging from 0.25% to 4%, to determine which chain extender functionality worked best with PHB. Molecular weight change was inferred from torque monitored during compounding, and from complex viscosity determined from parallel-plate rheology. None of the chain extenders changed the rate of degradation of PHB, although Joncryl increased the complex viscosity of the polymer. PHB was also blended with Poly(L-lactic acid), referred to as PLLA in PHB/PLLA ratios of 100/0, 75/25, 50/50, 25/75 and 0/100, to determine the effect of blending on the thermal stability of PHB. Again, thermal stability was determined by monitoring torque during compounding and by measuring complex viscosity through parallel-plate rheology. Blends in which PHB was the more abundant phase, as well as the 50% PHB/50% PLA blend continued to degrade, and the PLLA did not in these cases significantly increase complex viscosity. By contrast, the 25/75 PHB/PLLA blend had a complex viscosity equal to the neat PLLA blend, and both of the blends remained stable. All five blends were also produced with 1% Joncryl to observe the effect of Joncryl on the blends. In the 50/50 blend and the blends in which PLLA was the major component, complex viscosity increased by at least an order of magnitude, while in the 75/25 PHB/PLLA blend and the neat PHB blend, the effect of Joncryl was to increase complex viscosity only by a factor of 2. The effect of blending and of Joncryl on PHB-PLA blends was further investigated through uniaxial tensile stress testing of compression moulded samples of the blends, neat and with 1% Joncryl. The results showed an increase in tensile stress at yield and tensile strain at break for blends with the addition of Joncryl, although Young's modulus was somewhat diminished for these blends. In conclusion, chain extenders were not effective in reversing the effect of thermomechanical degradation, possibly because they do not change the resistance to bond rotation in PHB chains, or because they are not reactive with acrylates, although the exact cause has not been determined.

Reducing stock-outs of essential tuberculosis medicines: a system dynamics modelling approach to supply chain management.

PubMed

Bam, L; McLaren, Z M; Coetzee, E; von Leipzig, K H

2017-10-01

The under-performance of supply chains presents a significant hindrance to disease control in developing countries. Stock-outs of essential medicines lead to treatment interruption which can force changes in patient drug regimens, drive drug resistance and increase mortality. This study is one of few to quantitatively evaluate the effectiveness of supply chain policies in reducing shortages and costs. This study develops a systems dynamics simulation model of the downstream supply chain for amikacin, a second-line tuberculosis drug using 10 years of South African data. We evaluate current supply chain performance in terms of reliability, responsiveness and agility, following the widely-used Supply Chain Operation Reference framework. We simulate 141 scenarios that represent different combinations of supplier characteristics, inventory management strategies and demand forecasting methods to identify the Pareto optimal set of management policies that jointly minimize the number of shortages and total cost. Despite long supplier lead times and unpredictable demand, the amikacin supply chain is 98% reliable and agile enough to accommodate a 20% increase in demand without a shortage. However, this is accomplished by overstocking amikacin by 167%, which incurs high holding costs. The responsiveness of suppliers is low: only 57% of orders are delivered to the central provincial drug depot within one month. We identify three Pareto optimal safety stock management policies. Short supplier lead time can produce Pareto optimal outcomes even in the absence of other optimal policies. This study produces concrete, actionable guidelines to cost-effectively reduce stock-outs by implementing optimal supply chain policies. Preferentially selecting drug suppliers with short lead times accommodates unexpected changes in demand. Optimal supply chain management should be an essential component of national policy to reduce the mortality rate. © The Author 2017. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Detection of Neorickettsia risticii, the agent of Potomac horse fever, in a Gypsy Vanner stallion from Manitoba

PubMed Central

Durán, María Carolina; Marqués, Fernando J.

2016-01-01

A horse with colitis from Manitoba referred to the Veterinary Medical Centre, Western College of Veterinary Medicine, was diagnosed with Potomac horse fever (PHF). Polymerase chain reaction analysis of the feces confirmed Neorickettsia risticii infection. This is the first reported case of PHF in Manitoba. PMID:26933267

Assessing Beaked Whale Reproduction and Stress Response Relative to Sonar Activity at the Atlantic Undersea Test and Evaluation Center (AUTEC)

DTIC Science & Technology

2015-09-30

oil spills (unpublished data, Kellar). The second will be to conduct a more fine-scale analysis of the areas examined during this study. For this...REFERENCES Carlin BP , Chib S (1995) Bayesian model choice via Markov-chain Monte-Carlo methods. Journal of the Royal Statistical Society

Determination of alkylphenols by gas chromatography, elution liquid chromatography, and gel permeation chromatography

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

Wittmann, S.; Decsy, Z.; Regensperger, S.

1984-01-01

The separation and determination of groups of alkylphenols with C/sub 15/-C/sub 33/ isoalkane chains by gas chromatography, elution liquid chromatography, and gel permeation chromatography are described. Paraffinic hydrocarbons, monoalkylphenols, dialkylphenols, and bis(hydroxyphenyl)alkanes were identified in industrial alkylphenols by mass spectrometry. 7 references, 3 figures, 2 tables.

Small Engine Repair Course Outline.

ERIC Educational Resources Information Center

DeClouet, Fred

Small engines as referred to here are engines used on lawn mowers, chain saws, power plants, outboards, and cycles. It does not include engines used on automobiles. The course outlined is intended to show how small two-cycle and four-cycle gas engines are constructed, how they operate, what goes wrong, and how to service and repair them. It is…

Retail sector distribution chains for malaria treatment in the developing world: a review of the literature

PubMed Central

2010-01-01

Background In many low-income countries, the retail sector plays an important role in the treatment of malaria and is increasingly being considered as a channel for improving medicine availability. Retailers are the last link in a distribution chain and their supply sources are likely to have an important influence on the availability, quality and price of malaria treatment. This article presents the findings of a systematic literature review on the retail sector distribution chain for malaria treatment in low and middle-income countries. Methods Publication databases were searched using key terms relevant to the distribution chain serving all types of anti-malarial retailers. Organizations involved in malaria treatment and distribution chain related activities were contacted to identify unpublished studies. Results A total of 32 references distributed across 12 developing countries were identified. The distribution chain had a pyramid shape with numerous suppliers at the bottom and fewer at the top. The chain supplying rural and less-formal outlets was made of more levels than that serving urban and more formal outlets. Wholesale markets tended to be relatively concentrated, especially at the top of the chain where few importers accounted for most of the anti-malarial volumes sold. Wholesale price mark-ups varied across chain levels, ranging from 27% to 99% at the top of the chain, 8% at intermediate level (one study only) and 2% to 67% at the level supplying retailers directly. Retail mark-ups tended to be higher, and varied across outlet types, ranging from 3% to 566% in pharmacies, 29% to 669% in drug shops and 100% to 233% in general shops. Information on pricing determinants was very limited. Conclusions Evidence on the distribution chain for retail sector malaria treatment was mainly descriptive and lacked representative data on a national scale. These are important limitations in the advent of the Affordable Medicine Facility for Malaria, which aims to increase consumer access to artemisinin-based combination therapy (ACT), through a subsidy introduced at the top of the distribution chain. This review calls for rigorous distribution chain analysis, notably on the factors that influence ACT availability and prices in order to contribute to efforts towards improved access to effective malaria treatment. PMID:20149246

Trust in the early chain of healthcare: lifeworld hermeneutics from the patient's perspective.

PubMed

Norberg Boysen, Gabriella; Nyström, Maria; Christensson, Lennart; Herlitz, Johan; Wireklint Sundström, Birgitta

2017-12-01

Patients must be able to feel as much trust for caregivers and the healthcare system at the healthcare centre as at the emergency department. The aim of this study is to explain and understand the phenomenon of trust in the early chain of healthcare, when a patient has called an ambulance for a non-urgent condition and been referred to the healthcare centre. A lifeworld hermeneutic approach from the perspective of caring science was used. Ten patients participated: seven female and three male. The setting is the early chain of healthcare in south-western Sweden. The findings show that the phenomenon of trust does not automatically involve medical care. However, attention to the patient's lifeworld in a professional caring relationship enables the patient to trust the caregiver and the healthcare environment. It is clear that the "voice of the lifeworld" enables the patient to feel trust. Trust in the early chain of healthcare entails caregivers' ability to pay attention to both medical and existential issues in compliance with the patient's information and questions. Thus, the patient must be invited to participate in assessments and decisions concerning his or her own healthcare, in a credible manner and using everyday language.

Quality indicators to compare accredited independent pharmacies and accredited chain pharmacies in Thailand.

PubMed

Arkaravichien, Wiwat; Wongpratat, Apichaya; Lertsinudom, Sunee

2016-08-01

Background Quality indicators determine the quality of actual practice in reference to standard criteria. The Community Pharmacy Association (Thailand), with technical support from the International Pharmaceutical Federation, developed a tool for quality assessment and quality improvement at community pharmacies. This tool has passed validity and reliability tests, but has not yet had feasibility testing. Objective (1) To test whether this quality tool could be used in routine settings. (2) To compare quality scores between accredited independent and accredited chain pharmacies. Setting Accredited independent pharmacies and accredited chain pharmacies in the north eastern region of Thailand. Methods A cross sectional study was conducted in 34 accredited independent pharmacies and accredited chain pharmacies. Quality scores were assessed by observation and by interviewing the responsible pharmacists. Data were collected and analyzed by independent t-test and Mann-Whitney U test as appropriate. Results were plotted by histogram and spider chart. Main outcome measure Domain's assessable scores, possible maximum scores, mean and median of measured scores. Results Domain's assessable scores were close to domain's possible maximum scores. This meant that most indicators could be assessed in most pharmacies. The spider chart revealed that measured scores in the personnel, drug inventory and stocking, and patient satisfaction and health promotion domains of chain pharmacies were significantly higher than those of independent pharmacies (p < 0.05). There was no statistical difference between independent pharmacies and chain pharmacies in the premise and facility or dispensing and patient care domains. Conclusion Quality indicators developed by the Community Pharmacy Association (Thailand) could be used to assess quality of practice in pharmacies in routine settings. It is revealed that the quality scores of chain pharmacies were higher than those of independent pharmacies.

Simulation of a cellulose fiber in ionic liquid suggests a synergistic approach to dissolution

DOE PAGES

Mostofian, Barmak; Smith, Jeremy C.; Cheng, Xiaolin

2013-08-11

Ionic liquids dissolve cellulose in a more efficient and environmentally acceptable way than conventional methods in aqueous solution. An understanding of how ionic liquids act on cellulose is essential for improving pretreatment conditions and thus detailed knowledge of the interactions between the cations, anions and cellulose is necessary. Here in this study, to explore ionic liquid effects, we perform all-atom molecular dynamics simulations of a cellulose microfibril in 1-butyl-3-methylimidazolium chloride and analyze site–site interactions and cation orientations at the solute–solvent interface. The results indicate that Cl - anions predominantly interact with cellulose surface hydroxyl groups but with differences between chainsmore » of neighboring cellulose layers, referred to as center and origin chains; Cl- binds to C3-hydroxyls on the origin chains but to C2- and C6-hydroxyls on the center chains, thus resulting in a distinct pattern along glucan chains of the hydrophilic fiber surfaces. In particular, Cl - binding disrupts intrachain O3H–O5 hydrogen bonds on the origin chains but not those on the center chains. In contrast, Bmim + cations stack preferentially on the hydrophobic cellulose surface, governed by non-polar interactions with cellulose. Complementary to the polar interactions between Cl - and cellulose, the stacking interaction between solvent cation rings and cellulose pyranose rings can compensate the interaction between stacked cellulose layers, thus stabilizing detached cellulose chains. Moreover, a frequently occurring intercalation of Bmim + on the hydrophilic surface is observed, which by separating cellulose layers can also potentially facilitate the initiation of fiber disintegration. The results provide a molecular description why ionic liquids are ideal cellulose solvents, the concerted action of anions and cations on the hydrophobic and hydrophilic surfaces being key to the efficient dissolution of the amphiphilic carbohydrate.« less

Kinetics of Contact Formation and End-to-End Distance Distributions of Swollen Disordered Peptides

PubMed Central

Soranno, Andrea; Longhi, Renato; Bellini, Tommaso; Buscaglia, Marco

2009-01-01

Unstructured polypeptide chains are subject to various degrees of swelling or compaction depending on the combination of solvent condition and amino acid sequence. Highly denatured proteins generally behave like random-coils with excluded volume repulsion, whereas in aqueous buffer more compact conformations have been observed for the low-populated unfolded state of globular proteins as well as for naturally disordered sequences. To quantitatively account for the different mechanisms inducing the swelling of polypeptides, we have examined three 14-residues peptides in aqueous buffer and in denaturant solutions, including the well characterized AGQ repeat as a reference and two variants, in which we have successively introduced charged side chains and removed the glycines. Quenching of the triplet state of tryptophan by close contact with cysteine has been used in conjunction with Förster resonance energy transfer to study the equilibrium and kinetic properties of the peptide chains. The experiments enable accessing end-to-end root mean-square distance, probability of end-to-end contact formation and intrachain diffusion coefficient. The data can be coherently interpreted on the basis of a simple chain model with backbone angles obtained from a library of coil segments of proteins and hard sphere repulsion at each Cα position. In buffered water, we find that introducing charges in a glycine-rich sequence induces a mild chain swelling and a significant speed-up of the intrachain dynamics, whereas the removal of the glycines results in almost a two-fold increase of the chain volume and a drastic slowing down. In denaturants we observe a pronounced swelling of all the chains, with significant differences between the effect of urea and guanidinium chloride. PMID:19217868

[A monitor for the emergency psychiatric service chain].

PubMed

Salden, M E F H; van Kemenade, J F L M; van Dam, A; Mulder, C L

2014-01-01

Many organisations are involved in the delivery of psychiatric emergency care to patients in crisis. We therefore refer to these organisations as the Psychiatric Emergency Chain (PEC). The quality of the PEC determines the quality of the psychiatric emergency care in a region. In order to measure the quality of this type of care a monitor has been developed in collaboration with the main stakeholders in the region Western North Brabant (WNB). To develop a monitor to measure the quality of a PEC in a region, identify weak spots in the chain and feed back the results to the chain. By searching the literature, studying the primary process in the chain and by having interviews with stakeholders we compiled a questionnaire for monitoring the pec. The monitor was tested in the WNB region and adjusted on the basis of experiences with the respondents. Then the monitor was generalised and tested in another region (Eindhoven and the Kempen) in order to find out whether this instrument might also be applicable to other pecs in the Netherlands. The monitor provided the PEC with a common language for evaluating the chain. The monitor was able to pinpoint particular weak spots and collaboration problems such as the response time required to reach the emergency, communication between and within organisations and domain discussions between different stakeholders. Chain partners used the results of the monitor to negotiate better collaborative agreements and to improve their care. The monitor is able to pinpoint problem areas in the PEC and subsequently to generate feedback to its stakeholders. This creates opportunities for improvement in the PEC. Therefore the monitor is a useful instrument for evaluating a local PEC periodically.

Paraprotein-Related Kidney Disease: Evaluation and Treatment of Myeloma Cast Nephropathy.

PubMed

Finkel, Kevin W; Cohen, Eric P; Shirali, Anushree; Abudayyeh, Ala

2016-12-07

Nearly 50% of patients with multiple myeloma develop renal disease, most commonly from AKI caused by cast nephropathy. Development of AKI is associated with poor 1-year survival and reduces the therapeutic options available to patients. There is a great need for more effective therapies. Cast nephropathy is caused by the interaction and aggregation of filtered free light chains and Tamm-Horsfall protein causing intratubular obstruction and damage. The key to treating cast nephropathy is rapid lowering of free light chains, because this correlates with renal recovery. Newer chemotherapy agents rapidly lower free light chains and have been referred to as renoprotective. There is additional great interest in using extracorporeal therapies to remove serum free light chains. Small trials initially showed benefit of therapeutic plasma exchange to improve renal outcomes in cast nephropathy, but a large randomized trial of therapeutic plasma exchange failed to show benefit. A newer technique is extended high-cutoff hemodialysis. This modality uses a high molecular weight cutoff filter to remove free light chains. To date, trials of high-cutoff hemodialysis use in patients with cast nephropathy have been encouraging. However, there are no randomized trials showing the benefit of high-cutoff hemodialysis when used in addition to newer chemotherapeutic regimens. Until these studies are available, high-cutoff hemodialysis cannot be recommended as standard of care. Copyright © 2016 by the American Society of Nephrology.

Using Peer-Referral Chains with Incentives to Promote HIV Testing and Identify Undiagnosed HIV Infections Among Crack Users in San Salvador

PubMed Central

Glasman, Laura R.; Dickson-Gomez, Julia; Lechuga, Julia; Tarima, Sergey; Bodnar, Gloria; de Mendoza, Lorena Rivas

2016-01-01

In El Salvador, crack users are at high risk for HIV but they are not targeted by efforts to promote early HIV diagnosis. We evaluated the promise of peer-referral chains with incentives to increase HIV testing and identify undiagnosed HIV infections among networks of crack users in San Salvador. For 14 months, we offered HIV testing in communities with a high prevalence of crack use. For the following 14 months, we promoted chains in which crack users from these communities referred their peers to HIV testing and received a small monetary incentive. We recorded the monthly numbers of HIV testers, and their crack use, sexual risk behaviors and test results. After launching the referral chains, the monthly numbers of HIV testers increased significantly (Z = 6.90, p < .001) and decayed more slowly (Z = 5.93, p < .001), and the total number of crack-using testers increased nearly fourfold. Testers in the peer-referral period reported fewer HIV risk behaviors, but a similar percentage (~5 %) tested HIV positive in both periods. More women than men received an HIV-positive diagnosis throughout the study (χ2(1, N = 799) = 4.23, p = .040). Peer-referral chains with incentives can potentially increase HIV testing among networks of crack users while retaining a focus on high-risk individuals. PMID:26687093

Reference gene selection for quantitative reverse transcription-polymerase chain reaction normalization during in vitro adventitious rooting in Eucalyptus globulus Labill.

PubMed

de Almeida, Márcia R; Ruedell, Carolina M; Ricachenevsky, Felipe K; Sperotto, Raul A; Pasquali, Giancarlo; Fett-Neto, Arthur G

2010-09-20

Eucalyptus globulus and its hybrids are very important for the cellulose and paper industry mainly due to their low lignin content and frost resistance. However, rooting of cuttings of this species is recalcitrant and exogenous auxin application is often necessary for good root development. To date one of the most accurate methods available for gene expression analysis is quantitative reverse transcription-polymerase chain reaction (qPCR); however, reliable use of this technique requires reference genes for normalization. There is no single reference gene that can be regarded as universal for all experiments and biological materials. Thus, the identification of reliable reference genes must be done for every species and experimental approach. The present study aimed at identifying suitable control genes for normalization of gene expression associated with adventitious rooting in E. globulus microcuttings. By the use of two distinct algorithms, geNorm and NormFinder, we have assessed gene expression stability of eleven candidate reference genes in E. globulus: 18S, ACT2, EF2, EUC12, H2B, IDH, SAND, TIP41, TUA, UBI and 33380. The candidate reference genes were evaluated in microccuttings rooted in vitro, in presence or absence of auxin, along six time-points spanning the process of adventitious rooting. Overall, the stability profiles of these genes determined with each one of the algorithms were very similar. Slight differences were observed in the most stable pair of genes indicated by each program: IDH and SAND for geNorm, and H2B and TUA for NormFinder. Both programs identified UBI and 18S as the most variable genes. To validate these results and select the most suitable reference genes, the expression profile of the ARGONAUTE1 gene was evaluated in relation to the most stable candidate genes indicated by each algorithm. Our study showed that expression stability varied between putative reference genes tested in E. globulus. Based on the AGO1 relative expression profile obtained using the genes suggested by the algorithms, H2B and TUA were considered as the most suitable reference genes for expression studies in E. globulus adventitious rooting. UBI and 18S were unsuitable for use as controls in qPCR related to this process. These findings will enable more accurate and reliable normalization of qPCR results for gene expression studies in this economically important woody plant, particularly related to rooting and clonal propagation.

Reference gene selection for quantitative reverse transcription-polymerase chain reaction normalization during in vitro adventitious rooting in Eucalyptus globulus Labill

PubMed Central

2010-01-01

Background Eucalyptus globulus and its hybrids are very important for the cellulose and paper industry mainly due to their low lignin content and frost resistance. However, rooting of cuttings of this species is recalcitrant and exogenous auxin application is often necessary for good root development. To date one of the most accurate methods available for gene expression analysis is quantitative reverse transcription-polymerase chain reaction (qPCR); however, reliable use of this technique requires reference genes for normalization. There is no single reference gene that can be regarded as universal for all experiments and biological materials. Thus, the identification of reliable reference genes must be done for every species and experimental approach. The present study aimed at identifying suitable control genes for normalization of gene expression associated with adventitious rooting in E. globulus microcuttings. Results By the use of two distinct algorithms, geNorm and NormFinder, we have assessed gene expression stability of eleven candidate reference genes in E. globulus: 18S, ACT2, EF2, EUC12, H2B, IDH, SAND, TIP41, TUA, UBI and 33380. The candidate reference genes were evaluated in microccuttings rooted in vitro, in presence or absence of auxin, along six time-points spanning the process of adventitious rooting. Overall, the stability profiles of these genes determined with each one of the algorithms were very similar. Slight differences were observed in the most stable pair of genes indicated by each program: IDH and SAND for geNorm, and H2B and TUA for NormFinder. Both programs indentified UBI and 18S as the most variable genes. To validate these results and select the most suitable reference genes, the expression profile of the ARGONAUTE1 gene was evaluated in relation to the most stable candidate genes indicated by each algorithm. Conclusion Our study showed that expression stability varied between putative reference genes tested in E. globulus. Based on the AGO1 relative expression profile obtained using the genes suggested by the algorithms, H2B and TUA were considered as the most suitable reference genes for expression studies in E. globulus adventitious rooting. UBI and 18S were unsuitable for use as controls in qPCR related to this process. These findings will enable more accurate and reliable normalization of qPCR results for gene expression studies in this economically important woody plant, particularly related to rooting and clonal propagation. PMID:20854682

Test of the ``radical-like polymerization'' scheme in molecular dynamics on the behavior of polymers under shock loading

NASA Astrophysics Data System (ADS)

Lemarchand, Claire; Bousquet, David; Schnell, Benoît; Pineau, Nicolas

2017-06-01

The behavior of polymer melts under shock loading is a question attracting more and more attention because of applications such as polymer-bonded explosives, light-weight armor and civilian protective equipment, like sports and car equipment. Molecular dynamics (MD) simulations are a very good tool to characterize the microscopic response of the polymer to a shock wave. To do so, the initial configuration of the polymer melt needs to be realistic. The ``radical-like polymerization'' scheme is a method to obtain near equilibrium configurations of a melt of long polymer chains. It consists in adding one neighboring monomer at a time to each growing chain. Between each polymerization step an MD run is performed to relax the new configuration. We test how details of our implementation of the ``radical-like polymerization'' scheme can impact or not Hugoniot curves and changes of chain configuration under shock. We compare our results to other simulation and experimental results on reference polymers.

The spread model of food safety risk under the supply-demand disturbance.

PubMed

Wang, Jining; Chen, Tingqiang

2016-01-01

In this paper, based on the imbalance of the supply-demand relationship of food, we design a spreading model of food safety risk, which is about from food producers to consumers in the food supply chain. We use theoretical analysis and numerical simulation to describe the supply-demand relationship and government supervision behaviors' influence on the risk spread of food safety and the behaviors of the food producers and the food retailers. We also analyze the influence of the awareness of consumer rights protection and the level of legal protection of consumer rights on the risk spread of food safety. This model contributes to the explicit investigation of the influence relationship among supply-demand factors, the regulation behavioral choice of government, the behavioral choice of food supply chain members and food safety risk spread. And this paper provides a new viewpoint for considering food safety risk spread in the food supply chain, which has a great reference for food safety management.

Optimal Linear Responses for Markov Chains and Stochastically Perturbed Dynamical Systems

NASA Astrophysics Data System (ADS)

Antown, Fadi; Dragičević, Davor; Froyland, Gary

2018-03-01

The linear response of a dynamical system refers to changes to properties of the system when small external perturbations are applied. We consider the little-studied question of selecting an optimal perturbation so as to (i) maximise the linear response of the equilibrium distribution of the system, (ii) maximise the linear response of the expectation of a specified observable, and (iii) maximise the linear response of the rate of convergence of the system to the equilibrium distribution. We also consider the inhomogeneous, sequential, or time-dependent situation where the governing dynamics is not stationary and one wishes to select a sequence of small perturbations so as to maximise the overall linear response at some terminal time. We develop the theory for finite-state Markov chains, provide explicit solutions for some illustrative examples, and numerically apply our theory to stochastically perturbed dynamical systems, where the Markov chain is replaced by a matrix representation of an approximate annealed transfer operator for the random dynamical system.

[Equivalent Lever Principle of Ossicular Chain and Amplitude Reduction Effect of Internal Ear Lymph].

PubMed

Zhao, Xiaoyan; Qin, Renjia

2015-04-01

This paper makes persuasive demonstrations on some problems about the human ear sound transmission principle in existing physiological textbooks and reference books, and puts forward the authors' view to make up for its literature. Exerting the knowledge of lever in physics and the acoustics theory, we come up with an equivalent simplified model of manubrium mallei which is to meet the requirements as the long arm of the lever. We also set up an equivalent simplified model of ossicular chain--a combination of levers of ossicular chain. We disassemble the model into two simple levers, and make full analysis and demonstration on them. Through the calculation and comparison of displacement amplitudes in both external auditory canal air and internal ear lymph, we may draw a conclusion that the key reason, which the sound displacement amplitude is to be decreased to adapt to the endurance limit of the basement membrane, is that the density and sound speed in lymph is much higher than those in the air.

Development of a digital hearing aid to meet the Brazilian Government's Ordinance 587 (APAC).

PubMed

Penteado, Silvio Pires; Bento, Ricardo Ferreira

2010-01-01

The treatment of sensorineural hearing loss is based on hearing aids, also known as individual sound amplification devices. The hearing aids purchased by the Brazilian Government, aiming at fulfilling public policies, are based on dedicated components, which bring about benefits, but also render them expensive and may impair repair services after manufacture's warranty expires. to design digital behind-the-ear hearing aids built from standardized components coming from the very supply chain of these manufacturers. experimental. to identify the supply chain of these manufacturers, request samples and set up hearing aids in the laboratory. The developed hearing aids did not show lesser electroacoustic characteristics when compared to those acquired by the Government, also being tested by the same reference international technical standard. It is possible to develop digital behind-the-ear hearing aids based on off-the-shelf components from hearing aid manufacturers' supply chain. Their advantages include low operational costs - for acquisition (with clear advantages for the Government) and service (advantage for the patient).

Lipases as biocatalysts for the synthesis of structured lipids.

PubMed

Jala, Ram Chandra Reddy; Hu, Peng; Yang, Tiankui; Jiang, Yuanrong; Zheng, Yan; Xu, Xuebing

2012-01-01

Structured lipids (SL) are broadly referred to as modified or synthetic oils and fats or lipids with functional or pharmaceutical applications. Some structured lipids, such as triglycerides that contain both long-chain (mainly essential) fatty acids and medium- or short-chain fatty acids and also artificial products that mimic the structure of natural materials, namely human milk fat substitutes and cocoa butter equivalents, have been discussed. Further, other modified or synthetic lipids, such as structured phospholipids and synthetic phenolic lipids are also included in this chapter. For all the products described in this chapter, enzymatic production in industry has been already conducted in one way or another. Cocoa butter equivalents, healthy oil containing medium-chain fatty acids, phosphatidyl serine, and phenol lipids from enzyme technology have been reported for commercial operation. As the demand for better quality functional lipids is increasing, the production of structured lipids becomes an interesting area. Thus, in this chapter we have discussed latest developments as well as present industrial situation of all commercially important structured lipids.

Characterization and Uncertainty Analysis of a Reference Pressure Measurement System for Wind Tunnels

NASA Technical Reports Server (NTRS)

Amer, Tahani; Tripp, John; Tcheng, Ping; Burkett, Cecil; Sealey, Bradley

2004-01-01

This paper presents the calibration results and uncertainty analysis of a high-precision reference pressure measurement system currently used in wind tunnels at the NASA Langley Research Center (LaRC). Sensors, calibration standards, and measurement instruments are subject to errors due to aging, drift with time, environment effects, transportation, the mathematical model, the calibration experimental design, and other factors. Errors occur at every link in the chain of measurements and data reduction from the sensor to the final computed results. At each link of the chain, bias and precision uncertainties must be separately estimated for facility use, and are combined to produce overall calibration and prediction confidence intervals for the instrument, typically at a 95% confidence level. The uncertainty analysis and calibration experimental designs used herein, based on techniques developed at LaRC, employ replicated experimental designs for efficiency, separate estimation of bias and precision uncertainties, and detection of significant parameter drift with time. Final results, including calibration confidence intervals and prediction intervals given as functions of the applied inputs, not as a fixed percentage of the full-scale value are presented. System uncertainties are propagated beginning with the initial reference pressure standard, to the calibrated instrument as a working standard in the facility. Among the several parameters that can affect the overall results are operating temperature, atmospheric pressure, humidity, and facility vibration. Effects of factors such as initial zeroing and temperature are investigated. The effects of the identified parameters on system performance and accuracy are discussed.

Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs.

PubMed

Tsai, Pei-Chien; Breen, Matthew

2012-09-01

To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.

The Effectiveness of Circular Equating as a Criterion for Evaluating Equating.

ERIC Educational Resources Information Center

Wang, Tianyou; Hanson, Bradley A.; Harris, Deborah J.

Equating a test form to itself through a chain of equatings, commonly referred to as circular equating, has been widely used as a criterion to evaluate the adequacy of equating. This paper uses both analytical methods and simulation methods to show that this criterion is in general invalid in serving this purpose. For the random groups design done…

29 CFR 1910.6 - Incorporation by reference.

Code of Federal Regulations, 2013 CFR

2013-07-01

...); and 1910.111(d)(1) (ii) and (iii). (6) API 650 (1966) Welded Steel Tanks for Oil Storage, 3rd Ed., IBR... and Seamless Steel Pipe, IBR approved for §§ 1910.110 and 1910.111. (3) ASTM A 126-66, Gray Iron...-1968), Alloy Steel Chain, IBR approved for § 1910.184. (5) ASTM A 395-68, Ductile Iron for Use at...

29 CFR 1910.6 - Incorporation by reference.

Code of Federal Regulations, 2014 CFR

2014-07-01

...); and 1910.111(d)(1) (ii) and (iii). (6) API 650 (1966) Welded Steel Tanks for Oil Storage, 3rd Ed., IBR... and Seamless Steel Pipe, IBR approved for §§ 1910.110 and 1910.111. (3) ASTM A 126-66, Gray Iron...-1968), Alloy Steel Chain, IBR approved for § 1910.184. (5) ASTM A 395-68, Ductile Iron for Use at...

Anaerobic digestion of agricultural and other substrates--implications for greenhouse gas emissions.

PubMed

Pucker, J; Jungmeier, G; Siegl, S; Pötsch, E M

2013-06-01

The greenhouse gas (GHG) emissions, expressed in carbon dioxide equivalents (CO2-eq), of different Austrian biogas systems were analyzed and evaluated using life-cycle assessment (LCA) as part of a national project. Six commercial biogas plants were investigated and the analysis included the complete process chain: viz., the production and collection of substrates, the fermentation of the substrates in the biogas plant, the upgrading of biogas to biomethane (if applicable) and the use of the biogas or biomethane for heat and electricity or as transportation fuel. Furthermore, the LCA included the GHG emissions of construction, operation and dismantling of the major components involved in the process chain, as well as the use of by-products (e.g. fermentation residues used as fertilizers). All of the biogas systems reduced GHG emissions (in CO2-eq) compared with fossil reference systems. The potential for GHG reduction of the individual biogas systems varied between 60% and 100%. Type of feedstock and its reference use, agricultural practices, coverage of storage tanks for fermentation residues, methane leakage at the combined heat and power plant unit and the proportion of energy used as heat were identified as key factors influencing the GHG emissions of anaerobic digestion processes.

Development of two real-time polymerase chain reaction assays to detect Actinobacillus pleuropneumoniae serovars 1-9-11 and serovar 2.

PubMed

Marois-Créhan, Corinne; Lacouture, Sonia; Jacques, Mario; Fittipaldi, Nahuel; Kobisch, Marylène; Gottschalk, Marcelo

2014-01-01

Two real-time, or quantitative, polymerase chain reaction (qPCR) assays were developed to detect Actinobacillus pleuropneumoniae serovars 1-9-11 (highly related serovars with similar virulence potential) and serovar 2, respectively. The specificity of these assays was verified on a collection of 294 strains, which included all 16 reference A. pleuropneumoniae strains (including serovars 5a and 5b), 263 A. pleuropneumoniae field strains isolated between 1992 and 2009 in different countries, and 15 bacterial strains other than A. pleuropneumoniae. The detection levels of both qPCR tests were evaluated using 10-fold dilutions of chromosomal DNA from reference strains of A. pleuropneumoniae serovars 1 and 2, and the detection limit for both assays was 50 fg per assay. The analytical sensitivities of the qPCR tests were also estimated by using pure cultures and tonsils experimentally spiked with A. pleuropneumoniae. The detection threshold was 2.5 × 10(4) colony forming units (CFU)/ml and 2.9 × 10(5) CFU/0.1 g of tonsil, respectively, for both assays. These specific and sensitive tests can be used for the serotyping of A. pleuropneumoniae in diagnostic laboratories to control porcine pleuropneumonia.

Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements.

PubMed

He, Hua-Jun; Almeida, Jamie L; Lund, Steve P; Steffen, Carolyn R; Choquette, Steve; Cole, Kenneth D

2016-06-01

NIST standard reference material (SRM) 2373 was developed to improve the measurements of the HER2 gene amplification in DNA samples. SRM 2373 consists of genomic DNA extracted from five breast cancer cell lines with different amounts of amplification of the HER2 gene. The five components are derived from the human cell lines SK-BR-3, MDA-MB-231, MDA-MB-361, MDA-MB-453, and BT-474. The certified values are the ratios of the HER2 gene copy numbers to the copy numbers of selected reference genes DCK, EIF5B, RPS27A, and PMM1. The ratios were measured using quantitative polymerase chain reaction and digital PCR, methods that gave similar ratios. The five components of SRM 2373 have certified HER2 amplification ratios that range from 1.3 to 17.7. The stability and homogeneity of the reference materials were shown by repeated measurements over a period of several years. SRM 2373 is a well characterized genomic DNA reference material that can be used to improve the confidence of the measurements of HER2 gene copy number.

Comparative higher-order structure analysis of antibody biosimilars using combined bottom-up and top-down hydrogen-deuterium exchange mass spectrometry.

PubMed

Pan, Jingxi; Zhang, Suping; Borchers, Christoph H

2016-12-01

Hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) is a powerful technique for higher-order structural characterization of antibodies. Although the peptide-based bottom-up HDX approach and the protein-based top-down HDX approach have complementary advantages, the work done so far on biosimilars has involved only one or the other approach. Herein we have characterized the structures of two bevacizumab (BEV) biosimilars and compared them to the reference BEV using both methods. A sequence coverage of 87% was obtained for the heavy chain and 74% for the light chain in the bottom-up approach. The deuterium incorporation behavior of the peptic peptides from the three BEVs were compared side by side and showed no differences at various HDX time points. Top-down experiments were carried out using subzero temperature LC-MS, and the deuterium incorporation of the intact light chain and heavy chain were obtained. Top-down ETD was also performed to obtain amino acid-level HDX information that covered 100% of the light chain, but only 50% coverage is possible for the heavy chain. Consistent with the intact subunit level data, no differences were observed in the amino acid level HDX data. All these results indicate that there are no differences between the three BEV samples with respect to their high-order structures. The peptide level information from the bottom-up approach, and the residue level and intact subunit level information from the top-down approach were complementary and covered the entire antibody. Copyright © 2016 Elsevier B.V. All rights reserved.

Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation.

PubMed

Masè, Michela; Grasso, Margherita; Avogaro, Laura; D'Amato, Elvira; Tessarolo, Francesco; Graffigna, Angelo; Denti, Michela Alessandra; Ravelli, Flavia

2017-01-24

MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-C q , GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions.

Stable Reference Gene Selection for RT-qPCR Analysis in Nonviruliferous and Viruliferous Frankliniella occidentalis.

PubMed

Yang, Chunxiao; Li, Hui; Pan, Huipeng; Ma, Yabin; Zhang, Deyong; Liu, Yong; Zhang, Zhanhong; Zheng, Changying; Chu, Dong

2015-01-01

Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for measuring and evaluating gene expression during variable biological processes. To facilitate gene expression studies, normalization of genes of interest relative to stable reference genes is crucial. The western flower thrips Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), the main vector of tomato spotted wilt virus (TSWV), is a destructive invasive species. In this study, the expression profiles of 11 candidate reference genes from nonviruliferous and viruliferous F. occidentalis were investigated. Five distinct algorithms, geNorm, NormFinder, BestKeeper, the ΔCt method, and RefFinder, were used to determine the performance of these genes. geNorm, NormFinder, BestKeeper, and RefFinder identified heat shock protein 70 (HSP70), heat shock protein 60 (HSP60), elongation factor 1 α, and ribosomal protein l32 (RPL32) as the most stable reference genes, and the ΔCt method identified HSP60, HSP70, RPL32, and heat shock protein 90 as the most stable reference genes. Additionally, two reference genes were sufficient for reliable normalization in nonviruliferous and viruliferous F. occidentalis. This work provides a foundation for investigating the molecular mechanisms of TSWV and F. occidentalis interactions.

Selection of reference genes for expression analysis in the entomophthoralean fungus Pandora neoaphidis.

PubMed

Chen, Chun; Xie, Tingna; Ye, Sudan; Jensen, Annette Bruun; Eilenberg, Jørgen

2016-01-01

The selection of suitable reference genes is crucial for accurate quantification of gene expression and can add to our understanding of host-pathogen interactions. To identify suitable reference genes in Pandora neoaphidis, an obligate aphid pathogenic fungus, the expression of three traditional candidate genes including 18S rRNA(18S), 28S rRNA(28S) and elongation factor 1 alpha-like protein (EF1), were measured by quantitative polymerase chain reaction at different developmental stages (conidia, conidia with germ tubes, short hyphae and elongated hyphae), and under different nutritional conditions. We calculated the expression stability of candidate reference genes using four algorithms including geNorm, NormFinder, BestKeeper and Delta Ct. The analysis results revealed that the comprehensive ranking of candidate reference genes from the most stable to the least stable was 18S (1.189), 28S (1.414) and EF1 (3). The 18S was, therefore, the most suitable reference gene for real-time RT-PCR analysis of gene expression under all conditions. These results will support further studies on gene expression in P. neoaphidis. Copyright © 2015 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

The propagation and backscattering of soliton-like pulses in a chain of quartz beads and related problems. (II). Backscattering

NASA Astrophysics Data System (ADS)

Manciu, Marian; Sen, Surajit; Hurd, Alan J.

1999-12-01

We demonstrate that the propagation of solitons, soliton-like excitations and acoustic pulses discussed in the preceding article (M. Manciu, S. Sen and A.J. Hurd, Physica A, preceding article) can be used to detect buried impurities in a chain of elastic grains with Hertzian contacts. We also present preliminary data for 3D granular beds, where soliton-like objects can form and can be used to probe for buried impurities, thus suggesting that soliton-pulse spectroscopy has the potential to become a valuable tool for probing the structural properties of granular assemblies. The effects of restitution are briefly discussed. We refer to available experiments which support our contention.

The Effects of Partnership Management on Supply Chain Cooperative Performance: A Case Study of High-Tech Industry

NASA Astrophysics Data System (ADS)

Wu, Mei-Ying; Chang, Yun-Ju; Weng, Yung-Chien

2009-08-01

With the structural change of global supply chains, the relationship between manufacturers and suppliers has transformed into a long-term partnership. Thus, this study aims to explore the partnership between manufacturers and suppliers in Taiwan's high-tech industry. Four constructs, including partner characteristic, partnership quality, partnership closeness, and cooperative performance, induced from previous literatures are used to construct the research framework and hypotheses. A questionnaire survey is then performed on executives and staffs involved in the high-tech industry. The proposed framework and hypotheses are empirically validated through confirmatory factory analysis and structural equation modeling. It is expected that the research findings can serve as a reference for Taiwan's high-tech industry on building partnerships.

Cluster analysis for determining distribution center location

NASA Astrophysics Data System (ADS)

Lestari Widaningrum, Dyah; Andika, Aditya; Murphiyanto, Richard Dimas Julian

2017-12-01

Determination of distribution facilities is highly important to survive in the high level of competition in today’s business world. Companies can operate multiple distribution centers to mitigate supply chain risk. Thus, new problems arise, namely how many and where the facilities should be provided. This study examines a fast-food restaurant brand, which located in the Greater Jakarta. This brand is included in the category of top 5 fast food restaurant chain based on retail sales. There were three stages in this study, compiling spatial data, cluster analysis, and network analysis. Cluster analysis results are used to consider the location of the additional distribution center. Network analysis results show a more efficient process referring to a shorter distance to the distribution process.

Effects of predation efficiencies on the dynamics of a tritrophic food chain.

PubMed

Cassinari, Maria Paola; Groppi, Maria; Tebaldi, Claudio

2007-07-01

In this paper the dynamics of a tritrophic food chain (resource, consumer, top predator) is investigated, with particular attention not only to equilibrium states but also to cyclic behaviours that the system may exhibit. The analysis is performed in terms of two bifurcation parameters, denoted by p and q, which measure the efficiencies of the interaction processes. The persistence of the system is discussed, characterizing in the (p; q) plane the regions of existence and stability of biologically significant steady states and those of existence of limit cycles. The bifurcations occurring are discussed, and their implications with reference to biological control problems are considered. Examples of the rich dynamics exhibited by the model, including a chaotic regime, are described.

Interaction of nanoparticles with edible plants and their possible implications in the food chain

PubMed Central

Rico, Cyren M.; Majumdar, Sanghamitra; Duarte-Gardea, Maria; Peralta-Videa, Jose R.; Gardea-Torresdey, Jorge L.

2011-01-01

The uptake, bioaccumulation, biotransformation, and risks of nanomaterials (NMs) for the food crops are still not well understood. Very few NMs and plant species have been studied, mainly at the very early growth stages of the plants. Most of the studies, except one with multiwalled carbon nanotubes performed on the model plant Arabidopsis thaliana and another with ZnO nanoparticles (NPs) on ryegrass, reported the effect of NMs on seed germination or 15 day old seedlings. Very few references describe the biotransformation of NMs in food crops and the possible transmission of the NMs to the next generation of plants exposed to NMs is unknown. The possible biomagnification of NPs in the food chain is also unknown. PMID:21405020

Levelized cost of energy for a Backward Bent Duct Buoy

DOE PAGES

Bull, Diana; Jenne, D. Scott; Smith, Christopher S.; ...

2016-07-18

The Reference Model Project, supported by the U.S. Department of Energy, was developed to provide publicly available technical and economic benchmarks for a variety of marine energy converters. The methodology to achieve these benchmarks is to develop public domain designs that incorporate power performance estimates, structural models, anchor and mooring designs, power conversion chain designs, and estimates of the operations and maintenance, installation, and environmental permitting required. The reference model designs are intended to be conservative, robust, and experimentally verified. The Backward Bent Duct Buoy (BBDB) presented in this paper is one of three wave energy conversion devices studied withinmore » the Reference Model Project. Furthermore, comprehensive modeling of the BBDB in a Northern California climate has enabled a full levelized cost of energy (LCOE) analysis to be completed on this device.« less

Levelized cost of energy for a Backward Bent Duct Buoy

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

Bull, Diana; Jenne, D. Scott; Smith, Christopher S.

2016-12-01

The Reference Model Project, supported by the U.S. Department of Energy, was developed to provide publically available technical and economic benchmarks for a variety of marine energy converters. The methodology to achieve these benchmarks is to develop public domain designs that incorporate power performance estimates, structural models, anchor and mooring designs, power conversion chain designs, and estimates of the operations and maintenance, installation, and environmental permitting required. The reference model designs are intended to be conservative, robust, and experimentally verified. The Backward Bent Duct Buoy (BBDB) presented in this paper is one of three wave energy conversion devices studied withinmore » the Reference Model Project. Comprehensive modeling of the BBDB in a Northern California climate has enabled a full levelized cost of energy (LCOE) analysis to be completed on this device.« less

Selection of Suitable Reference Genes for RT-qPCR Normalization under Abiotic Stresses and Hormone Stimulation in Persimmon (Diospyros kaki Thunb)

PubMed Central

Wang, Peihong; Xiong, Aisheng; Gao, Zhihong; Yu, Xinyi; Li, Man; Hou, Yingjun; Sun, Chao; Qu, Shenchun

2016-01-01

The success of quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) to quantify gene expression depends on the stability of the reference genes used for data normalization. To date, systematic screening for reference genes in persimmon (Diospyros kaki Thunb) has never been reported. In this study, 13 candidate reference genes were cloned from 'Nantongxiaofangshi' using information available in the transcriptome database. Their expression stability was assessed by geNorm and NormFinder algorithms under abiotic stress and hormone stimulation. Our results showed that the most suitable reference genes across all samples were UBC and GAPDH, and not the commonly used persimmon reference gene ACT. In addition, UBC combined with RPII or TUA were found to be appropriate for the "abiotic stress" group and α-TUB combined with PP2A were found to be appropriate for the "hormone stimuli" group. For further validation, the transcript level of the DkDREB2C homologue under heat stress was studied with the selected genes (CYP, GAPDH, TUA, UBC, α-TUB, and EF1-α). The results suggested that it is necessary to choose appropriate reference genes according to the test materials or experimental conditions. Our study will be useful for future studies on gene expression in persimmon. PMID:27513755

Validation of reference genes for quantitative gene expression analysis in experimental epilepsy.

PubMed

Sadangi, Chinmaya; Rosenow, Felix; Norwood, Braxton A

2017-12-01

To grasp the molecular mechanisms and pathophysiology underlying epilepsy development (epileptogenesis) and epilepsy itself, it is important to understand the gene expression changes that occur during these phases. Quantitative real-time polymerase chain reaction (qPCR) is a technique that rapidly and accurately determines gene expression changes. It is crucial, however, that stable reference genes are selected for each experimental condition to ensure that accurate values are obtained for genes of interest. If reference genes are unstably expressed, this can lead to inaccurate data and erroneous conclusions. To date, epilepsy studies have used mostly single, nonvalidated reference genes. This is the first study to systematically evaluate reference genes in male Sprague-Dawley rat models of epilepsy. We assessed 15 potential reference genes in hippocampal tissue obtained from 2 different models during epileptogenesis, 1 model during chronic epilepsy, and a model of noninjurious seizures. Reference gene ranking varied between models and also differed between epileptogenesis and chronic epilepsy time points. There was also some variance between the four mathematical models used to rank reference genes. Notably, we found novel reference genes to be more stably expressed than those most often used in experimental epilepsy studies. The consequence of these findings is that reference genes suitable for one epilepsy model may not be appropriate for others and that reference genes can change over time. It is, therefore, critically important to validate potential reference genes before using them as normalizing factors in expression analysis in order to ensure accurate, valid results. © 2017 Wiley Periodicals, Inc.

Counter Unmanned Aerial System Decision-Aid Logic Process (C-UAS DALP)

DTIC Science & Technology

decision -aid or logic process that bridges the middle elements of the kill... of use, location, general logic process , and reference mission. This is the framework for the IDEF0 functional architecture diagrams, decision -aid diagrams, logic process , and modeling and simulation....chain between detection to countermeasure response. This capstone project creates the logic for a decision process that transitions from the

Evaluation of Organisational Interoperabiity in a Network Centric Warfare Environment

DTIC Science & Technology

2004-09-01

understanding developed. Command and Coordination examines issues related to command structure, command and leadership styles . Ethos covers socio...harmonisation of command arrangements and the accommodation of differences in command and leadership styles . 3.2.4 Ethos Future warfare will... leadership styles . • changes to give less emphasis to hierarchy and command and more to coordination. Any reference to a single chain of command has been

26 CFR 1.883-1 - Exclusion of income from the international operation of ships or aircraft.

Code of Federal Regulations, 2014 CFR

2014-04-01

... charter), space, slot, or block-seat charter, or dry lease, as those terms are defined in paragraph (e)(5... connection with passenger aircraft this sort of charter may be referred to as the sale of block seats. (ix... how the ship or aircraft is used by the lowest-tier lessee in the chain of lessees (as provided in...

26 CFR 1.883-1 - Exclusion of income from the international operation of ships or aircraft.

Code of Federal Regulations, 2013 CFR

2013-04-01

... charter), space, slot, or block-seat charter, or dry lease, as those terms are defined in paragraph (e)(5... connection with passenger aircraft this sort of charter may be referred to as the sale of block seats. (ix... how the ship or aircraft is used by the lowest-tier lessee in the chain of lessees (as provided in...

26 CFR 1.883-1 - Exclusion of income from the international operation of ships or aircraft.

Code of Federal Regulations, 2011 CFR

2011-04-01

... charter), space, slot, or block-seat charter, or dry lease, as those terms are defined in paragraph (e)(5... connection with passenger aircraft this sort of charter may be referred to as the sale of block seats. (ix... how the ship or aircraft is used by the lowest-tier lessee in the chain of lessees (as provided in...

26 CFR 1.883-1 - Exclusion of income from the international operation of ships or aircraft.

Code of Federal Regulations, 2012 CFR

2012-04-01

... charter), space, slot, or block-seat charter, or dry lease, as those terms are defined in paragraph (e)(5... connection with passenger aircraft this sort of charter may be referred to as the sale of block seats. (ix... how the ship or aircraft is used by the lowest-tier lessee in the chain of lessees (as provided in...

A biomonitoring plan for assessing potential radionuclide exposure using Amchitka Island in the Aleutian chain of Alaska as a case study.

PubMed

Burger, Joanna; Gochfeld, Michael; Kosson, D S; Powers, Charles W

2007-01-01

With the ending of the Cold War, the US and other nations were faced with a legacy of nuclear wastes. For some sites where hazardous nuclear wastes will remain in place, methods must be developed to protect human health and the environment. Biomonitoring is one method of assessing the status and trends of potential radionuclide exposure from nuclear waste sites, and of providing the public with early warning of any potential harmful exposure. Amchitka Island (51 degrees N lat, 179 degrees E long) was the site of three underground nuclear tests from 1965 to 1971. Following a substantive study of radionuclide levels in biota from the marine environment around Amchitka and a reference site, we developed a suite of bioindicators (with suggested isotopes) that can serve as a model for other sites contaminated with radionuclides. Although the species selection was site-specific, the methods can provide a framework for other sites. We selected bioindicators using five criteria: (1) occurrence at all three test shots (and reference site), (2) receptor groups (subsistence foods, commercial species, and food chain nodes), (3) species groups (plants, invertebrates, fish, and birds), (4) trophic levels, and (5) an accumulator of one or several radionuclides. Our major objective was to identify bioindicators that could serve for both human health and the ecosystem, and were abundant enough to collect adjacent to the three test sites and at the reference site. Site-specific information on both biota availability and isotope levels was essential in the final selection of bioindicators. Actinides bioaccumulated in algae and invertebrates, while radiocesium accumulated in higher trophic level birds and fish. Thus, unlike biomonitoring schemes developed for heavy metals or other contaminants, top-level predators are not sufficient to evaluate potential radionuclide exposure at Amchitka. The process described in this paper resulted in the selection of Fucus, Alaria fistulosa, blue mussel (Mytilus trossulus), dolly varden (Salvelinus malma), black rockfish (Sebastes melanops), Pacific cod (Gadus macrocephalus), Pacific halibut (Hippoglossus stenolepis), and glaucous-winged gull (Larus glaucescens) as bioindicators. This combination of species included mainly subsistence foods, commercial fish, and nodes on different food chains.

Effect of short chain inulin on the rheological and sensory characteristics of reduced fat set coconut milk yoghurt.

PubMed

Adegoke, Samuel Chetachukwu; Thongraung, Chakree; Yupanqui, Chutha Takahashi

2018-06-23

The effect of short-chain inulin on the rheological and sensory properties of reduced fat set coconut milk yoghurt was studied with whole fat coconut milk yoghurt as reference. The concentration of short-chain inulin was varied at 0, 5, 10, 15, and 20% w/v respectively. All the yoghurt samples displayed higher elastic modulus G' than viscous modulus G". However, 15% inulin yoghurt had the highest value for G' & G". The 15 and 20% inulin yoghurts displayed high yield stress (1036.7 ± 2.39 & 368.23 ± 0.30 Pa). Addition threshold of 15% was established, beyond this level there was a significant decrease in the yield stress, firmness, cohesiveness and consistency values of the reduced fat yoghurts. Using Pearson correlation analysis, no correlation was observed between firmness and yield stress, Similarly, there was significant correlation between the yield stress and instrumental viscosity r = 0.957; p < 0.01. Furthermore, all yoghurt samples displayed strain thinning behavior except whole fat yoghurt. Carbohydrate was affected by inulin incorporation. Addition of short chain inulin improved sensorial characteristics such as taste, and flavor, but did not display significant difference in color and odor of yoghurt samples. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Trust in the early chain of healthcare: lifeworld hermeneutics from the patient’s perspective

PubMed Central

Norberg Boysen, Gabriella; Nyström, Maria; Christensson, Lennart; Herlitz, Johan; Wireklint Sundström, Birgitta

2017-01-01

ABSTRACT Purpose: Patients must be able to feel as much trust for caregivers and the healthcare system at the healthcare centre as at the emergency department. The aim of this study is to explain and understand the phenomenon of trust in the early chain of healthcare, when a patient has called an ambulance for a non-urgent condition and been referred to the healthcare centre. Method: A lifeworld hermeneutic approach from the perspective of caring science was used. Ten patients participated: seven female and three male. The setting is the early chain of healthcare in south-western Sweden. Results: The findings show that the phenomenon of trust does not automatically involve medical care. However, attention to the patient’s lifeworld in a professional caring relationship enables the patient to trust the caregiver and the healthcare environment. It is clear that the “voice of the lifeworld” enables the patient to feel trust. Conclusion: Trust in the early chain of healthcare entails caregivers’ ability to pay attention to both medical and existential issues in compliance with the patient’s information and questions. Thus, the patient must be invited to participate in assessments and decisions concerning his or her own healthcare, in a credible manner and using everyday language. PMID:28793852

Systematic Review of Ossicular Chain Anatomy: Strategic Planning for Development of Novel Middle Ear Prostheses.

PubMed

Kamrava, Brandon; Roehm, Pamela C

2017-08-01

Objective To systematically review the anatomy of the ossicular chain. Data Sources Google Scholar, PubMed, and otologic textbooks. Review Methods A systematic literature search was performed on January 26, 2015. Search terms used to discover articles consisted of combinations of 2 keywords. One keyword from both groups was used: [ ossicular, ossicle, malleus, incus, stapes] and [ morphology, morphometric, anatomy, variation, physiology], yielding more than 50,000 hits. Articles were then screened by title and abstract if they did not contain information relevant to human ossicular chain anatomy. In addition to this search, references of selected articles were studied as well as suggested relevant articles from publication databases. Standard otologic textbooks were screened using the search criteria. Results Thirty-three sources were selected for use in this review. From these studies, data on the composition, physiology, morphology, and morphometrics were acquired. In addition, any correlations or lack of correlations between features of the ossicular chain and other features of the ossicular chain or patient were noted, with bilateral symmetry between ossicles being the only important correlation reported. Conclusion There was significant variation in all dimensions of each ossicle between individuals, given that degree of variation, custom fitting, or custom manufacturing of prostheses for each patient could optimize prosthesis fit. From published data, an accurate 3-dimensional model of the malleus, incus, and stapes can be created, which can then be further modified for each patient's individual anatomy.

Using Peer-Referral Chains with Incentives to Promote HIV Testing and Identify Undiagnosed HIV Infections Among Crack Users in San Salvador.

PubMed

Glasman, Laura R; Dickson-Gomez, Julia; Lechuga, Julia; Tarima, Sergey; Bodnar, Gloria; de Mendoza, Lorena Rivas

2016-06-01

In El Salvador, crack users are at high risk for HIV but they are not targeted by efforts to promote early HIV diagnosis. We evaluated the promise of peer-referral chains with incentives to increase HIV testing and identify undiagnosed HIV infections among networks of crack users in San Salvador. For 14 months, we offered HIV testing in communities with a high prevalence of crack use. For the following 14 months, we promoted chains in which crack users from these communities referred their peers to HIV testing and received a small monetary incentive. We recorded the monthly numbers of HIV testers, and their crack use, sexual risk behaviors and test results. After launching the referral chains, the monthly numbers of HIV testers increased significantly (Z = 6.90, p < .001) and decayed more slowly (Z = 5.93, p < .001), and the total number of crack-using testers increased nearly fourfold. Testers in the peer-referral period reported fewer HIV risk behaviors, but a similar percentage (~5 %) tested HIV positive in both periods. More women than men received an HIV-positive diagnosis throughout the study (χ(2)(1, N = 799) = 4.23, p = .040). Peer-referral chains with incentives can potentially increase HIV testing among networks of crack users while retaining a focus on high-risk individuals.

Developing a competitive advantage in the market for radiology services.

PubMed

Kropf, R; Szafran, A J

1988-01-01

This article describes how managers of outpatient diagnostic radiology services can develop a competitive advantage by increasing the value of services to patients and referring physicians. A method is presented to identify changes to services that increase their value. The method requires the definition of the "value chains" of patients and referring physicians. Particular attention is paid to the use of information systems technology to suggest and implement service changes. A narrow range of health services was selected because the approach requires a detailed understanding of consumers and how they use services. The approach should, however, be examined carefully by managers seeking to develop a competitive advantage for a wide range of health services.

RefPrimeCouch—a reference gene primer CouchApp

PubMed Central

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html PMID:24368831

RefPrimeCouch--a reference gene primer CouchApp.

PubMed

Silbermann, Jascha; Wernicke, Catrin; Pospisil, Heike; Frohme, Marcus

2013-01-01

To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Database URL: http://hpclife.th-wildau.de:5984/rpc/_design/rpc/view.html.

Hawaii bibliographic database

USGS Publications Warehouse

Wright, T.L.; Takahashi, T.J.

1998-01-01

The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and abstracts or (if no abstract) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

Real-time PCR assay for the diagnosis of pleural tuberculosis

PubMed Central

Cárdenas Bernal, Ana María; Giraldo-Cadavid, Luis Fernando; Prieto Diago, Enrique; Santander, Sandra Paola

2017-01-01

Abstract Introduction: The diagnosis of pleural tuberculosis requires an invasive and time-consuming reference method. Polymerase chain reaction (PCR) is rapid, but validation in pleural tuberculosis is still weak. Objective: To establish the operating characteristics of real-time polymerase chain reaction (RT-PCR) hybridization probes for the diagnosis of pleural tuberculosis. Methods: The validity of the RT-PCR hybridization probes was evaluated compared to a composite reference method by a cross-sectional study at the Hospital Universitario de la Samaritana. 40 adults with lymphocytic pleural effusion were included. Pleural tuberculosis was confirmed (in 9 patients) if the patient had at least one of three tests using the positive reference method: Ziehl-Neelsen or Mycobacterium tuberculosis culture in fluid or pleural tissue, or pleural biopsy with granulomas. Pleural tuberculosis was ruled out (in 31 patients) if all three tests were negative. The operating characteristics of the RT-PCR, using the Mid-P Exact Test, were determined using the OpenEpi 2.3 Software (2009). Results: The RT-PCR hybridization probes showed a sensitivity of 66.7% (95% CI: 33.2%-90.7%) and a specificity of 93.5% (95% CI: 80.3%-98.9%). The PPV was 75.0% (95% CI: 38.8%-95.6%) and a NPV of 90.6% (95% CI: 76.6%-97.6%). Two false positives were found for the test, one with pleural mesothelioma and the other with chronic pleuritis with mesothelial hyperplasia. Conclusions: The RT-PCR hybridization probes had good specificity and acceptable sensitivity, but a negative value cannot rule out pleural tuberculosis. PMID:29021638

Filling reference gaps via assembling DNA barcodes using high-throughput sequencing—moving toward barcoding the world

PubMed Central

Zhou, Chengran

2017-01-01

Abstract Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)–based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from more than 78% of the polymerase chain reactions that didn’t show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform Pacbio confirmed the accuracy of the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about one-tenth of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes. PMID:29077841

Filling reference gaps via assembling DNA barcodes using high-throughput sequencing-moving toward barcoding the world.

PubMed

Liu, Shanlin; Yang, Chentao; Zhou, Chengran; Zhou, Xin

2017-12-01

Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)-based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from more than 78% of the polymerase chain reactions that didn't show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform Pacbio confirmed the accuracy of the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about one-tenth of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes. © The Authors 2017. Published by Oxford University Press.

Quantifying the Impact of Feedstock Quality on the Design of Bioenergy Supply Chain Networks

DOE PAGES

Castillo-Villar, Krystel; Minor-Popocatl, Hertwin; Webb, Erin

2016-03-01

Logging residues, which refer to the unused portions of trees cut during logging, are important sources of biomass for the emerging biofuel industry and are critical feedstocks for the first-type biofuel facilities (e.g., corn-ethanol facilities). Logging residues are under-utilized sources of biomass for energetic purposes. To support the scaling-up of the bioenergy industry, it is essential to design cost-effective biofuel supply chains that not only minimize costs, but also consider the biomass quality characteristics. The biomass quality is heavily dependent upon the moisture and the ash contents. Ignoring the biomass quality characteristics and its intrinsic costs may yield substantial economicmore » losses that will only be discovered after operations at a biorefinery have begun. Here this paper proposes a novel bioenergy supply chain network design model that minimizes operational costs and includes the biomass quality-related costs. The proposed model is unique in the sense that it supports decisions where quality is not unrealistically assumed to be perfect. The effectiveness of the proposed methodology is proven by assessing a case study in the state of Tennessee, USA. The results demonstrate that the ash and moisture contents of logging residues affect the performance of the supply chain (in monetary terms). Higher-than-target moisture and ash contents incur in additional quality-related costs. The quality-related costs in the optimal solution (with final ash content of 1% and final moisture of 50%) account for 27% of overall supply chain cost. In conclusion, based on the numeral experimentation, the total supply chain cost increased 7%, on average, for each additional percent in the final ash content.« less

Mechanical response of wild-type and Alport murine lens capsules during osmotic swelling.

PubMed

Gyoneva, Lazarina; Segal, Yoav; Dorfman, Kevin D; Barocas, Victor H

2013-08-01

The mechanical support of basement membranes, such as the lens capsule, is believed to arise from one of their main constituents - collagen IV. The basement membranes of the lens, kidney, and ear normally contain two different types of collagen IV networks, referred to as the major and minor chain networks. In Alport syndrome, a mutation in one of the minor chain COL4 genes leads to the absence of the minor chain network, causing life-threatening disturbances. We hypothesized that the absence of the minor chain network increases basement membrane distensibility, as measured in wild-type (n = 25) and Alport syndrome (n = 21) mice using the lens capsule as a model. Osmotic swelling experiments revealed direction-dependent changes. As a reflection of lens capsule properties, Alport lenses strained significantly more than wild-type lenses in the anterior-posterior direction, i.e. along their thickness, but not in the equatorial direction (p = 0.03 and p = 0.08, respectively). This is consistent with clinical data: Alport patients develop conical protrusions on the anterior and posterior lenticular poles. There was no evidence of significant change in total amount of collagen between Alport and wild-type lenses (p = 0.6). The observed differences in distensibility could indicate that the major chain network alone cannot fully compensate for the absence of the more highly cross-linked minor chain network, which is believed to be stronger, more stable, and resistant to deformation. The addition of mechanical information on Alport syndrome to the currently available biological data provides a fuller picture into the progression of the disease. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quantifying the Impact of Feedstock Quality on the Design of Bioenergy Supply Chain Networks

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

Castillo-Villar, Krystel; Minor-Popocatl, Hertwin; Webb, Erin

Logging residues, which refer to the unused portions of trees cut during logging, are important sources of biomass for the emerging biofuel industry and are critical feedstocks for the first-type biofuel facilities (e.g., corn-ethanol facilities). Logging residues are under-utilized sources of biomass for energetic purposes. To support the scaling-up of the bioenergy industry, it is essential to design cost-effective biofuel supply chains that not only minimize costs, but also consider the biomass quality characteristics. The biomass quality is heavily dependent upon the moisture and the ash contents. Ignoring the biomass quality characteristics and its intrinsic costs may yield substantial economicmore » losses that will only be discovered after operations at a biorefinery have begun. Here this paper proposes a novel bioenergy supply chain network design model that minimizes operational costs and includes the biomass quality-related costs. The proposed model is unique in the sense that it supports decisions where quality is not unrealistically assumed to be perfect. The effectiveness of the proposed methodology is proven by assessing a case study in the state of Tennessee, USA. The results demonstrate that the ash and moisture contents of logging residues affect the performance of the supply chain (in monetary terms). Higher-than-target moisture and ash contents incur in additional quality-related costs. The quality-related costs in the optimal solution (with final ash content of 1% and final moisture of 50%) account for 27% of overall supply chain cost. In conclusion, based on the numeral experimentation, the total supply chain cost increased 7%, on average, for each additional percent in the final ash content.« less

Synthesis and synchrotron X-ray characterization of two 2D Hoffman related compounds [Ni(p-Xylylenediamine)nNi(CN)4] and [Ni(p-tetrafluoroxylylenediamine)nNi(CN)4

NASA Astrophysics Data System (ADS)

Wong-Ng, W.; Culp, J. T.; Siderius, D. W.; Chen, Y. S.

2018-07-01

Synchrotron X-ray single crystal structure determination of two 2D Hofmann-related compounds, [Ni(p-Xylyenediamine)n-tetracyanonickelate] (abbreviated as Ni-pXdam) and [Ni(tetrafluoro-p-Xylyenediamine)n-tetracyanonickelate] (abbreviated as Ni-pXdamF4), have been conducted. Both the pXdam and pXdamF4 ligands contain two short chains of -CH2NH2 at the para-positions of a phenyl ring. These flexible chains link the 6-fold coordinated Ni2 sites throughout the network. In Ni-pXdam, the closed-2D network of [Ni-(CN-Ni1/4-)4]∞ is broken into 1D chains, leaving the C≡N groups at the trans-positions of the Ni(CN)4 moiety unbridged. The resulting 1D chains [(trans-)-NC-Ni(CN)2-CN-Ni-]∞ runs along the [010] direction of the unit cell. The pXdam ligands bridge in pair between the Ni atoms of the adjacent chains. The catenation structure of [Ni{(pXdam)}]∞ could be referred to as double -1D. In Ni-pXdamF4, the -CH2NH2 ligands connect the neighboring chains via the 6-fold Ni2 site. Surrounding the 4-fold Ni1 site, the two trans terminal C≡N groups were replaced by the Lewis base NH3 during the synthesis process, therefore preventing the propagation of the 2D net to form a 3D network. Computed pore volume of both compounds indicated that there is not sufficient space in the structure to accommodate gas molecules. In both compounds, hydrogen bonds were found, and solvent of crystallization was absent due to the limited free space in the structure.

A novel T cell receptor single-chain signaling complex mediates antigen-specific T cell activity and tumor control

PubMed Central

Stone, Jennifer D.; Harris, Daniel T.; Soto, Carolina M.; Chervin, Adam S.; Aggen, David H.; Roy, Edward J.; Kranz, David M.

2014-01-01

Adoptive transfer of genetically modified T cells to treat cancer has shown promise in several clinical trials. Two main strategies have been applied to redirect T cells against cancer: 1) introduction of a full-length T cell receptor (TCR) specific for a tumor-associated peptide-MHC, or 2) introduction of a chimeric antigen receptor (CAR), including an antibody fragment specific for a tumor cell surface antigen, linked intracellularly to T cell signaling domains. Each strategy has advantages and disadvantages for clinical applications. Here, we present data on the in vitro and in vivo effectiveness of a single-chain signaling receptor incorporating a TCR variable fragment as the targeting element (referred to as TCR-SCS). This receptor contained a single-chain TCR (Vβ-linker-Vα) from a high-affinity TCR called m33, linked to the intracellular signaling domains of CD28 and CD3ζ. This format avoided mispairing with endogenous TCR chains, and mediated specific T cell activity when expressed in either CD4 or CD8 T cells. TCR-SCS-transduced CD8-negative cells showed an intriguing sensitivity, compared to full-length TCRs, to higher densities of less stable pepMHC targets. T cells that expressed this peptide-specific receptor persisted in vivo, and exhibited polyfunctional responses. Growth of metastatic antigen-positive tumors was significantly inhibited by T cells that expressed this receptor, and tumor cells that escaped were antigen loss variants. TCR-SCS receptors represent an alternative targeting receptor strategy that combines the advantages of single-chain expression, avoidance of TCR chain mispairing, and targeting of intracellular antigens presented in complex with MHC proteins. PMID:25082071

Modeling of anaerobic degradation of solid slaughterhouse waste: inhibition effects of long-chain fatty acids or ammonia.

PubMed

Lokshina, L Y; Vavilin, V A; Salminen, E; Rintala, J

2003-01-01

The anaerobic bioconversion of solid poultry slaughterhouse wastes was kinetically investigated. The modified version of simulation model was applied for description of experimental data in mesophilic laboratory digester and assays. Additionally, stages of formation and consumption of long chain fatty acids (LCFA) were included in the model. Batch data on volatile solids, ammonium, acetate, butyrate, propionate, LCFA concentrations, pH level, cumulative volume, and methane partial pressure were used for model calibration. As a reference, the model was used to describe digestion of solid sorted household waste. Simulation results showed that an inhibition of polymer hydrolysis by volatile fatty acids and acetogenesis by NH3 or LCFA could be responsible for the complex system dynamics during degradation of lipid- and protein-rich wastes.

Model-oriented review and multi-body simulation of the ossicular chain of the human middle ear.

PubMed

Volandri, G; Di Puccio, F; Forte, P; Manetti, S

2012-11-01

The ossicular chain of the human middle ear has a key role in sound conduction since it transfers vibrations from the tympanic membrane to the cochlea, connecting the outer and the inner part of the hearing organ. This study reports firstly a description of the main anatomical features of the middle ear to introduce a detailed survey of its biomechanics, focused on model development, with a collection of geometric, inertial and mechanical/material parameters. The joint issues are particularly discussed from the perspective of developing a model of the middle ear both explanatory and predictive. Such a survey underlines the remarkable dispersion of data, due also to the lack of a standardization of the experimental techniques and conditions. Subsequently, a 3D multi-body model of the ossicular chain and other structures of the middle ear is described. Such an approach is justified as the ossicles were proven to behave as rigid bodies in the human hearing range and was preferred to the more widely used finite element one as it simplifies the model development and improves joint modeling. The displacement of the umbo (a reference point of the tympanic membrane) in the 0.3-6kHz frequency range was defined as input of the model, while the stapes footplate displacement as output. A parameter identification procedure was used to find parameter values for reproducing experimental and numerical reference curves taken from the literature. This simple model might represent a valid alternative to more complex models and might provide a useful tool to simulate pathological/post-surgical/post-traumatic conditions and evaluate ossicular replacement prostheses. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.

The role of higher-order terms in perturbation approaches to the monomer and\\xA0bonding contributions in a SAFT-type equation of state for square-well chain\\xA0fluids

NASA Astrophysics Data System (ADS)

Solana, J. R.; Akhouri, B. P.

2018-07-01

A perturbation theory for square-well chain fluids is developed within the scheme of the (generalised) Wertheim thermodynamic perturbation theory. The theory is based on the Pavlyukhin parametrisations [Y. T. Pavlyukhin, J. Struct. Chem. 53, 476 (2012)] of their simulation data for the first four perturbation terms in the high temperature expansion of the Helmholtz free energy of square-well monomer fluids combined with a second-order perturbation theory for the contact value of the radial distribution function of the square-well monomer fluid that enters into bonding contribution. To obtain the latter perturbation terms, we have performed computer simulations in the hard-sphere reference system. The importance of the perturbation terms beyond the second-order one for the monomer fluid and of the approximations of different orders in the bonding contribution for the chain fluids in the predicted equation of state, excess energy and liquid-vapour coexistence densities is analysed.

ASSESSMENT OF HOUSEHOLD CARBON FOOTPRINT REDUCTION POTENTIALS

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

Kramer, Klaas Jan; Homan, Greg; Brown, Rich

2009-04-15

The term ?household carbon footprint? refers to the total annual carbon emissions associated with household consumption of energy, goods, and services. In this project, Lawrence Berkeley National Laboratory developed a carbon footprint modeling framework that characterizes the key underlying technologies and processes that contribute to household carbon footprints in California and the United States. The approach breaks down the carbon footprint by 35 different household fuel end uses and 32 different supply chain fuel end uses. This level of end use detail allows energy and policy analysts to better understand the underlying technologies and processes contributing to the carbon footprintmore » of California households. The modeling framework was applied to estimate the annual home energy and supply chain carbon footprints of a prototypical California household. A preliminary assessment of parameter uncertainty associated with key model input data was also conducted. To illustrate the policy-relevance of this modeling framework, a case study was conducted that analyzed the achievable carbon footprint reductions associated with the adoption of energy efficient household and supply chain technologies.« less

Model Reduction via Principe Component Analysis and Markov Chain Monte Carlo (MCMC) Methods

NASA Astrophysics Data System (ADS)

Gong, R.; Chen, J.; Hoversten, M. G.; Luo, J.

2011-12-01

Geophysical and hydrogeological inverse problems often include a large number of unknown parameters, ranging from hundreds to millions, depending on parameterization and problems undertaking. This makes inverse estimation and uncertainty quantification very challenging, especially for those problems in two- or three-dimensional spatial domains. Model reduction technique has the potential of mitigating the curse of dimensionality by reducing total numbers of unknowns while describing the complex subsurface systems adequately. In this study, we explore the use of principal component analysis (PCA) and Markov chain Monte Carlo (MCMC) sampling methods for model reduction through the use of synthetic datasets. We compare the performances of three different but closely related model reduction approaches: (1) PCA methods with geometric sampling (referred to as 'Method 1'), (2) PCA methods with MCMC sampling (referred to as 'Method 2'), and (3) PCA methods with MCMC sampling and inclusion of random effects (referred to as 'Method 3'). We consider a simple convolution model with five unknown parameters as our goal is to understand and visualize the advantages and disadvantages of each method by comparing their inversion results with the corresponding analytical solutions. We generated synthetic data with noise added and invert them under two different situations: (1) the noised data and the covariance matrix for PCA analysis are consistent (referred to as the unbiased case), and (2) the noise data and the covariance matrix are inconsistent (referred to as biased case). In the unbiased case, comparison between the analytical solutions and the inversion results show that all three methods provide good estimates of the true values and Method 1 is computationally more efficient. In terms of uncertainty quantification, Method 1 performs poorly because of relatively small number of samples obtained, Method 2 performs best, and Method 3 overestimates uncertainty due to inclusion of random effects. However, in the biased case, only Method 3 correctly estimates all the unknown parameters, and both Methods 1 and 2 provide wrong values for the biased parameters. The synthetic case study demonstrates that if the covariance matrix for PCA analysis is inconsistent with true models, the PCA methods with geometric or MCMC sampling will provide incorrect estimates.

Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation

PubMed Central

Masè, Michela; Grasso, Margherita; Avogaro, Laura; D’Amato, Elvira; Tessarolo, Francesco; Graffigna, Angelo; Denti, Michela Alessandra; Ravelli, Flavia

2017-01-01

MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-Cq, GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions. PMID:28117343

Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis1[w

PubMed Central

Czechowski, Tomasz; Stitt, Mark; Altmann, Thomas; Udvardi, Michael K.; Scheible, Wolf-Rüdiger

2005-01-01

Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future. PMID:16166256

Stable Reference Gene Selection for RT-qPCR Analysis in Nonviruliferous and Viruliferous Frankliniella occidentalis

PubMed Central

Pan, Huipeng; Ma, Yabin; Zhang, Deyong; Liu, Yong; Zhang, Zhanhong; Zheng, Changying; Chu, Dong

2015-01-01

Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for measuring and evaluating gene expression during variable biological processes. To facilitate gene expression studies, normalization of genes of interest relative to stable reference genes is crucial. The western flower thrips Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), the main vector of tomato spotted wilt virus (TSWV), is a destructive invasive species. In this study, the expression profiles of 11 candidate reference genes from nonviruliferous and viruliferous F. occidentalis were investigated. Five distinct algorithms, geNorm, NormFinder, BestKeeper, the ΔC t method, and RefFinder, were used to determine the performance of these genes. geNorm, NormFinder, BestKeeper, and RefFinder identified heat shock protein 70 (HSP70), heat shock protein 60 (HSP60), elongation factor 1 α, and ribosomal protein l32 (RPL32) as the most stable reference genes, and the ΔC t method identified HSP60, HSP70, RPL32, and heat shock protein 90 as the most stable reference genes. Additionally, two reference genes were sufficient for reliable normalization in nonviruliferous and viruliferous F. occidentalis. This work provides a foundation for investigating the molecular mechanisms of TSWV and F. occidentalis interactions. PMID:26244556

Acid-induced changes in DOC quality in an experimental whole-lake manipulation

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

Donahue, W.F.; Schindler, D.W.; Page, S.J.

1998-10-01

Fluorescence analyses of archived water samples were used to typify dissolved organic carbon (DOC) quality in experimentally acidified lakes and reference lakes at the Experimental Lakes Area, in northwestern Ontario. Carbon-specific DOC fluorescence (CSF) during peak acidification was 40--50% of that for a high-DOC reference lake and similar to a low-DOC reference lake. Reference lakes showed similar but smaller decreases in CSF during several years of prolonged drought in the late 1980s. During the 1990s, recovery from acidification resulted in increased CSF, whereas reference lakes remained unchanged during the same time period. In addition to causing decreased [DOC], acidification causesmore » changes in fluorescence-peak geometry that indicate a switch in DOC quality from allochthonous to autochthonous-like during acidification. The acid-induced change in DOC quality was likely due to increased chemical oxidation or precipitation of the UV-absorbent aromatic portions of allochthonous DOC molecules, leaving more UV-transparent aliphatic chains. The change in the nature of DOC following acidification and drought may have an important role in physical, biological, and chemical processes within these lakes. With recovery from acidification, DOC quality has also recovered.« less

Magneto-structural correlation in a series of bimetallic alternating chain complexes of [CrIIIL(CN)4]n[MnIII(salpn)]n.nsolvents (L=2,2'-bipy or 9,10-phen, salpn=substituted salicyldehyde, solvents=water and methanol).

PubMed

Pan, Feng; Wang, Zhe-Ming; Gao, Song

2007-11-26

Five chain compounds based on the building block of [Cr(L)(CN)4]- (L=2,2'-bipy, 1-4; L=9,10-phen, 5) and [Mn(salpn)]+ (salpn=substituted salicyldehyde-type Schiff base in Scheme 1) have been prepared and characterized structurally and magnetically. The four compounds (1-4) consisting of [Cr(bipy)(CN)4]- units possess straight bimetallic chains as the [Cr(bpy)(CN)4]- unit links the two neighbor [Mn(salpn)]+ units with the two trans-cyanide ligands, while in 5 the chain is zigzag because the [Cr(phen)(CN)4]- unit connects the [Mn(salpn)]+ units with its two cis-cyanide ligands. The bond angles of Mn-N-C-Cr are adjusted by different coligands of salpn and bipy/phen. The chains are stacking via mainly the aromatic pi-pi-type interactions. All compounds show 3D antiferromagnetic ordering with Néel temperatures ranging from 3.7 to 8.1 K, and they are metamagnets displaying antiferromagnetic to ferrimagnetic transition at critical fields of 4.0-13.1 kOe at 1.9 K. This is due to weak interchain antiferromagnetic interactions between the ferrimagnetic bimetallic chains in the materials. The intrachain couplings (J, in cm(-1)) in the materials, between cyanide-bridged CrIII and MnIII ions, from -1.84 to -5.35 cm(-1), follow a linear relationship (J=-33+0.18alpha) to the Mn-N-C angles (alpha, in deg). In addition, the weak interchain antiferromagnetic interactions and critical fields for antiferromagnetic-ferrimagnetic transition are closely related to some of their structural factors, which were studied very superficially only referring to the separations of nearest chains in each material.

Interlaboratory Reproducibility of Droplet Digital Polymerase Chain Reaction Using a New DNA Reference Material Format.

PubMed

Pinheiro, Leonardo B; O'Brien, Helen; Druce, Julian; Do, Hongdo; Kay, Pippa; Daniels, Marissa; You, Jingjing; Burke, Daniel; Griffiths, Kate; Emslie, Kerry R

2017-11-07

Use of droplet digital PCR technology (ddPCR) is expanding rapidly in the diversity of applications and number of users around the world. Access to relatively simple and affordable commercial ddPCR technology has attracted wide interest in use of this technology as a molecular diagnostic tool. For ddPCR to effectively transition to a molecular diagnostic setting requires processes for method validation and verification and demonstration of reproducible instrument performance. In this study, we describe the development and characterization of a DNA reference material (NMI NA008 High GC reference material) comprising a challenging methylated GC-rich DNA template under a novel 96-well microplate format. A scalable process using high precision acoustic dispensing technology was validated to produce the DNA reference material with a certified reference value expressed in amount of DNA molecules per well. An interlaboratory study, conducted using blinded NA008 High GC reference material to assess reproducibility among seven independent laboratories demonstrated less than 4.5% reproducibility relative standard deviation. With the exclusion of one laboratory, laboratories had appropriate technical competency, fully functional instrumentation, and suitable reagents to perform accurate ddPCR based DNA quantification measurements at the time of the study. The study results confirmed that NA008 High GC reference material is fit for the purpose of being used for quality control of ddPCR systems, consumables, instrumentation, and workflow.

Reference genes for reverse transcription quantitative PCR in canine brain tissue.

PubMed

Stassen, Quirine E M; Riemers, Frank M; Reijmerink, Hannah; Leegwater, Peter A J; Penning, Louis C

2015-12-09

In the last decade canine models have been used extensively to study genetic causes of neurological disorders such as epilepsy and Alzheimer's disease and unravel their pathophysiological pathways. Reverse transcription quantitative polymerase chain reaction is a sensitive and inexpensive method to study expression levels of genes involved in disease processes. Accurate normalisation with stably expressed so-called reference genes is crucial for reliable expression analysis. Following the minimum information for publication of quantitative real-time PCR experiments precise guidelines, the expression of ten frequently used reference genes, namely YWHAZ, HMBS, B2M, SDHA, GAPDH, HPRT, RPL13A, RPS5, RPS19 and GUSB was evaluated in seven brain regions (frontal lobe, parietal lobe, occipital lobe, temporal lobe, thalamus, hippocampus and cerebellum) and whole brain of healthy dogs. The stability of expression varied between different brain areas. Using the GeNorm and Normfinder software HMBS, GAPDH and HPRT were the most reliable reference genes for whole brain. Furthermore based on GeNorm calculations it was concluded that as little as two to three reference genes are sufficient to obtain reliable normalisation, irrespective the brain area. Our results amend/extend the limited previously published data on canine brain reference genes. Despite the excellent expression stability of HMBS, GAPDH and HRPT, the evaluation of expression stability of reference genes must be a standard and integral part of experimental design and subsequent data analysis.

Identification of TMEM208 and PQLC2 as reference genes for normalizing mRNA expression in colorectal cancer treated with aspirin

PubMed Central

Zhu, Yuanyuan; Yang, Chao; Weng, Mingjiao; Zhang, Yan; Yang, Chunhui; Jin, Yinji; Yang, Weiwei; He, Yan; Wu, Yiqi; Zhang, Yuhua; Wang, Guangyu; RajkumarEzakiel Redpath, Riju James; Zhang, Lei; Jin, Xiaoming; Liu, Ying; Sun, Yuchun; Ning, Ning; Qiao, Yu; Zhang, Fengmin; Li, Zhiwei; Wang, Tianzhen; Zhang, Yanqiao; Li, Xiaobo

2017-01-01

Numerous evidences indicate that aspirin usage causes a significant reduction in colorectal cancer. However, the molecular mechanisms about aspirin preventing colon cancer are largely unknown. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a most frequently used method to identify the target molecules regulated by certain compound. However, this method needs stable internal reference genes to analyze the expression change of the targets. In this study, the transcriptional stabilities of several traditional reference genes were evaluated in colon cancer cells treated with aspirin, and also, the suitable internal reference genes were screened by using a microarray and were further identified by using the geNorm and NormFinder softwares, and then were validated in more cell lines and xenografts. We have showed that three traditional internal reference genes, β-actin, GAPDH and α-tubulin, are not suitable for studying gene transcription in colon cancer cells treated with aspirin, and we have identified and validated TMEM208 and PQLC2 as the ideal internal reference genes for detecting the molecular targets of aspirin in colon cancer in vitro and in vivo. This study reveals stable internal reference genes for studying the target genes of aspirin in colon cancer, which will contribute to identify the molecular mechanism behind aspirin preventing colon cancer. PMID:28184026

Identification of TMEM208 and PQLC2 as reference genes for normalizing mRNA expression in colorectal cancer treated with aspirin.

PubMed

Zhu, Yuanyuan; Yang, Chao; Weng, Mingjiao; Zhang, Yan; Yang, Chunhui; Jin, Yinji; Yang, Weiwei; He, Yan; Wu, Yiqi; Zhang, Yuhua; Wang, Guangyu; RajkumarEzakiel Redpath, Riju James; Zhang, Lei; Jin, Xiaoming; Liu, Ying; Sun, Yuchun; Ning, Ning; Qiao, Yu; Zhang, Fengmin; Li, Zhiwei; Wang, Tianzhen; Zhang, Yanqiao; Li, Xiaobo

2017-04-04

Numerous evidences indicate that aspirin usage causes a significant reduction in colorectal cancer. However, the molecular mechanisms about aspirin preventing colon cancer are largely unknown. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a most frequently used method to identify the target molecules regulated by certain compound. However, this method needs stable internal reference genes to analyze the expression change of the targets. In this study, the transcriptional stabilities of several traditional reference genes were evaluated in colon cancer cells treated with aspirin, and also, the suitable internal reference genes were screened by using a microarray and were further identified by using the geNorm and NormFinder softwares, and then were validated in more cell lines and xenografts. We have showed that three traditional internal reference genes, β-actin, GAPDH and α-tubulin, are not suitable for studying gene transcription in colon cancer cells treated with aspirin, and we have identified and validated TMEM208 and PQLC2 as the ideal internal reference genes for detecting the molecular targets of aspirin in colon cancer in vitro and in vivo. This study reveals stable internal reference genes for studying the target genes of aspirin in colon cancer, which will contribute to identify the molecular mechanism behind aspirin preventing colon cancer.

Inter-laboratory quality control for hormone-dependent gene expression in human breast tumors using real-time reverse transcription-polymerase chain reaction.

PubMed

de Cremoux, P; Bieche, I; Tran-Perennou, C; Vignaud, S; Boudou, E; Asselain, B; Lidereau, R; Magdelénat, H; Becette, V; Sigal-Zafrani, B; Spyratos, F

2004-09-01

Quantitative reverse transcription-polymerase chain reaction (RT-PCR) used to detect minor changes in specific mRNA concentrations may be associated with poor reproducibility. Stringent quality control is therefore essential at each step of the protocol, including the PCR procedure. We performed inter-laboratory quality control of quantitative PCR between two independent laboratories, using in-house RT-PCR assays on a series of hormone-related target genes in a retrospective consecutive series of 79 breast tumors. Total RNA was reverse transcribed in a single center. Calibration curves were performed for five target genes (estrogen receptor (ER)alpha, ERbeta, progesterone receptor (PR), CYP19 (aromatase) and Ki 67) and for two reference genes (human acidic ribosomal phosphoprotein PO (RPLPO) and TATA box-binding protein (TBP)). Amplification efficiencies of the calibrator were determined for each run and used to calculate mRNA expression. Correlation coefficients were evaluated for each target and each reference gene. A good correlation was observed for all target and reference genes in both centers using their own protocols and kits (P < 0.0001). The correlation coefficients ranged from 0.90 to 0.98 for the various target genes in the two centers. A good correlation was observed between the level of expression of the ERalpha and the PR transcripts (P < 0.001). A weak inverse correlation was observed in both centers between ERalpha and ERbeta levels, but only when TBP was the reference gene. No other correlation was observed with other parameters. Real-time PCR assays allow convenient quantification of target mRNA transcripts and quantification of target-derived nucleic acids in clinical specimens. This study addresses the importance of inter-laboratory quality controls for the use of a panel of real-time PCR assays devoted to clinical samples and protocols and to ensure their appropriate accuracy. This can also facilitate exchanges and multicenter comparison of data.

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking

DTIC Science & Technology

2007-04-01

optimization methodology we introduce. State-of-the-art protein - protein docking approaches start by identifying conformations with good surface /chemical com...side-chains on the interface ). The protein - protein docking literature (e.g., [8] and the references therein) is predominantly treating the docking...mations by various measures of surface complementarity which can be efficiently computed using fast Fourier correlation tech- niques (FFTs). However, when

Oil rigs and offshore sport fishing in Louisiana

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

Dugas, R.; Guillory, V.; Fischer, M.

Forty years ago, offshore sport fishing in Louisiana was almost nonexistent. Offshore oil drilling platforms are the primary cause of the present increase in sport fishing in this area. Algae and other organisms forming the first step in the food chain cluster around the subsurface structures of the rigs, attracting fish that seek food and shelter. Major game species frequenting these rigs are identified. (3 photos, 22 references, 2 tables)

Fundamental Investigations of Durability at a Polymer Electrolyte-Electrode Interface

DTIC Science & Technology

2008-04-01

before before σ -σ σ after before before σ -σ σ Cleavage of the side chain ether linkage (Fig. 3), which intrudes into the hydrophilic ionic cluster...directly correlated to peroxide yields measured Figure 3: ATR-FTIR Spectrum of Nafion ®112 (H-form) indicating absorption bands obtained using...electrocatalyst-based fuel cell electrode (referred as sacrificial electrode) directly into the liquid electrolyte, in which oxygen reduction was

GPSS and Modeling of Computer Communication Networks.

DTIC Science & Technology

1982-04-01

chains are used to alter the normal "flows" of transactions in a user defined manner. Transaction "flow" may be controlled on the basis of group ...authors refer to loops and rings interchangeably, including those who have designed loop networks with distributed control mechanisms [8,9,10,11,121...that detailed simulation of character by character transmission does not take place; rather, [ control message--data message-- control message! groupings

PTTI Capabilities of the Modernized LORAN System

DTIC Science & Technology

2008-12-01

Cape Elizabeth LCCS Carolina Beach 9960-Y Dana 9960-Z Seneca 9960-M LSU 9960-T Sandy Hook Plumbrook Dunbar Forest LCCS Transmitting Station ...reference clocks at the individual transmitting stations , the intra-chain timing between stations , and the overall system synchronization to UTC. Each... station has three cesium clocks installed, and new Time and Frequency Equipment (TFE) was installed at the stations , beginning in the spring of 2003

Privacy Preservation in Context-Aware Systems

DTIC Science & Technology

2011-01-01

Policies and the Semantic Web The Semantic Web refers to both a vision and a set of technologies. The vision was first articulated by Tim Berners - Lee ... Berners - lee 2005) is a distributed framework for describing and reasoning over policies in the Semantic Web. It supports N3 rules ( Berners - Lee ...Connolly 2008), ( Berners - Lee et al. 2005) for representing intercon- nections between policies and resources and uses the CWM forward-chaining reasoning

Protein-Backbone Thermodynamics across the Membrane Interface.

PubMed

Bereau, Tristan; Kremer, Kurt

2016-07-07

The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups.

New statistical potential for quality assessment of protein models and a survey of energy functions

PubMed Central

2010-01-01

Background Scoring functions, such as molecular mechanic forcefields and statistical potentials are fundamentally important tools in protein structure modeling and quality assessment. Results The performances of a number of publicly available scoring functions are compared with a statistical rigor, with an emphasis on knowledge-based potentials. We explored the effect on accuracy of alternative choices for representing interaction center types and other features of scoring functions, such as using information on solvent accessibility, on torsion angles, accounting for secondary structure preferences and side chain orientation. Partially based on the observations made, we present a novel residue based statistical potential, which employs a shuffled reference state definition and takes into account the mutual orientation of residue side chains. Atom- and residue-level statistical potentials and Linux executables to calculate the energy of a given protein proposed in this work can be downloaded from http://www.fiserlab.org/potentials. Conclusions Among the most influential terms we observed a critical role of a proper reference state definition and the benefits of including information about the microenvironment of interaction centers. Molecular mechanical potentials were also tested and found to be over-sensitive to small local imperfections in a structure, requiring unfeasible long energy relaxation before energy scores started to correlate with model quality. PMID:20226048

Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization.

PubMed

Hartenfeller, Markus; Proschak, Ewgenij; Schüller, Andreas; Schneider, Gisbert

2008-07-01

We present a fast stochastic optimization algorithm for fragment-based molecular de novo design (COLIBREE, Combinatorial Library Breeding). The search strategy is based on a discrete version of particle swarm optimization. Molecules are represented by a scaffold, which remains constant during optimization, and variable linkers and side chains. Different linkers represent virtual chemical reactions. Side-chain building blocks were obtained from pseudo-retrosynthetic dissection of large compound databases. Here, ligand-based design was performed using chemically advanced template search (CATS) topological pharmacophore similarity to reference ligands as fitness function. A weighting scheme was included for particle swarm optimization-based molecular design, which permits the use of many reference ligands and allows for positive and negative design to be performed simultaneously. In a case study, the approach was applied to the de novo design of potential peroxisome proliferator-activated receptor subtype-selective agonists. The results demonstrate the ability of the technique to cope with large combinatorial chemistry spaces and its applicability to focused library design. The technique was able to perform exploitation of a known scheme and at the same time explorative search for novel ligands within the framework of a given molecular core structure. It thereby represents a practical solution for compound screening in the early hit and lead finding phase of a drug discovery project.

Biomass Scenario Model Documentation: Data and References

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

Lin, Y.; Newes, E.; Bush, B.

2013-05-01

The Biomass Scenario Model (BSM) is a system dynamics model that represents the entire biomass-to-biofuels supply chain, from feedstock to fuel use. The BSM is a complex model that has been used for extensive analyses; the model and its results can be better understood if input data used for initialization and calibration are well-characterized. It has been carefully validated and calibrated against the available data, with data gaps filled in using expert opinion and internally consistent assumed values. Most of the main data sources that feed into the model are recognized as baseline values by the industry. This report documentsmore » data sources and references in Version 2 of the BSM (BSM2), which only contains the ethanol pathway, although subsequent versions of the BSM contain multiple conversion pathways. The BSM2 contains over 12,000 total input values, with 506 distinct variables. Many of the variables are opportunities for the user to define scenarios, while others are simply used to initialize a stock, such as the initial number of biorefineries. However, around 35% of the distinct variables are defined by external sources, such as models or reports. The focus of this report is to provide insight into which sources are most influential in each area of the supply chain.« less

A Complementary Isothermal Amplification Method to the U.S. EPA Quantitative Polymerase Chain Reaction Approach for the Detection of Enterococci in Environmental Waters

PubMed Central

2017-01-01

We report a novel molecular assay, based on helicase-dependent amplification (HDA), for the detection of enterococci as markers for fecal pollution in water. This isothermal assay targets the same Enterococcus 23S rRNA gene region as the existing quantitative polymerase chain reaction (qPCR) assays of U.S. Environmental Protection Agency Methods 1611 and 1609 but can be entirely performed on a simple heating block. The developed Enterococcus HDA assay successfully discriminated 15 enterococcal from 15 non-enterococcal reference strains and reliably detected 48 environmental isolates of enterococci. The limit of detection was 25 target copies per reaction, only 3 times higher than that of qPCR. The applicability of the assay was tested on 30 environmental water sample DNA extracts, simulating a gradient of fecal pollution. Despite the isothermal nature of the reaction, the HDA results were consistent with those of the qPCR reference. Given this performance, we conclude that the developed Enterococcus HDA assay has great potential as a qualitative molecular screening method for resource-limited settings when combined with compatible up- and downstream processes. This amplification strategy can pave the way for developing a new generation of rapid, low-cost, and field-deployable molecular diagnostic tools for water quality monitoring. PMID:28541661

Novel Miscanthus Germplasm-Based Value Chains: A Life Cycle Assessment

PubMed Central

Wagner, Moritz; Kiesel, Andreas; Hastings, Astley; Iqbal, Yasir; Lewandowski, Iris

2017-01-01

In recent years, considerable progress has been made in miscanthus research: improvement of management practices, breeding of new genotypes, especially for marginal conditions, and development of novel utilization options. The purpose of the current study was a holistic analysis of the environmental performance of such novel miscanthus-based value chains. In addition, the relevance of the analyzed environmental impact categories was assessed. A Life Cycle Assessment was conducted to analyse the environmental performance of the miscanthus-based value chains in 18 impact categories. In order to include the substitution of a reference product, a system expansion approach was used. In addition, a normalization step was applied. This allowed the relevance of these impact categories to be evaluated for each utilization pathway. The miscanthus was cultivated on six sites in Europe (Aberystwyth, Adana, Moscow, Potash, Stuttgart and Wageningen) and the biomass was utilized in the following six pathways: (1) small-scale combustion (heat)—chips; (2) small-scale combustion (heat)—pellets; (3) large-scale combustion (CHP)—biomass baled for transport and storage; (4) large-scale combustion (CHP)—pellets; (5) medium-scale biogas plant—ensiled miscanthus biomass; and (6) large-scale production of insulation material. Thus, in total, the environmental performance of 36 site × pathway combinations was assessed. The comparatively high normalized results of human toxicity, marine, and freshwater ecotoxicity, and freshwater eutrophication indicate the relevance of these impact categories in the assessment of miscanthus-based value chains. Differences between the six sites can almost entirely be attributed to variations in biomass yield. However, the environmental performance of the utilization pathways analyzed varied widely. The largest differences were shown for freshwater and marine ecotoxicity, and freshwater eutrophication. The production of insulation material had the lowest impact on the environment, with net benefits in all impact categories expect three (marine eutrophication, human toxicity, agricultural land occupation). This performance can be explained by the multiple use of the biomass, first as material and subsequently as an energy carrier, and by the substitution of an emission-intensive reference product. The results of this study emphasize the importance of assessing all environmental impacts when selecting appropriate utilization pathways. PMID:28642784

Normalization of Reverse Transcription Quantitative PCR Data During Ageing in Distinct Cerebral Structures.

PubMed

Bruckert, G; Vivien, D; Docagne, F; Roussel, B D

2016-04-01

Reverse transcription quantitative-polymerase chain reaction (RT-qPCR) has become a routine method in many laboratories. Normalization of data from experimental conditions is critical for data processing and is usually achieved by the use of a single reference gene. Nevertheless, as pointed by the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, several reference genes should be used for reliable normalization. Ageing is a physiological process that results in a decline of many expressed genes. Reliable normalization of RT-qPCR data becomes crucial when studying ageing. Here, we propose a RT-qPCR study from four mouse brain regions (cortex, hippocampus, striatum and cerebellum) at different ages (from 8 weeks to 22 months) in which we studied the expression of nine commonly used reference genes. With the use of two different algorithms, we found that all brain structures need at least two genes for a good normalization step. We propose specific pairs of gene for efficient data normalization in the four brain regions studied. These results underline the importance of reliable reference genes for specific brain regions in ageing.

Evaluation of RNA extraction methods and identification of putative reference genes for real-time quantitative polymerase chain reaction expression studies on olive (Olea europaea L.) fruits.

PubMed

Nonis, Alberto; Vezzaro, Alice; Ruperti, Benedetto

2012-07-11

Genome wide transcriptomic surveys together with targeted molecular studies are uncovering an ever increasing number of differentially expressed genes in relation to agriculturally relevant processes in olive (Olea europaea L). These data need to be supported by quantitative approaches enabling the precise estimation of transcript abundance. qPCR being the most widely adopted technique for mRNA quantification, preliminary work needs to be done to set up robust methods for extraction of fully functional RNA and for the identification of the best reference genes to obtain reliable quantification of transcripts. In this work, we have assessed different methods for their suitability for RNA extraction from olive fruits and leaves and we have evaluated thirteen potential candidate reference genes on 21 RNA samples belonging to fruit developmental/ripening series and to leaves subjected to wounding. By using two different algorithms, GAPDH2 and PP2A1 were identified as the best reference genes for olive fruit development and ripening, and their effectiveness for normalization of expression of two ripening marker genes was demonstrated.

Free fatty acids chain length distribution affects the permeability of skin lipid model membranes.

PubMed

Uchiyama, Masayuki; Oguri, Masashi; Mojumdar, Enamul H; Gooris, Gert S; Bouwstra, Joke A

2016-09-01

The lipid matrix in the stratum corneum (SC) plays an important role in the barrier function of the skin. The main lipid classes in this lipid matrix are ceramides (CERs), cholesterol (CHOL) and free fatty acids (FFAs). The aim of this study was to determine whether a variation in CER subclass composition and chain length distribution of FFAs affect the permeability of this matrix. To examine this, we make use of lipid model membranes, referred to as stratum corneum substitute (SCS). We prepared SCS containing i) single CER subclass with either a single FFA or a mixture of FFAs and CHOL, or ii) a mixture of various CER subclasses with either a single FFA or a mixture of FFAs and CHOL. In vitro permeation studies were performed using ethyl-p-aminobenzoic acid (E-PABA) as a model drug. The flux of E-PABA across the SCS containing the mixture of FFAs was higher than that across the SCS containing a single FA with a chain length of 24 C atoms (FA C24), while the E-PABA flux was not effected by the CER composition. To select the underlying factors for the changes in permeability, the SCSs were examined by Fourier transform infrared spectroscopy (FTIR) and Small angle X-ray scattering (SAXS). All lipid models demonstrated a similar phase behavior. However, when focusing on the conformational ordering of the individual FFA chains, the shorter chain FFA (with a chain length of 16, 18 or 20 C atoms forming only 11m/m% of the total FFA level) had a higher conformational disordering, while the conformational ordering of the chains of the CER and FA C24 and FA C22 hardly did not change irrespective of the composition of the SCS. In conclusion, the conformational mobility of the short chain FFAs present only at low levels in the model SC lipid membranes has a great impact on the permeability of E-PABA. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT-PCR under Aluminum, Cadmium, and Heat Stresses in Soybean.

PubMed

Gao, Mengmeng; Liu, Yaping; Ma, Xiao; Shuai, Qin; Gai, Junyi; Li, Yan

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used to analyze the relative gene expression level, however, the accuracy of qRT-PCR is greatly affected by the stability of reference genes, which is tissue- and environment- dependent. Therefore, choosing the most stable reference gene in a specific tissue and environment is critical to interpret gene expression patterns. Aluminum (Al), cadmium (Cd), and heat stresses are three important abiotic factors limiting soybean (Glycine max) production in southern China. To identify the suitable reference genes for normalizing the expression levels of target genes by qRT-PCR in soybean response to Al, Cd and heat stresses, we studied the expression stability of ten commonly used housekeeping genes in soybean roots and leaves under these three abiotic stresses, using five approaches, BestKeeper, Delta Ct, geNorm, NormFinder and RefFinder. We found TUA4 is the most stable reference gene in soybean root tips under Al stress. Under Cd stress, Fbox and UKN2 are the most stable reference genes in roots and leaves, respectively, while 60S is the most suitable reference gene when analyzing both roots and leaves together. For heat stress, TUA4 and UKN2 are the most stable housekeeping genes in roots and leaves, respectively, and UKN2 is the best reference gene for analysis of roots and leaves together. To validate the reference genes, we quantified the relative expression levels of six target genes that were involved in soybean response to Al, Cd or heat stresses, respectively. The expression patterns of these target genes differed between using the most and least stable reference genes, suggesting the selection of a suitable reference gene is critical for gene expression studies.

Barriers and facilitators of consumer use of nutrition labels at sit-down restaurant chains.

PubMed

Auchincloss, Amy H; Young, Candace; Davis, Andrea L; Wasson, Sara; Chilton, Mariana; Karamanian, Vanesa

2013-12-01

Numerous localities have mandated that chain restaurants post nutrition information at the point of purchase. However, some studies suggest that consumers are not highly responsive to menu labelling. The present qualitative study explored influences on full-service restaurant customers’ noticing and using menu labelling. Five focus groups were conducted with thirty-six consumers. A semi-structured script elicited barriers and facilitators to using nutrition information by showing excerpts of real menus from full-service chain restaurants. Participants were recruited from a full-service restaurant chain in Philadelphia, Pennsylvania, USA, in September 2011. Focus group participants were mostly female, African American, with incomes <$US 60 000, mean age 36 years and education 14·5 years. At recruitment, 33 % (n 12) reported changing their order after seeing nutrition information on the menu. Three themes characterized influences on label use in restaurants: nutrition knowledge, menu design and display, and normative attitudes and behaviours. Barriers to using labels were low prior knowledge of nutrition; displaying nutrition information using codes; low expectations of the nutritional quality of restaurant food; and restaurant discounts, promotions and social influences that overwhelmed interest in nutrition and reinforced disinterest in nutrition. Facilitators were higher prior knowledge of recommended daily intake; spending time reading the menu; having strong prior interest in nutrition/healthy eating; and being with people who reinforced dietary priorities. Menu labelling use may increase if consumers learn a few key recommended dietary reference values, understand basic energy intake/expenditure scenarios and if chain restaurants present nutrition information in a user-friendly way and promote healthier items.

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

PubMed

Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

2016-11-23

The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com.

Polymerase chain reaction-based identification of clinically relevant Pasteurellaceae isolated from cats and dogs in Poland.

PubMed

Król, Jaroslaw; Bania, Jacek; Florek, Magdalena; Pliszczak-Król, Aleksandra; Staroniewicz, Zdzislaw

2011-05-01

A set of polymerase chain reaction (PCR) assays for identification of the most important Pasteurellaceae species encountered in cats and dogs were developed. Primers for Pasteurella multocida were designed to detect a fragment of the kmt, a gene encoding the outer-membrane protein. Primers specific to Pasteurella canis, Pasteurella dagmatis, and Pasteurella stomatis were based on the manganese-dependent superoxide dismutase gene (sodA) and those specific to [Haemophilus] haemoglobinophilus on species-specific sequences of the 16S ribosomal RNA gene. All the primers were tested on respective reference and control strains and applied to the identification of 47 canine and feline field isolates of Pasteurellaceae. The PCR assays were shown to be species specific, providing a valuable supplement to phenotypic identification of species within this group of bacteria. © 2011 The Author(s)

AL (Light-Chain) Cardiac Amyloidosis: A Review of Diagnosis and Therapy.

PubMed

Falk, Rodney H; Alexander, Kevin M; Liao, Ronglih; Dorbala, Sharmila

2016-09-20

The amyloidoses are a group of protein-folding disorders in which ≥1 organ is infiltrated by proteinaceous deposits known as amyloid. The deposits are derived from 1 of several amyloidogenic precursor proteins, and the prognosis of the disease is determined both by the organ(s) involved and the type of amyloid. Amyloid involvement of the heart (cardiac amyloidosis) carries the worst prognosis of any involved organ, and light-chain (AL) amyloidosis is the most serious form of the disease. The last decade has seen considerable progress in understanding the amyloidoses. In this review, current and novel approaches to the diagnosis and treatment of cardiac amyloidosis are discussed, with particular reference to AL amyloidosis in the heart. Copyright © 2016 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

Smart polymers as surface modifiers for bioanalytical devices and biomaterials: theory and practice

NASA Astrophysics Data System (ADS)

Ivanov, A. E.; Zubov, V. P.

2016-06-01

Smart, or responsive polymers can reversibly change their state of aggregation, thus switching from water-soluble to insoluble state, in response to minor changes in temperature, pH or solvent composition. Grafting of these polymers to solid surfaces imparts the surfaces with controllable wettability and adsorption behaviour. The review summarizes the theoretical models and the results of physical measurements of the conformational transitions in grafted polymer chains and polymer brushes. Primary attention is paid to the grafting density and the length and spatial arrangement of grafted chains, the role of polystyrene, organosilane or alkanethiol sublayers and their effects on adsorption of proteins and adhesion of cells. The key applications of grafted smart polymers such as cell culture and tissue engineering, cell and protein separation, biosensing and targeted drug delivery are surveyed. The bibliography includes 174 references.

Use of an ecosystem model for testing ecosystem response to inaccuracies of root and microflora productivity estimates

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

Petersen, H.; O'Neill, R.V.; Gardner, R.H.

1984-01-01

A seventy-compartment model for a Danish beech forest ecosystem is described in outline. The unmodified model predicts considerable accumulation of wood litter and decreasing accumulation through secondary to final decomposition products. Increment rates are similar for all components of the detritus based food chain. Modification of fine root production rate produces strong, positive response for root litter, and less, but still significant, response for detritus, humus and the components of the decomposer food chain. Increase of microbial biomass with adjustments of metabolism and production causes reduced accumulation of detritus and humus. The soil organisms respond according to food source. Themore » use of the model for testing the sensitivity of the ecosystem to inaccuracies of rroot- and microflora estimates is discussed. 21 references, 3 figures, 1 table.« less

A methodology for cloud masking uncalibrated lidar signals

NASA Astrophysics Data System (ADS)

Binietoglou, Ioannis; D'Amico, Giuseppe; Baars, Holger; Belegante, Livio; Marinou, Eleni

2018-04-01

Most lidar processing algorithms, such as those included in EARLINET's Single Calculus Chain, can be applied only to cloud-free atmospheric scenes. In this paper, we present a methodology for masking clouds in uncalibrated lidar signals. First, we construct a reference dataset based on manual inspection and then train a classifier to separate clouds and cloud-free regions. Here we present details of this approach together with an example cloud masks from an EARLINET station.

Construct Demo Input Deck

DTIC Science & Technology

2010-06-01

information diffusion patterns when bridging agents span two otherwise separate groups ? and then how such a simulation would be simulated using ...All users may find it more useful to use the table of contents in order to read sections of interest and reference chain to other parts of the...expression evaluates to 0+20-1 = 19, which would be the end-value expected for a zero-indexed group of twenty agents. Similar calculation can be used to

Discovery and Testing of Ricin Therapeutics

DTIC Science & Technology

2011-06-01

reticulum (ER) lumen. While in the ER, the ricin A chain co-opts ER quality control to gain access to the cytosol by a process referred to as...containing N-linked oligosaccharides characteristic of ER-resident molecules (21). RTAE177D and RTA! polypeptides with the predicted molecular weight...U373RTA! cells by pulse - chase analysis (Figure 2B and C). The cells were metabolically labeled with 35S-methionine for 15 min and Lane 1

Chemical modification of electrolytes for lithium batteries

NASA Astrophysics Data System (ADS)

Afanas'ev, Vladimir N.; Grechin, Aleksandr G.

2002-09-01

Modern approaches to modifying chemically electrolytes for lithium batteries are analysed with the aim of optimising the charge-transfer processes in liquid-phase and solid (polymeric) media. The main regularities of transport properties of lithium electrolyte solutions containing complex (encapsulated) ions in aprotic solvents and polymers are discussed. The prospects for the development of electrolytic solvosystems with the chain (ionotropic) mechanism of conduction with respect to lithium ions are outlined. The bibliography includes 126 references.

Current instrument status of the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS)

NASA Technical Reports Server (NTRS)

Eastwood, Michael L.; Sarture, Charles M.; Chrien, Thomas G.; Green, Robert O.; Porter, Wallace M.

1991-01-01

An upgraded version of AVIRIS, an airborne imaging spectrometer based on a whiskbroom-type scanner coupled via optical fibers to four dispersive spectrometers, that has been in operation since 1987 is described. Emphasis is placed on specific AVIRIS subsystems including foreoptics, fiber optics, and an in-flight reference source; spectrometers and detector dewars; a scan drive mechanism; a signal chain; digital electronics; a tape recorder; calibration systems; and ground support requirements.

Clinical and preclinical validation of the serum free light chain assay: identification of the critical difference for optimized clinical use.

PubMed

Hansen, Charlotte T; Münster, Anna-Marie; Nielsen, Lars; Pedersen, Per; Abildgaard, Niels

2012-12-01

The use of the assay for the measurements of free light chains in serum (sFLCs) is increasing. However, there are technical limitations that potentially affect the use in serial measurements. We need further knowledge on the standards of analytical precision, the utility of conventional population-based reference values and the critical difference (CD) between serial results required for significance. To answer these questions, the biological variation must be known. We determined the biological variation in healthy individuals and patients with plasma cell dyscrasia (PCD). We assessed the imprecision of the analysis in use from FreeLite™. We determined the reference interval (RI) in 170 healthy individuals. The biological variation is identical for healthy individuals and patients with PCD. The imprecision of the sFLC analysis cannot fulfil the desirable performance standards for a laboratory test, but are within the manufacturer's ±20% variation for quality control samples. RI showed a significant increase for κ FLC and κ/λ ratio with age, but not for λ. Critical difference was calculated to be 24% and 23% for κ and λ, respectively. We suggest the use of an age-dependent RI. When monitoring patients with PCD, their own former results are the best reference, and knowledge on CD is a valuable tool, which we describe for the first time. Also, it challenges the recently proposed International Myeloma Working Group 'paraprotein relapse criteria', recommending an increase of more than 25% in the involved FLC to indicate the need for initiation of retreatment. We recommend revision of this criterion. © 2012 John Wiley & Sons A/S.

Specificity of monoclonal antibodies to strains of Dickeya sp. that cause bacterial heart rot of pineapple.

PubMed

Peckham, Gabriel D; Kaneshiro, Wendy S; Luu, Van; Berestecky, John M; Alvarez, Anne M

2010-10-01

During a severe outbreak of bacterial heart rot that occurred in pineapple plantations on Oahu, Hawaii, in 2003 and years following, 43 bacterial strains were isolated from diseased plants or irrigation water and identified as Erwinia chrysanthemi (now Dickeya sp.) by phenotypic, molecular, and pathogenicity assays. Rep-PCR fingerprint patterns grouped strains from pineapple plants and irrigation water into five genotypes (A-E) that differed from representatives of other Dickeya species, Pectobacterium carotovorum and other enteric saprophytes isolated from pineapple. Monoclonal antibodies produced following immunization of mice with virulent type C Dickeya sp. showed only two specificities. MAb Pine-1 (2D11G1, IgG1 with kappa light chain) reacted to all 43 pineapple/water strains and some reference strains (D. dianthicola, D. chrysanthemi, D. paradisiaca, some D. dadantii, and uncharacterized Dickeya sp.) but did not react to reference strains of D. dieffenbachiae, D. zeae, or one of the two Malaysian pineapple strains. MAb Pine-2 (2A7F2, IgG3 with kappa light chain) reacted to all type B, C, and D strains but not to any A or E strains or any reference strains except Dickeya sp. isolated from Malaysian pineapple. Pathogenicity tests showed that type C strains were more aggressive than type A strains when inoculated during cool months. Therefore, MAb Pine-2 distinguishes the more virulent type C strains from less virulent type A pineapple strains and type E water strains. MAbs with these two specificities enable development of rapid diagnostic tests that will distinguish the systemic heart rot pathogen from opportunistic bacteria associated with rotted tissues. Use of the two MAbs in field assays also permits the monitoring of a known subpopulation and provides additional decision tools for disease containment and management practices.

Identification of suitable reference genes in bone marrow stromal cells from osteoarthritic donors.

PubMed

Schildberg, Theresa; Rauh, Juliane; Bretschneider, Henriette; Stiehler, Maik

2013-11-01

Bone marrow stromal cells (BMSCs) are key cellular components for musculoskeletal tissue engineering strategies. Furthermore, recent data suggest that BMSCs are involved in the development of Osteoarthritis (OA) being a frequently occurring degenerative joint disease. Reliable reference genes for the molecular evaluation of BMSCs derived from donors exhibiting OA as a primary co-morbidity have not been reported on yet. Hence, the aim of the study was to identify reference genes suitable for comparative gene expression analyses using OA-BMSCs. Passage 1 bone marrow derived BMSCs were isolated from n=13 patients with advanced stage idiopathic hip osteoarthritis and n=15 age-matched healthy donors. The expression of 31 putative reference genes was analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using a commercially available TaqMan(®) assay. Calculating the coefficient of variation (CV), mRNA expression stability was determined and afterwards validated using geNorm and NormFinder algorithms. Importin 8 (IPO8), TATA box binding protein (TBP), and cancer susceptibility candidate 3 (CASC3) were identified as the most stable reference genes. Notably, commonly used reference genes, e.g. beta-actin (ACTB) and beta-2-microglobulin (B2M) were among the most unstable genes. For normalization of gene expression data of OA-BMSCs the combined use of IPO8, TBP, and CASC3 gene is recommended. © 2013.

Reference intervals for plasma-free amino acid in a Japanese population.

PubMed

Yamamoto, Hiroyuki; Kondo, Kazuhiro; Tanaka, Takayuki; Muramatsu, Takahiko; Yoshida, Hiroo; Imaizumi, Akira; Nagao, Kenji; Noguchi, Yasushi; Miyano, Hiroshi

2016-05-01

Plasma amino acid concentrations vary with various diseases. Although reference intervals are useful in daily clinical practice, no reference intervals have been reported for plasma amino acids in a large Japanese population. Reference individuals were selected from 7685 subjects examined with the Japanese Ningen Dock in 2008. A total of 1890 individuals were selected based on exclusion criteria, and the reference samples were selected after the outlier samples for each amino acid concentration were excluded. The lower limit of the reference intervals for the plasma amino acid concentrations was set at the 2.5th percentile and the upper limit at the 97.5th percentile. By use of the nested analysis of variance, we analysed a large dataset of plasma samples and the effects of background factors (sex, age and body mass index [BMI]) on the plasma amino acid concentrations. Most amino acid concentrations were related to sex, especially those of branched-chained amino acid. The citrulline, glutamine, ornithine and lysine concentrations were related to age. The glutamate concentration was related to body mass index. The concentrations of most amino acids are more strongly related to sex than to age or body mass index. Our results indicate that the reference intervals for plasma amino acid concentrations should be stratified by sex when the background factors of age and body mass index are considered. © The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Selection of reference genes for quantitative real time RT-PCR during dimorphism in the zygomycete Mucor circinelloides.

PubMed

Valle-Maldonado, Marco I; Jácome-Galarza, Irvin E; Gutiérrez-Corona, Félix; Ramírez-Díaz, Martha I; Campos-García, Jesús; Meza-Carmen, Víctor

2015-03-01

Mucor circinelloides is a dimorphic fungal model for studying several biological processes including cell differentiation (yeast-mold transitions) as well as biodiesel and carotene production. The recent release of the first draft sequence of the M. circinelloides genome, combined with the availability of analytical methods to determine patterns of gene expression, such as quantitative Reverse transcription-Polymerase chain reaction (qRT-PCR), and the development of molecular genetic tools for the manipulation of the fungus, may help identify M. circinelloides gene products and analyze their relevance in different biological processes. However, no information is available on M. circinelloides genes of stable expression that could serve as internal references in qRT-PCR analyses. One approach to solve this problem consists in the use of housekeeping genes as internal references. However, validation of the usability of these reference genes is a fundamental step prior to initiating qRT-PCR assays. This work evaluates expression of several constitutive genes by qRT-PCR throughout the morphological differentiation stages of M. circinelloides; our results indicate that tfc-1 and ef-1 are the most stable genes for qRT-PCR assays during differentiation studies and they are proposed as reference genes to carry out gene expression studies in this fungus.

Identification of Reference Genes and Analysis of Heat Shock Protein Gene Expression in Lingzhi or Reishi Medicinal Mushroom, Ganoderma lucidum, after Exposure to Heat Stress.

PubMed

Liu, Yong-Nan; Lu, Xiao-Xiao; Ren, Ang; Shi, Liang; Jiang, Ai-Liang; Yu, Han-Shou; Zhao, Ming-Wen

2017-01-01

Ganoderma lucidum has been considered an emerging model species for studying how environmental factors regulate the growth, development, and secondary metabolism of Basidiomycetes. Heat stress, which is one of the most important environmental abiotic stresses, seriously affects the growth, development, and yield of microorganisms. Understanding the response to heat stress has gradually become a hotspot in microorganism research. But suitable reference genes for expression analysis under heat stress have not been reported in G. lucidum. In this study, we systematically identified 11 candidate reference genes that were measured using reverse transcriptase quantitative polymerase chain reaction, and the gene expression stability was analyzed under heat stress conditions using geNorm and NormFinder. The results show that 5 reference genes-CYP and TIF, followed by UCE2, ACTIN, and UBQ1-are the most stable genes under our experimental conditions. Moreover, the relative expression levels of 3 heat stress response genes (hsp17.4, hsp70, and hsp90) were analyzed under heat stress conditions with different normalization strategies. The results show that use of a gene with unstable expression (SAND) as the reference gene leads to biased data and misinterpretations of the target gene expression level under heat stress.

Identification of Reference Genes for Real-Time Quantitative PCR Experiments in the Liverwort Marchantia polymorpha

PubMed Central

Dolan, Liam; Langdale, Jane A.

2015-01-01

Real-time quantitative polymerase chain reaction (qPCR) has become widely used as a method to compare gene transcript levels across different conditions. However, selection of suitable reference genes to normalize qPCR data is required for accurate transcript level analysis. Recently, Marchantia polymorpha has been adopted as a model for the study of liverwort development and land plant evolution. Identification of appropriate reference genes has therefore become a necessity for gene expression studies. In this study, transcript levels of eleven candidate reference genes have been analyzed across a range of biological contexts that encompass abiotic stress, hormone treatment and different developmental stages. The consistency of transcript levels was assessed using both geNorm and NormFinder algorithms, and a consensus ranking of the different candidate genes was then obtained. MpAPT and MpACT showed relatively constant transcript levels across all conditions tested whereas the transcript levels of other candidate genes were clearly influenced by experimental conditions. By analyzing transcript levels of phosphate and nitrate starvation reporter genes, we confirmed that MpAPT and MpACT are suitable reference genes in M. polymorpha and also demonstrated that normalization with an inappropriate gene can lead to erroneous analysis of qPCR data. PMID:25798897

Selection of reference genes for qRT-PCR analysis of gene expression in sea cucumber Apostichopus japonicus during aestivation

NASA Astrophysics Data System (ADS)

Zhao, Ye; Chen, Muyan; Wang, Tianming; Sun, Lina; Xu, Dongxue; Yang, Hongsheng

2014-11-01

Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a technique that is widely used for gene expression analysis, and its accuracy depends on the expression stability of the internal reference genes used as normalization factors. However, many applications of qRT-PCR used housekeeping genes as internal controls without validation. In this study, the expression stability of eight candidate reference genes in three tissues (intestine, respiratory tree, and muscle) of the sea cucumber Apostichopus japonicus was assessed during normal growth and aestivation using the geNorm, NormFinder, delta CT, and RefFinder algorithms. The results indicate that the reference genes exhibited significantly different expression patterns among the three tissues during aestivation. In general, the β-tubulin (TUBB) gene was relatively stable in the intestine and respiratory tree tissues. The optimal reference gene combination for intestine was 40S ribosomal protein S18 (RPS18), TUBB, and NADH dehydrogenase (NADH); for respiratory tree, it was β-actin (ACTB), TUBB, and succinate dehydrogenase cytochrome B small subunit (SDHC); and for muscle it was α-tubulin (TUBA) and NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 (NDUFA13). These combinations of internal control genes should be considered for use in further studies of gene expression in A. japonicus during aestivation.

Monitoring the freely dissolved concentrations of polycyclic aromatic hydrocarbons (PAH) and alkylphenols (AP) around a Norwegian oil platform by holistic passive sampling.

PubMed

Harman, Christopher; Thomas, Kevin V; Tollefsen, Knut Erik; Meier, Sonnich; Bøyum, Olav; Grung, Merete

2009-11-01

In order to assess the environmental impact of aquatic discharges from the offshore oil industry, polar organic chemical integrative samplers (POCIS) and semipermeable membrane devices (SPMDs) were deployed around an oil platform and at reference locations in the North Sea. Exposure to polycyclic aromatic hydrocarbons (PAH) and alkylated phenols (AP) was determined from passive sampler accumulations using an empirical uptake model, the dissipation of performance reference compounds and adjusted laboratory derived sampling rates. Exposure was relatively similar within 1-2 km of the discharge point, with levels dominated by short chained C1-C3 AP isomers (19-51 ngL(-1)) and alkylated naphthalenes, phenanthrenes and dibenzothiophenes (NPD, 29-45 ngL(-1)). Exposure stations showed significant differences to reference sites for NPD, but not always for more hydrophobic PAH. These concentrations are several orders of magnitude lower than those reported to give both acute and sub-lethal effects, although their long term consequences are unknown.

Optimal Reference Genes for Gene Expression Normalization in Trichomonas vaginalis.

PubMed

dos Santos, Odelta; de Vargas Rigo, Graziela; Frasson, Amanda Piccoli; Macedo, Alexandre José; Tasca, Tiana

2015-01-01

Trichomonas vaginalis is the etiologic agent of trichomonosis, the most common non-viral sexually transmitted disease worldwide. This infection is associated with several health consequences, including cervical and prostate cancers and HIV acquisition. Gene expression analysis has been facilitated because of available genome sequences and large-scale transcriptomes in T. vaginalis, particularly using quantitative real-time polymerase chain reaction (qRT-PCR), one of the most used methods for molecular studies. Reference genes for normalization are crucial to ensure the accuracy of this method. However, to the best of our knowledge, a systematic validation of reference genes has not been performed for T. vaginalis. In this study, the transcripts of nine candidate reference genes were quantified using qRT-PCR under different cultivation conditions, and the stability of these genes was compared using the geNorm and NormFinder algorithms. The most stable reference genes were α-tubulin, actin and DNATopII, and, conversely, the widely used T. vaginalis reference genes GAPDH and β-tubulin were less stable. The PFOR gene was used to validate the reliability of the use of these candidate reference genes. As expected, the PFOR gene was upregulated when the trophozoites were cultivated with ferrous ammonium sulfate when the DNATopII, α-tubulin and actin genes were used as normalizing gene. By contrast, the PFOR gene was downregulated when the GAPDH gene was used as an internal control, leading to misinterpretation of the data. These results provide an important starting point for reference gene selection and gene expression analysis with qRT-PCR studies of T. vaginalis.

Optimal Reference Genes for Gene Expression Normalization in Trichomonas vaginalis

PubMed Central

dos Santos, Odelta; de Vargas Rigo, Graziela; Frasson, Amanda Piccoli; Macedo, Alexandre José; Tasca, Tiana

2015-01-01

Trichomonas vaginalis is the etiologic agent of trichomonosis, the most common non-viral sexually transmitted disease worldwide. This infection is associated with several health consequences, including cervical and prostate cancers and HIV acquisition. Gene expression analysis has been facilitated because of available genome sequences and large-scale transcriptomes in T. vaginalis, particularly using quantitative real-time polymerase chain reaction (qRT-PCR), one of the most used methods for molecular studies. Reference genes for normalization are crucial to ensure the accuracy of this method. However, to the best of our knowledge, a systematic validation of reference genes has not been performed for T. vaginalis. In this study, the transcripts of nine candidate reference genes were quantified using qRT-PCR under different cultivation conditions, and the stability of these genes was compared using the geNorm and NormFinder algorithms. The most stable reference genes were α-tubulin, actin and DNATopII, and, conversely, the widely used T. vaginalis reference genes GAPDH and β-tubulin were less stable. The PFOR gene was used to validate the reliability of the use of these candidate reference genes. As expected, the PFOR gene was upregulated when the trophozoites were cultivated with ferrous ammonium sulfate when the DNATopII, α-tubulin and actin genes were used as normalizing gene. By contrast, the PFOR gene was downregulated when the GAPDH gene was used as an internal control, leading to misinterpretation of the data. These results provide an important starting point for reference gene selection and gene expression analysis with qRT-PCR studies of T. vaginalis. PMID:26393928

Identification of Reliable Reference Genes for Quantification of MicroRNAs in Serum Samples of Sulfur Mustard-Exposed Veterans.

PubMed

Gharbi, Sedigheh; Shamsara, Mehdi; Khateri, Shahriar; Soroush, Mohammad Reza; Ghorbanmehr, Nassim; Tavallaei, Mahmood; Nourani, Mohammad Reza; Mowla, Seyed Javad

2015-01-01

In spite of accumulating information about pathological aspects of sulfur mustard (SM), the precise mechanism responsible for its effects is not well understood. Circulating microRNAs (miRNAs) are promising biomarkers for disease diagnosis and prognosis. Accurate normalization using appropriate reference genes, is a critical step in miRNA expression studies. In this study, we aimed to identify appropriate reference gene for microRNA quantification in serum samples of SM victims. In this case and control experimental study, using quantitative real-time polymerase chain reaction (qRT-PCR), we evaluated the suitability of a panel of small RNAs including SNORD38B, SNORD49A, U6, 5S rRNA, miR-423-3p, miR-191, miR-16 and miR-103 in sera of 28 SM-exposed veterans of Iran-Iraq war (1980-1988) and 15 matched control volunteers. Different statistical algorithms including geNorm, Normfinder, best-keeper and comparative delta-quantification cycle (Cq) method were employed to find the least variable reference gene. miR-423-3p was identified as the most stably expressed reference gene, and miR- 103 and miR-16 ranked after that. We demonstrate that non-miRNA reference genes have the least stabil- ity in serum samples and that some house-keeping miRNAs may be used as more reliable reference genes for miRNAs in serum. In addition, using the geometric mean of two reference genes could increase the reliability of the normalizers.

[Two patients with mitochondrial respiratory chain disease].

PubMed

Bangma, H R; Smit, G P A; Kuks, J B M; Grevink, R G; Wolffenbuttel, B H R

2008-10-18

A 23-year-old woman and a 13-year-old boy were diagnosed with mitochondrial respiratory chain disease. The woman had muscle pain, fatigue and bilateral ophthalmoplegia--symptoms consistent with Kearns-Sayre syndrome. The boy had aspecific symptoms; eventually, reduced activity of complex 1 was found to be the cause of the mitochondrial respiratory chain disease in the boy and his mother, who had suffered from unexplained fatigue and muscle pain for 15 years. Mitochondrial diseases often involve several organ systems. Diagnosis can be difficult, because laboratory tests such as serum and urinary lactate and creatine kinase have low sensitivity and specificity. Biochemical assessment of muscle biopsy can reveal reduced oxidation ATP synthesis and sometimes specific abnormalities in individual protein complexes. DNA analysis may be helpful in demonstrating mitochondrial or nuclear mutations or deletions. The goal of treatment is to increase mitochondrial ATP production, improve clinical symptoms and enhance stamina. Replacement of the following substances (also referred to as cofactors) may be attempted: co-enzyme Q10, antioxidants (lipoic acid, vitamins C and E), riboflavin, thiamine, creatine and carnitine. Evidence regarding the optimal treatment approach is lacking; one usually has to rely on observing effects in the individual patient.

Symmetry Breaking in Side Chains Leading to Mixed Orientations and Improved Charge Transport in Isoindigo-alt-Bithiophene Based Polymer Thin Films.

PubMed

Xue, Guobiao; Zhao, Xikang; Qu, Ge; Xu, Tianbai; Gumyusenge, Aristide; Zhang, Zhuorui; Zhao, Yan; Diao, Ying; Li, Hanying; Mei, Jianguo

2017-08-02

The selection of side chains is important in design of conjugated polymers. It not only affects their intrinsic physical properties, but also has an impact on thin film morphologies. Recent reports suggested that a face-on/edge-on bimodal orientation observed in polymer thin films may be responsible for a three-dimensional (3D) charge transport and leads to dramatically improved mobility in donor-acceptor based conjugated polymers. To achieve a bimodal orientation in thin films has been seldom explored from the aspect of molecular design. Here, we demonstrate a design strategy involving the use of asymmetric side chains that enables an isoindigo-based polymer to adopt a distinct bimodal orientation, confirmed by the grazing incidence X-ray diffraction. As a result, the polymer presents an average high mobility of 3.8 ± 0.7 cm 2 V -1 s -1 with a maximum value of 5.1 cm 2 V -1 s -1 , in comparison with 0.47 and 0.51 cm 2 V -1 s -1 obtained from the two reference polymers. This study exemplifies a new strategy to develop the next generation polymers through understanding the property-structure relationship.

Reviewing the importance of the cold chain in the distribution of vaccines.

PubMed

Purssell, Edward

2015-10-01

Vaccination is an effective public health measure to prevent and control a number of infectious diseases. However, since vaccines are biological products and are sensitive to both heat and cold, they need to be maintained within a narrow range of temperatures, often referred to as the 'cold-chain'. This range, which is between +2°C and +8°C with a target +5°C, does not allow for refreezing or storage at room temperature. This paper discusses the importance of the cold chain, what should be done both to maintain it, and the actions to be taken, should a break be noted. It is important to note the product information supplied with vaccines, which is taken from the summary of product characteristics that forms part of the licensing requirements for each vaccine, and which will state how it should be stored. Using a vaccine that has not been stored according to these instructions constitutes off-label use, for which the individual practitioner must take responsibility. It also emphasises the fragile nature of many public health interventions, maintenance of which require constant vigilance and close cooperation between many groups and individuals.

On the occurrence of polyproline II structure in elastin

NASA Astrophysics Data System (ADS)

Martino, M.; Bavoso, A.; Guantieri, V.; Coviello, A.; Tamburro, A. M.

2000-02-01

To shed light on the occurrence of the polyproline II (PP II) structure in the elastomeric protein elastin, the octapeptide sequence ALGGGALG of the N-terminal region of human elastin was studied in its monomeric and polymeric form, both in solution and in the solid state. Furthermore, the polymer poly(PG), chosen by us as an a priori reference compound for investigating the stability of PP II structure in presence of alternating proline and glycine residues along the polypeptide chain, was studied by circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Its "monomeric" form Boc-PG-OH, was also analyzed by X-ray diffraction. It was shown that, in the solid state the presence of PG or GGG sequences in polypeptide chains and even in a short peptide as Boc-PG-OH induces the acquisition of the PP II structural motif. However, in solution this conformation appears to be much more unstable even in the case of long polypeptide chains. The finding that at room temperature the PP II structure is always in equilibrium with other conformers suggests that its dynamics could also contribute to the molecular mechanism of elastin elasticity.

USSR and Eastern Europe Scientific Abstracts, Physics and Mathematics, Number 39

DTIC Science & Technology

1978-01-17

examination of a monoclinic single crystal has revealed a U022+ iön, and helical polyphosphate chains with six PO4 tetrahedra per link. Corrugated uranyl...mean mass temperature and local Nusselt number. Figures 5; references 13: 3 Russian, 10 Western. USSR UDC 535.334 DETERMINATION OF THE PARAMETERS...Nuclear Research [Abstract] The theory of pion condensation predicts the existence of super- dense nuclei, on the basis of the structure of the

Effects of Moisture and Other Contaminants in Friction Composites

DTIC Science & Technology

1993-01-30

NC 126, (Cardolite Corporation, Newark, NJ), a cashew nut shell liquid modified phenolic resin. NC126 is different from a straight phenolic resin in...that there is an alkyl chain substituent in the meta position of the phenol. The resin is derived from cashew nut shell liquid and is a solid...crosslinked cashew resin and is often referred to as cashew particles. The friction materials were processed by compression molding at 160 °C and 1000 psi

Nanofiber-Based Bulk-Heterojunction Organic Solar Cells Using Coaxial Electrospinning

DTIC Science & Technology

2012-01-01

chains are likely oriented with the [010] direction, perpendicular to the substrate, in the fi lm device. Glancing incidence X - ray diffraction (GIXD...Electron and X - ray diffraction measurements were per- formed in order to study the structural order in annealed fi bers and devices. For reference... angle X - ray scattering (SAXS/WAXS) beamline 7.3.3 of the Advanced Light Source at Lawrence Berkeley National Laboratory at 10 keV (1.24 Å) from a bend

JPRS Report, Science & Technology, Japan

DTIC Science & Technology

1990-10-22

34 Particularly, details of the "Comparison with Other Countries" have been described in a series of this journal since the first edition. Also, the...transportation. Comparison of energy efficiency between different means of transportation was done by von Karman 2 but, for walking, he referred to living things...Federation Lecture Meeting, 1988, pp 333-334. 6. Kumar, V.R. and Waldron,. K.J,.. ""Force Distribution in Cl6sed’Kinematics Chains," IEEE J. ROBOTICS AND

An Adaptive Planning Framework for Situation Assessment and Decision-making on an Autonomous Ground Vehicle

DTIC Science & Technology

2006-12-01

robot is referred to as “emergent” since it is likely that the observed behavior is some extemporaneous blend of the possible behaviors that the...Report Meta Data message to contain data of any permissible type, arranged in any combination, and assembled extemporaneously by the publishing component...system (and especially the Decision Broker) to use the inferencing chain to extemporaneously assemble an explanation of how a certain conclusion has been

Analytical Approaches to Verify Food Integrity: Needs and Challenges.

PubMed

Stadler, Richard H; Tran, Lien-Anh; Cavin, Christophe; Zbinden, Pascal; Konings, Erik J M

2016-09-01

A brief overview of the main analytical approaches and practices to determine food authenticity is presented, addressing, as well, food supply chain and future requirements to more effectively mitigate food fraud. Food companies are introducing procedures and mechanisms that allow them to identify vulnerabilities in their food supply chain under the umbrella of a food fraud prevention management system. A key step and first line of defense is thorough supply chain mapping and full transparency, assessing the likelihood of fraudsters to penetrate the chain at any point. More vulnerable chains, such as those where ingredients and/or raw materials are purchased through traders or auctions, may require a higher degree of sampling, testing, and surveillance. Access to analytical tools is therefore pivotal, requiring continuous development and possibly sophistication in identifying chemical markers, data acquisition, and modeling. Significant progress in portable technologies is evident already today, for instance, as in the rapid testing now available at the agricultural level. In the near future, consumers may also have the ability to scan products in stores or at home to authenticate labels and food content. For food manufacturers, targeted analytical methods complemented by untargeted approaches are end control measures at the factory gate when the material is delivered. In essence, testing for food adulterants is an integral part of routine QC, ideally tailored to the risks in the individual markets and/or geographies or supply chains. The development of analytical methods is a first step in verifying the compliance and authenticity of food materials. A next, more challenging step is the successful establishment of global consensus reference methods as exemplified by the AOAC Stakeholder Panel on Infant Formula and Adult Nutritionals initiative, which can serve as an approach that could also be applied to methods for contaminants and adulterants in food. The food industry has taken these many challenges aboard, working closely with all stakeholders and continuously communicating on progress in a fully transparent manner.

Molecular Characteristics of Hb New York [β113(G15)Val→Glu, HBB: c.341T>A] in Thailand.

PubMed

Chaibunruang, Attawut; Singha, Kritsada; Srivorakun, Hataichanok; Fucharoen, Goonnapa; Fucharoen, Supan

2018-01-01

Hb New York or Hb Kaohsiung [β113(G15)Val→Glu (GTG>GAG), HBB: c.341T>A] has been considered a rare β hemoglobin (Hb) variant found originally in an Iranian woman and later in diverse populations but its genetic origin has not been elucidated. Here we report molecular and hematological descriptions of this variant found in the Thai population. Among 5643 subjects referred for hemoglobinopathy investigation during January 2015 to September 2017, 183 (3.2%) were found to carry several Hb variants, including β chain variants (n = 135, 2.4%), α chain variants (n = 33, 0.6%), Hb Lepore-Hollandia (NG_000007.3: g.63290_70702del) and Hb Lepore-Boston-Washington (NG_000007.3: g.63632_71046del) (δβ hybrid Hb) (n = 12, 0.2%) and δ chain variants (n = 3, 0.05%). Of patients with β chain variants, six with normal high performance liquid chromatography (HPLC) patterns, had an abnormal Hb in zone 11 of capillary electrophoresis (CE), the amounts of which ranged from 29.6-45.4% with normal levels of Hb A 2 and Hb F. DNA analysis identified a heterozygous Hb New York mutation in all cases. Further screening of α-thalassemia (α-thal) identified coinheritance of α + - and α 0 -thal in two of them who had reduced levels of Hb New York. Haplotype analysis suggested that the Thai Hb New York was likely associated with a single β-globin haplotype [+ - - - - + +], indicating that it was of the same origin. Hematological findings and simple DNA assay based on allele-specific polymerase chain reaction (PCR) for rapid detection of Hb New York are presented.

Internal Light Source-Driven Photoelectrochemical 3D-rGO/Cellulose Device Based on Cascade DNA Amplification Strategy Integrating Target Analog Chain and DNA Mimic Enzyme.

PubMed

Lan, Feifei; Liang, Linlin; Zhang, Yan; Li, Li; Ren, Na; Yan, Mei; Ge, Shenguang; Yu, Jinghua

2017-11-01

In this work, a chemiluminescence-driven collapsible greeting card-like photoelectrochemical lab-on-paper device (GPECD) with hollow channel was demonstrated, in which target-triggering cascade DNA amplification strategy was ingeniously introduced. The GPECD had the functions of reagents storage and signal collection, and the change of configuration could control fluidic path, reaction time and alterations in electrical connectivity. In addition, three-dimentional reduced graphene oxide affixed Au flower was in situ grown on paper cellulose fiber for achieving excellent conductivity and biocompatibility. The cascade DNA amplification strategy referred to the cyclic formation of target analog chain and its trigger action to hybridization chain reaction (HCR), leading to the formation of numerous hemin/G-quadruplex DNA mimic enzyme with the presence of hemin. Subjected to the catalysis of hemin/G-quadruplex, the strong chemiluminiscence of luminol-H 2 O 2 system was obtained, which then was used as internal light source to excite photoactive materials realizing the simplification of instrument. In this analyzing process, thrombin served as proof-of-concept, and the concentration of target was converted into the DNA signal output by the specific recognition of aptamer-protein and target analog chain recycling. The target analog chain was produced in quantity with the presence of target, which further triggered abundant HCR and introduced hemin/G-quadruplex into the system. The photocurrent signal was obtained after the nitrogen-doped carbon dots sensitized ZnO was stimulated by chemiluminescence. The proposed GPECD exhibited excellent specificity and sensitivity toward thrombin with a detection limit of 16.7 fM. This judiciously engineered GPECD paved a luciferous way for detecting other protein with trace amounts in bioanalysis and clinical biomedicine.

Structured medium and long chain triglycerides show short-term increases in fat oxidation, but no changes in adiposity in men.

PubMed

Roynette, Catherine E; Rudkowska, Iwona; Nakhasi, Dilip K; Jones, Peter J H

2008-05-01

Medium chain triglycerides (MCT) have been suggested as modulators of human energy expenditure (EE) and thus may influence total and regional body fat distribution. To investigate in overweight men the effects of structured medium and long chain triglycerides on EE, substrate oxidation and body adiposity, compared to extra virgin olive oil (OO). In a 6 week single-blind crossover study, 23 overweight men were randomly assigned to consume a standard high-fat diet of which 75% total fat was provided as either structured medium and long chain triglycerides referred to as structured oil (StO), or OO. EE and body composition were measured using indirect calorimetry and magnetic resonance imaging, respectively, at weeks 1 and 6 of each phase. Body weight decreased (p<0.01) from baseline to end-point during consumption of both the StO (-1.46+/-0.4k g) and OO (-1.17+/-0.4 kg); however, no significant treatment differences were observed. There were no changes in body composition among treatment groups. No differences between diets for EE measurements were reported. Fat oxidation rates did not differ between oils, but were reduced (p<0.05) in the StO group between baseline (0.0020+/-0.0003 g/kg fat free mass per min) in comparison to after week 6 (0.0013+/-0.0001 g/kg fat free mass per min). No differences in carbohydrate oxidation rate were noted across diets or time. The present structured medium and long chain triglyceride oil increases short-term fat oxidation but fails to modulate body weight or adiposity through a change in EE.

Identification and validation of reference genes for quantitative real-time PCR normalization and its applications in lycium.

PubMed

Zeng, Shaohua; Liu, Yongliang; Wu, Min; Liu, Xiaomin; Shen, Xiaofei; Liu, Chunzhao; Wang, Ying

2014-01-01

Lycium barbarum and L. ruthenicum are extensively used as traditional Chinese medicinal plants. Next generation sequencing technology provides a powerful tool for analyzing transcriptomic profiles of gene expression in non-model species. Such gene expression can then be confirmed with quantitative real-time polymerase chain reaction (qRT-PCR). Therefore, use of systematically identified suitable reference genes is a prerequisite for obtaining reliable gene expression data. Here, we calculated the expression stability of 18 candidate reference genes across samples from different tissues and grown under salt stress using geNorm and NormFinder procedures. The geNorm-determined rank of reference genes was similar to those defined by NormFinder with some differences. Both procedures confirmed that the single most stable reference gene was ACNTIN1 for L. barbarum fruits, H2B1 for L. barbarum roots, and EF1α for L. ruthenicum fruits. PGK3, H2B2, and PGK3 were identified as the best stable reference genes for salt-treated L. ruthenicum leaves, roots, and stems, respectively. H2B1 and GAPDH1+PGK1 for L. ruthenicum and SAMDC2+H2B1 for L. barbarum were the best single and/or combined reference genes across all samples. Finally, expression of salt-responsive gene NAC, fruit ripening candidate gene LrPG, and anthocyanin genes were investigated to confirm the validity of the selected reference genes. Suitable reference genes identified in this study provide a foundation for accurately assessing gene expression and further better understanding of novel gene function to elucidate molecular mechanisms behind particular biological/physiological processes in Lycium.

Identification and validation of superior reference gene for gene expression normalization via RT-qPCR in staminate and pistillate flowers of Jatropha curcas - A biodiesel plant.

PubMed

Karuppaiya, Palaniyandi; Yan, Xiao-Xue; Liao, Wang; Wu, Jun; Chen, Fang; Tang, Lin

2017-01-01

Physic nut (Jatropha curcas L) seed oil is a natural resource for the alternative production of fossil fuel. Seed oil production is mainly depended on seed yield, which was restricted by the low ratio of staminate flowers to pistillate flowers. Further, the mechanism of physic nut flower sex differentiation has not been fully understood yet. Quantitative Real Time-Polymerase Chain Reaction is a reliable and widely used technique to quantify the gene expression pattern in biological samples. However, for accuracy of qRT-PCR, appropriate reference gene is highly desirable to quantify the target gene level. Hence, the present study was aimed to identify the stable reference genes in staminate and pistillate flowers of J. curcas. In this study, 10 candidate reference genes were selected and evaluated for their expression stability in staminate and pistillate flowers, and their stability was validated by five different algorithms (ΔCt, BestKeeper, NormFinder, GeNorm and RefFinder). Resulting, TUB and EF found to be the two most stably expressed reference for staminate flower; while GAPDH1 and EF found to be the most stably expressed reference gene for pistillate flowers. Finally, RT-qPCR assays of target gene AGAMOUS using the identified most stable reference genes confirmed the reliability of selected reference genes in different stages of flower development. AGAMOUS gene expression levels at different stages were further proved by gene copy number analysis. Therefore, the present study provides guidance for selecting appropriate reference genes for analyzing the expression pattern of floral developmental genes in staminate and pistillate flowers of J. curcas.

Identification and validation of superior reference gene for gene expression normalization via RT-qPCR in staminate and pistillate flowers of Jatropha curcas – A biodiesel plant

PubMed Central

Karuppaiya, Palaniyandi; Yan, Xiao-Xue; Liao, Wang; Chen, Fang; Tang, Lin

2017-01-01

Physic nut (Jatropha curcas L) seed oil is a natural resource for the alternative production of fossil fuel. Seed oil production is mainly depended on seed yield, which was restricted by the low ratio of staminate flowers to pistillate flowers. Further, the mechanism of physic nut flower sex differentiation has not been fully understood yet. Quantitative Real Time—Polymerase Chain Reaction is a reliable and widely used technique to quantify the gene expression pattern in biological samples. However, for accuracy of qRT-PCR, appropriate reference gene is highly desirable to quantify the target gene level. Hence, the present study was aimed to identify the stable reference genes in staminate and pistillate flowers of J. curcas. In this study, 10 candidate reference genes were selected and evaluated for their expression stability in staminate and pistillate flowers, and their stability was validated by five different algorithms (ΔCt, BestKeeper, NormFinder, GeNorm and RefFinder). Resulting, TUB and EF found to be the two most stably expressed reference for staminate flower; while GAPDH1 and EF found to be the most stably expressed reference gene for pistillate flowers. Finally, RT-qPCR assays of target gene AGAMOUS using the identified most stable reference genes confirmed the reliability of selected reference genes in different stages of flower development. AGAMOUS gene expression levels at different stages were further proved by gene copy number analysis. Therefore, the present study provides guidance for selecting appropriate reference genes for analyzing the expression pattern of floral developmental genes in staminate and pistillate flowers of J. curcas. PMID:28234941

An optical transduction chain for the AURIGA detector

NASA Astrophysics Data System (ADS)

Conti, L.; Marin, F.; de Rosa, M.; Prodi, G. A.; Taffarello, L.; Zendri, J. P.; Cerdonio, M.; Vitale, S.

2000-06-01

We describe the principle of operation of an opto-mechanical readout for resonant mass gravitational wave detectors; with such a device the AURIGA detector is expected to reach a sensitivity at the level of Shh=10-22/Hz over a bandwidth of about 40Hz. Recent developments in the implementation of this transduction chain are also reported. In particular we achieve quantum limited laser power noise in the frequency range of 200Hz around the bar fundamental frequency (about 1kHz) by means of active stabilization. We also set up a reference cavity of finesse 40000 with optically contacted mirrors on a 0.2m long Zerodur spacer. The cavity can be heated from room temperature to about 100 °C and temperature stabilized with fluctuations within 1mK over a period of several days. The cavity is under vacuum and isolated from mechanical disturbancies by means of a double stage cantilever system. .

Simultaneous detection of hemagglutinin and neuraminidase genes of novel influenza A (H7N9) by duplex real-time reverse transcription polymerase chain reaction.

PubMed

Li, Yan; Wu, Tao; Qi, Xian; Ge, Yiyue; Guo, Xiling; Wu, Bin; Yu, Huiyan; Zhu, Yefei; Shi, Zhiyang; Wang, Hua; Cui, Lunbiao; Zhou, Minghao

2013-12-01

A novel reassortant influenza A (H7N9) virus emerged recently in China. In this study, a duplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay was developed for the simultaneous detection of hemagglutinin (HA) and neuraminidase (NA) genes of H7N9 influenza viruses. The sensitivity of the assay was determined to be 10 RNA copies per reaction for both HA and NA genes. No cross-reactivity was observed with other influenza virus subtypes or respiratory tract viruses. One hundred and forty-six clinical and environmental specimens were tested and compared with reference methods and were found to be consistent. The assay is suitable for large-scale screening due to short turnaround times and high specificity, sensitivity, and reproducibility. Copyright © 2013 Elsevier B.V. All rights reserved.

Recursive thoughts on the simulation of the flexible multibody dynamics of slender offshore structures

NASA Astrophysics Data System (ADS)

Schilder, J.; Ellenbroek, M.; de Boer, A.

2017-12-01

In this work, the floating frame of reference formulation is used to create a flexible multibody model of slender offshore structures such as pipelines and risers. It is shown that due to the chain-like topology of the considered structures, the equation of motion can be expressed in terms of absolute interface coordinates. In the presented form, kinematic constraint equations are satisfied explicitly and the Lagrange multipliers are eliminated from the equations. Hence, the structures can be conveniently coupled to finite element or multibody models of for example seabed and vessel. The chain-like topology enables the efficient use of recursive solution procedures for both transient dynamic analysis and equilibrium analysis. For this, the transfer matrix method is used. In order to improve the convergence of the equilibrium analysis, the analytical solution of an ideal catenary is used as an initial configuration, reducing the number of required iterations.

An Organizational Knowledge Ontology for Automotive Supply Chains

NASA Astrophysics Data System (ADS)

Hellingrath, Bernd; Witthaut, Markus; Böhle, Carsten; Brügger, Stephan

The currently completed ILIPT (Intelligent Logistics for Innovative Product Technologies) project was concerned with the concept of the “5 day car” (a customized car that is delivered within five days after its ordering) and encompassed extensive research on the required production and logistics network structures and processes. As car manufacturers in the automotive industry (commonly referred to as OEMs) rely heavily on their suppliers, the major challenge lies in the organization of inter-enterprise cooperation supported by information systems (IS) in an efficient manner. A common understanding of supply chain concepts is indispensable for this. Ontologies as formal representations of concepts can be used as a semantic basis for cooperation. Relevant results from ILIPT are presented followed by a concept as well as a prototype of how to transfer the theoretical findings to a practical implementation, in this case a multi-agent system.

Identification of the five human Plasmodium species including P. knowlesi by real-time polymerase chain reaction.

PubMed

Oddoux, O; Debourgogne, A; Kantele, A; Kocken, C H; Jokiranta, T S; Vedy, S; Puyhardy, J M; Machouart, M

2011-04-01

Recently, Plasmodium knowlesi has been recognised as the fifth Plasmodium species causing malaria in humans. Hundreds of human cases infected with this originally simian Plasmodium species have been described in Asian countries and increasing numbers are reported in Europe from travellers. The growing impact of tourism and economic development in South and Southeast Asia are expected to subsequently lead to a further increase in cases both among locals and among travellers. P. knowlesi is easily misidentified in microscopy as P. malariae or P. falciparum. We developed new primers for the rapid and specific detection of this species by low-cost real-time polymerase chain reaction (PCR) and added this method to an already existing panel of primers used for the molecular identification of the other four species in one reaction. Reference laboratories should now be able to identify undisputably and rapidly P. knowlesi, as it is a potentially fatal pathogen.

Quantum recurrence and fractional dynamic localization in ac-driven perfect state transfer Hamiltonians

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

Longhi, Stefano, E-mail: stefano.longhi@fisi.polimi.it

Quantum recurrence and dynamic localization are investigated in a class of ac-driven tight-binding Hamiltonians, the Krawtchouk quantum chain, which in the undriven case provides a paradigmatic Hamiltonian model that realizes perfect quantum state transfer and mirror inversion. The equivalence between the ac-driven single-particle Krawtchouk Hamiltonian H{sup -hat} (t) and the non-interacting ac-driven bosonic junction Hamiltonian enables to determine in a closed form the quasi energy spectrum of H{sup -hat} (t) and the conditions for exact wave packet reconstruction (dynamic localization). In particular, we show that quantum recurrence, which is predicted by the general quantum recurrence theorem, is exact for themore » Krawtchouk quantum chain in a dense range of the driving amplitude. Exact quantum recurrence provides perfect wave packet reconstruction at a frequency which is fractional than the driving frequency, a phenomenon that can be referred to as fractional dynamic localization.« less

Polymerase chain reaction technology as analytical tool in agricultural biotechnology.

PubMed

Lipp, Markus; Shillito, Raymond; Giroux, Randal; Spiegelhalter, Frank; Charlton, Stacy; Pinero, David; Song, Ping

2005-01-01

The agricultural biotechnology industry applies polymerase chain reaction (PCR) technology at numerous points in product development. Commodity and food companies as well as third-party diagnostic testing companies also rely on PCR technology for a number of purposes. The primary use of the technology is to verify the presence or absence of genetically modified (GM) material in a product or to quantify the amount of GM material present in a product. This article describes the fundamental elements of PCR analysis and its application to the testing of grains. The document highlights the many areas to which attention must be paid in order to produce reliable test results. These include sample preparation, method validation, choice of appropriate reference materials, and biological and instrumental sources of error. The article also discusses issues related to the analysis of different matrixes and the effect they may have on the accuracy of the PCR analytical results.

A high-fidelity weather time series generator using the Markov Chain process on a piecewise level

NASA Astrophysics Data System (ADS)

Hersvik, K.; Endrerud, O.-E. V.

2017-12-01

A method is developed for generating a set of unique weather time-series based on an existing weather series. The method allows statistically valid weather variations to take place within repeated simulations of offshore operations. The numerous generated time series need to share the same statistical qualities as the original time series. Statistical qualities here refer mainly to the distribution of weather windows available for work, including durations and frequencies of such weather windows, and seasonal characteristics. The method is based on the Markov chain process. The core new development lies in how the Markov Process is used, specifically by joining small pieces of random length time series together rather than joining individual weather states, each from a single time step, which is a common solution found in the literature. This new Markov model shows favorable characteristics with respect to the requirements set forth and all aspects of the validation performed.

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.

The Study of Interpenetration Length between dPS Films and PS-grafted Layers

NASA Astrophysics Data System (ADS)

Lee, Hoyeon; Jo, Seongjun; Hirata, Toyoaki; Yamada, Norifumi L.; Tanaka, Keiji; Ryu, Du Yeol

In polymer thin film system, the type of interfacial interaction is a critical parameter to determining the thermal and physical properties of polymer films. Interestingly, the interfacial energy of grafted substrates with polymer chains is remarkably altered by simply controlling grafting density, which has been referred to as autophobicity. In this study, we investigated the interpenetrating interfaces between deuterated polystyrene (dPS) and grafted substrates with the same chemical identity. PS-grafted substrates were prepared using a grafting-to approach with hydroxyl end-functionalized polystyrene (PSOH) in a dry brush regime, where the brush thickness and grafting density were determined based on the chain length (or molecular weight, Mn) of PSOHs. The interpenetration lengths (ξ) at interfaces between dPS and PS-grafted layers were characterized using neutron reflectivity (NR) measurements (performed at the SOFIA beam-line at J-PARC, Japan). Academic adviser.

Research on Optimization of Pooling System and Its Application in Drug Supply Chain Based on Big Data Analysis

PubMed Central

2017-01-01

Reform of drug procurement is being extensively implemented and expanded in China, especially in today's big data environment. However, the pattern of supply mode innovation lags behind procurement improvement. Problems in financial strain and supply break frequently occur, which affect the stability of drug supply. Drug Pooling System is proposed and applied in a few pilot cities to resolve these problems. From the perspective of supply chain, this study analyzes the process of setting important parameters and sets out the tasks of involved parties in a pooling system according to the issues identified in the pilot run. The approach is based on big data analysis and simulation using system dynamic theory and modeling of Vensim software to optimize system performance. This study proposes a theoretical framework to resolve problems and attempts to provide a valuable reference for future application of pooling systems. PMID:28293258

A study on the stability of a motorcycle wheel-swingarm suspension with chain transmission

NASA Astrophysics Data System (ADS)

Sorrentino, S.; Leonelli, L.

2017-11-01

The present study describes a possible driving mechanism for a self-excited oscillation observed in motorcycle dynamics, often referred to as chatter. This phenomenon, affecting the performance of road racing motorcycles, has been simulated in straight running braking manoeuvres with multibody motorcycle models. It involves rear suspension bounce and driveline oscillation in the frequency range between 17 and 22 Hz. A simplified model of a motorcycle rear suspension with chain transmission is proposed and its stability in equilibrium configurations is studied via eigenvalue analysis. The sensitivity with respect to all its governing parameters is analysed by means of stability maps and the self-excitation mechanism is explained with the aid of energy balance analysis and phase diagrams. It is found that the key role for the instability onset is played by the gradient of the nonlinear characteristic slip function of the tyre.

A new viscosupplement based on partially hydrophobic hyaluronic acid: a comparative study.

PubMed

Finelli, Ivana; Chiessi, Ester; Galesso, Devis; Renier, Davide; Paradossi, Gaio

2011-01-01

A novel partially hydrophobized derivative of hyaluronic acid (HYADD® 4), containing a low number of C16 side-chains per polysaccharide backbone, provides injectable hydrogels stabilized by side-chain hydrophobic interactions. The rheological properties of Hymovis®, a physical hydrogel based on the hyaluronic acid derivative HYADD® 4, were evaluated using as reference a solution of the parent natural polysaccharide, hyaluronic acid. The rheological measurements were performed both in flow and oscillation regimes at the physiological frequency values of the knee, typically spanning the range from 0.5 Hz (walking frequency) to 3 Hz (running frequency). Moreover, the viscoelastic features of Hymovis® were compared with the market-available viscosupplementation products in view of its use in joint diseases.The different behavior of the investigated materials in crossover frequency measurements and in structure recovery experiments can be explained on the basis of the structural and dynamic properties of the polymeric systems.

Short Chain Fatty Acids (SCFA) Reprogram Gene Expression in Human Malignant Epithelial and Lymphoid Cells

PubMed Central

Astakhova, Lidiia; Ngara, Mtakai; Babich, Olga; Prosekov, Aleksandr; Asyakina, Lyudmila; Dyshlyuk, Lyubov; Midtvedt, Tore; Zhou, Xiaoying; Ernberg, Ingemar; Matskova, Liudmila

2016-01-01

The effect of short chain fatty acids (SCFAs) on gene expression in human, malignant cell lines was investigated, with a focus on signaling pathways. The commensal microbial flora produce high levels of SCFAs with established physiologic effects in humans. The most abundant SCFA metabolite in the human microflora is n-butyric acid. It is well known to activate endogenous latent Epstein-Barr virus (EBV), that was used as a reference read out system and extended to EBV+ epithelial cancer cell lines. N-butyric acid and its salt induced inflammatory and apoptotic responses in tumor cells of epithelial and lymphoid origin. Epithelial cell migration was inhibited. The n-butyric gene activation was reduced by knock-down of the cell membrane transporters MCT-1 and -4 by siRNA. N-butyric acid show biologically significant effects on several important cellular functions, also with relevance for tumor cell phenotype. PMID:27441625

[Pseudo-radicular referred leg pain].

PubMed

von Heymann, W

2015-12-01

Pseudo-radicular leg pain as initially described by Bruegger more than 55 years ago was at that time a genius explanation for so many non-radicular pain syndromes that needed not any kind of surgical intervention but in first line a manual treatment or a treatment by therapeutic local anesthetics. Today we describe this pain as a "referred pain" originating from other anatomic structures that may occur during the development of chronic pain. Nevertheless this pain is found in many patients and it still seems to be a big problem for many physicians and surgeons. Imaging does not help either. The history and the clinical symptoms, the examinations, the chain reactions in the motor system as well as the treatment options from the point of view of manual medicine are described.

A Markov Random Field Framework for Protein Side-Chain Resonance Assignment

NASA Astrophysics Data System (ADS)

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

Nuclear magnetic resonance (NMR) spectroscopy plays a critical role in structural genomics, and serves as a primary tool for determining protein structures, dynamics and interactions in physiologically-relevant solution conditions. The current speed of protein structure determination via NMR is limited by the lengthy time required in resonance assignment, which maps spectral peaks to specific atoms and residues in the primary sequence. Although numerous algorithms have been developed to address the backbone resonance assignment problem [68,2,10,37,14,64,1,31,60], little work has been done to automate side-chain resonance assignment [43, 48, 5]. Most previous attempts in assigning side-chain resonances depend on a set of NMR experiments that record through-bond interactions with side-chain protons for each residue. Unfortunately, these NMR experiments have low sensitivity and limited performance on large proteins, which makes it difficult to obtain enough side-chain resonance assignments. On the other hand, it is essential to obtain almost all of the side-chain resonance assignments as a prerequisite for high-resolution structure determination. To overcome this deficiency, we present a novel side-chain resonance assignment algorithm based on alternative NMR experiments measuring through-space interactions between protons in the protein, which also provide crucial distance restraints and are normally required in high-resolution structure determination. We cast the side-chain resonance assignment problem into a Markov Random Field (MRF) framework, and extend and apply combinatorial protein design algorithms to compute the optimal solution that best interprets the NMR data. Our MRF framework captures the contact map information of the protein derived from NMR spectra, and exploits the structural information available from the backbone conformations determined by orientational restraints and a set of discretized side-chain conformations (i.e., rotamers). A Hausdorff-based computation is employed in the scoring function to evaluate the probability of side-chain resonance assignments to generate the observed NMR spectra. The complexity of the assignment problem is first reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is used to find a set of optimal side-chain resonance assignments that best fit the NMR data. We have tested our algorithm on NMR data for five proteins, including the FF Domain 2 of human transcription elongation factor CA150 (FF2), the B1 domain of Protein G (GB1), human ubiquitin, the ubiquitin-binding zinc finger domain of the human Y-family DNA polymerase Eta (pol η UBZ), and the human Set2-Rpb1 interacting domain (hSRI). Our algorithm assigns resonances for more than 90% of the protons in the proteins, and achieves about 80% correct side-chain resonance assignments. The final structures computed using distance restraints resulting from the set of assigned side-chain resonances have backbone RMSD 0.5 - 1.4 Å and all-heavy-atom RMSD 1.0 - 2.2 Å from the reference structures that were determined by X-ray crystallography or traditional NMR approaches. These results demonstrate that our algorithm can be successfully applied to automate side-chain resonance assignment and high-quality protein structure determination. Since our algorithm does not require any specific NMR experiments for measuring the through-bond interactions with side-chain protons, it can save a significant amount of both experimental cost and spectrometer time, and hence accelerate the NMR structure determination process.

Fabrication and Characterization of a Stabilized Thin Film Ag/AgCl Reference Electrode Modified with Self-Assembled Monolayer of Alkane Thiol Chains for Rapid Biosensing Applications.

PubMed

Rahman, Tanzilur; Ichiki, Takanori

2017-10-13

The fabrication of miniaturized electrical biosensing devices can enable the rapid on-chip detection of biomarkers such as miRNA molecules, which is highly important in early-stage cancer detection. The challenge in realizing such devices remains in the miniaturization of the reference electrodes, which is an integral part of electrical detection. Here, we report on a novel thin film Ag/AgCl reference electrode (RE) that has been fabricated on top of a Au-sputtered glass surface, which was coated with a self-assembled monolayer (SAM) of 6-mercepto-1-hexanol (MCH). The electrode showed very little measurement deviation (-1.5 mv) from a commercial Ag/AgCl reference electrode and exhibited a potential drift of only ± 0.2 mV/h. In addition, the integration of this SAM-modified microfabricated thin film RE enabled the rapid detection (<30 min) of miRNA (let-7a). The electrode can be integrated seamlessly into a microfluidic device, allowing the highly stable and fast measurement of surface potential and is expected to be very useful for the development of miniature electrical biosensors.

Comparison of molecular orientation and phase transition behaviors in the two kinds of ordered ultrathin films of reversed duckweed polymer ES-3 studied by infrared grazing reflection-absorption spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Qiang; Xu, Weiqing; Zhao, Bing

2003-03-01

A multilayer LB film and a casting film of reversed duckweed polymer ES-3 on Au-evaporated glass slides were investigated by Fourier Transform infrared grazing reflection-absorption spectroscopy. It is found that the two kinds of ordered ultrathin films have different orientation of alkyl chains, nearly perpendicular to the substrate surface for the LB film while rather tilted for the casting film. The studies on their thermal transition behaviors indicate that both of the films have three phase transition processes, respectively, occurring near 65, 105 and 140 °C for the former while near 80, 105 and 140 °C for the latter, but show different transition behavior in the each corresponding transition process. It is referred that at room temperature there are island-like domain structures formed in the LB film, but no ones in the casting film; however, the latter can form the domain structures between the first two transition points due to the desorption of solvents. The formation of domain structure seems to play two important roles, one of which is to make alkyl chains more perpendicular to the substrate surface, and the other to make alkyl chains more packed closely. Thermal cyclic experiments reveal that neither of the films could return to its original state after thermal cyclic treatment up to the temperature, which is above the third transition point, although its alkyl chain becomes highly ordered again.

Anisotropic planar Heisenberg model of the quantum heterobimetallic zigzag chains with bridged ReIV-CuII magnetic complexes

NASA Astrophysics Data System (ADS)

Sobczak, P.; Barasiński, A.; Kamieniarz, G.; Drzewiński, A.

2011-12-01

An anisotropic quantum planar Heisenberg model is proposed and thoroughly analyzed within the numerical density-matrix renormalization group approach. The model takes into account the site-dependent alternating directions of the local coordination system for the ReIV ions and both the axial and the rhombic single-ion anisotropy terms. Thermodynamic properties of a simpler collinear model without the rhombic term and its Ising counterpart as well as some previous approximations for ReIV-ion-containing compounds are discussed to point out the importance of quantum effects and deficiencies of classical approaches. For the noncollinear model with the alternating uniaxial local z axis tilted by the angle θ from the global chain axis formed by copper ions, some symmetries for the single-crystal susceptibilities are found. In the strong-anisotropy limit some striking maxima in the corresponding single-crystal χT products are revealed and their relation to the experimental determination of the anisotropy parameters is emphasized. Some cases to which the collinear model for zigzag chains is fully applicable are indicated. Finally, fitting the reference experimental data for a powder sample of given chloro- and cyanobridged zigzag chains, the weaker magnetic coupling and the uniaxial single-ion anisotropy term parameters have been found. The corrected value of the ferromagnetic interaction parameter implies that for the cyanobridge compound the record of the highest superexchange through cyanide has not been beaten.

A novel sputum transport solution eliminates cold chain and supports routine tuberculosis testing in Nepal.

PubMed

Maharjan, Bhagwan; Shrestha, Bhabana; Weirich, Alexandra; Stewart, Andrew; Kelly-Cirino, Cassandra D

2016-12-01

This preliminary study evaluated the transport reagent OMNIgene SPUTUM (OMS) in a real-world, resource-limited setting: a zonal hospital and national tuberculosis (TB) reference laboratory, Nepal. The objectives were to: (1) assess the performance of OMS for transporting sputum from peripheral sites without cold chain stabilization; and (2) compare with Nepal's standard of care (SOC) for Mycobacterium tuberculosis smear and culture diagnostics. Sixty sputa were manually split into a SOC sample (airline-couriered to the laboratory, conventional processing) and an OMS sample (OMS added at collection, no cold chain transport or processing). Smear microscopy and solid culture were performed. Transport was 0-8days. Forty-one samples (68%) were smear-positive using both methods. Of the OMS cultures, 37 (62%) were positive, 22 (36%) were negative, and one (2%) was contaminated. Corresponding SOC results were 32 (53%), 21 (35%), and seven (12%). OMS "rescued" six (i.e., missed using SOC) compared with one rescue using SOC. Of smear-positives, six SOC samples produced contaminated cultures whereas only one OMS sample was contaminated. OMS reduced culture contamination from 12% to 2%, and improved TB detection by 9%. The results suggest that OMS could perform well as a no cold chain, long-term transport solution for smear and culture testing. The findings provide a basis for larger feasibility studies. Copyright © 2016 Ministry of Health, Saudi Arabia. Published by Elsevier Ltd. All rights reserved.

Structure-guided mutational analysis of the nucleotidyltransferase domain of Escherichia coli NAD+-dependent DNA ligase (LigA).

PubMed

Zhu, Hui; Shuman, Stewart

2005-04-01

NAD+-dependent DNA ligase (LigA) is essential for bacterial growth and a potential target for antimicrobial drug discovery. Here we queried the role of 14 conserved amino acids of Escherichia coli LigA by alanine scanning and thereby identified five new residues within the nucleotidyltransferase domain as being essential for LigA function in vitro and in vivo. Structure activity relationships were determined by conservative mutagenesis for the Glu-173, Arg-200, Arg-208, and Arg-277 side chains, as well as four other essential side chains that had been identified previously (Lys-115, Asp-117, Asp-285, and Lys-314). In addition, we identified Lys-290 as important for LigA activity. Reference to the structure of Enterococcus faecalis LigA allowed us to discriminate three classes of essential/important side chains that: (i) contact NAD+ directly (Lys-115, Glu-173, Lys-290, and Lys-314); (ii) comprise the interface between the NMN-binding domain (domain Ia) and the nucleotidyltransferase domain or comprise part of a nick-binding site on the surface of the nucleotidyltransferase domain (Arg-200 and Arg-208); or (iii) stabilize the active site fold of the nucleotidyltransferase domain (Arg-277). Analysis of mutational effects on the isolated ligase adenylylation and phosphodiester formation reactions revealed different functions for essential side chains at different steps of the DNA ligase pathway, consistent with the proposal that the active site is serially remodeled as the reaction proceeds.

Effect of polyoxyethylene n-alkyl ethers on carrier-mediated transport of lanthanide ions through cellulose triacetate membranes

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

Sugiura, Masaaki

1992-02-01

Fluxes of 14 kinds of lanthanides across cellulose triacetate membranes were determined by using mixtures of o-nitrophenyl n-octyl ether and a series of polyoxythylene n-alkyl ethers (POE ethers) as plasticizers, and hinokitiol as carrier. Effects of alkyl and polyoxyethylene (POE) chains of POE ether on the flux were demonstrated. The transport of the lanthanides was coupled to a flow of hydrogen ions. The POE ethers used (C{sub n}H{sub 2n+1}(OCH{sub 2}CH{sub 2}){sub x}OH, referred to as C{sub n}E{sub x}) were C{sub 10}E{sub 3}, C{sub 12}E{sub 3}, C{sub 14}E{sub 3}, C{sub 16}E{sub 3}, C{sub 12}E{sub 2}, C{sub 12}E{sub 4}, C{sub 12}E{sub 6}more » and C{sub 12}E{sub 8}, In all cases, high fluxes were observed for the lanthanides from samarium to lutetium. On the contrary, the fluxes for lanthanum to neodymium were extremely low. In experiments testing the effect of the alkyl chain, the order of the POE ethers in the lanthanide flux for samarium to lutetium was C{sub 12}E{sub 3} > C{sub 10}E{sub 3} > C{sub 14}E{sub 3} >C{sub 16}E{sub 3}. In experiments testing the effect of the POE chain, the flux decreased with an increase in the chain length.« less

Building oceanographic and atmospheric observation networks by composition: unmanned vehicles, communication networks, and planning and execution control frameworks

NASA Astrophysics Data System (ADS)

Sousa, J. T.; Pinto, J.; Martins, R.; Costa, M.; Ferreira, F.; Gomes, R.

2014-12-01

The problem of developing mobile oceanographic and atmospheric observation networks (MOAO) with coordinated air and ocean vehicles is discussed in the framework of the communications and control software tool chain developed at Underwater Systems and Technologies Laboratory (LSTS) from Porto University. This is done with reference to field experiments to illustrate key capabilities and to assess future MOAO operations. First, the motivation for building MOAO by "composition" of air and ocean vehicles, communication networks, and planning and execution control frameworks is discussed - in networked vehicle systems information and commands are exchanged among multiple vehicles and operators, and the roles, relative positions, and dependencies of these vehicles and operators change during operations. Second, the planning and execution control framework developed at LSTS for multi-vehicle systems is discussed with reference to key concepts such as autonomy, mixed-initiative interactions, and layered organization. Third, the LSTS tool software tool chain is presented to show how to develop MOAO by composition. The tool chain comprises the Neptus command and control framework for mixed initiative interactions, the underlying IMC messaging protocol, and the DUNE on-board software. Fourth, selected LSTS operational deployments illustrate MOAO capability building. In 2012 we demonstrated the use of UAS to "ferry" data from UUVs located beyond line of sight (BLOS). In 2013 we demonstrated coordinated observations of coastal fronts with small UAS and UUVs, "bent" BLOS through the use of UAS as communication relays, and UAS tracking of juvenile hammer-head sharks. In 2014 we demonstrated UUV adaptive sampling with the closed loop controller of the UUV residing on a UAS; this was done with the help of a Wave Glider ASV with a communications gateway. The results from these experiments provide a background for assessing potential future UAS operations in a compositional MOAO.

Equilibrating high-molecular-weight symmetric and miscible polymer blends with hierarchical back-mapping.

PubMed

Ohkuma, Takahiro; Kremer, Kurt; Daoulas, Kostas

2018-05-02

Understanding properties of polymer alloys with computer simulations frequently requires equilibration of samples comprised of microscopically described long molecules. We present the extension of an efficient hierarchical backmapping strategy, initially developed for homopolymer melts, to equilibrate high-molecular-weight binary blends. These mixtures present significant interest for practical applications and fundamental polymer physics. In our approach, the blend is coarse-grained into models representing polymers as chains of soft blobs. Each blob stands for a subchain with N b microscopic monomers. A hierarchy of blob-based models with different resolution is obtained by varying N b . First the model with the largest N b is used to obtain an equilibrated blend. This configuration is sequentially fine-grained, reinserting at each step the degrees of freedom of the next in the hierarchy blob-based model. Once the blob-based description is sufficiently detailed, the microscopic monomers are reinserted. The hard excluded volume is recovered through a push-off procedure and the sample is re-equilibrated with molecular dynamics (MD), requiring relaxation on the order of the entanglement time. For the initial method development we focus on miscible blends described on microscopic level through a generic bead-spring model, which reproduces hard excluded volume, strong covalent bonds, and realistic liquid density. The blended homopolymers are symmetric with respect to molecular architecture and liquid structure. To parameterize the blob-based models and validate equilibration of backmapped samples, we obtain reference data from independent hybrid simulations combining MD and identity exchange Monte Carlo moves, taking advantage of the symmetry of the blends. The potential of the backmapping strategy is demonstrated by equilibrating blend samples with different degree of miscibility, containing 500 chains with 1000 monomers each. Equilibration is verified by comparing chain conformations and liquid structure in backmapped blends with the reference data. Possible directions for further methodological developments are discussed.

Equilibrating high-molecular-weight symmetric and miscible polymer blends with hierarchical back-mapping

NASA Astrophysics Data System (ADS)

Ohkuma, Takahiro; Kremer, Kurt; Daoulas, Kostas

2018-05-01

Understanding properties of polymer alloys with computer simulations frequently requires equilibration of samples comprised of microscopically described long molecules. We present the extension of an efficient hierarchical backmapping strategy, initially developed for homopolymer melts, to equilibrate high-molecular-weight binary blends. These mixtures present significant interest for practical applications and fundamental polymer physics. In our approach, the blend is coarse-grained into models representing polymers as chains of soft blobs. Each blob stands for a subchain with N b microscopic monomers. A hierarchy of blob-based models with different resolution is obtained by varying N b. First the model with the largest N b is used to obtain an equilibrated blend. This configuration is sequentially fine-grained, reinserting at each step the degrees of freedom of the next in the hierarchy blob-based model. Once the blob-based description is sufficiently detailed, the microscopic monomers are reinserted. The hard excluded volume is recovered through a push-off procedure and the sample is re-equilibrated with molecular dynamics (MD), requiring relaxation on the order of the entanglement time. For the initial method development we focus on miscible blends described on microscopic level through a generic bead-spring model, which reproduces hard excluded volume, strong covalent bonds, and realistic liquid density. The blended homopolymers are symmetric with respect to molecular architecture and liquid structure. To parameterize the blob-based models and validate equilibration of backmapped samples, we obtain reference data from independent hybrid simulations combining MD and identity exchange Monte Carlo moves, taking advantage of the symmetry of the blends. The potential of the backmapping strategy is demonstrated by equilibrating blend samples with different degree of miscibility, containing 500 chains with 1000 monomers each. Equilibration is verified by comparing chain conformations and liquid structure in backmapped blends with the reference data. Possible directions for further methodological developments are discussed.

Dual Combined Real-Time Reverse Transcription Polymerase Chain Reaction Assay for the Diagnosis of Lyssavirus Infection.

PubMed

Dacheux, Laurent; Larrous, Florence; Lavenir, Rachel; Lepelletier, Anthony; Faouzi, Abdellah; Troupin, Cécile; Nourlil, Jalal; Buchy, Philippe; Bourhy, Herve

2016-07-01

The definitive diagnosis of lyssavirus infection (including rabies) in animals and humans is based on laboratory confirmation. The reference techniques for post-mortem rabies diagnosis are still based on direct immunofluorescence and virus isolation, but molecular techniques, such as polymerase chain reaction (PCR) based methods, are increasingly being used and now constitute the principal tools for diagnosing rabies in humans and for epidemiological analyses. However, it remains a key challenge to obtain relevant specificity and sensitivity with these techniques while ensuring that the genetic diversity of lyssaviruses does not compromise detection. We developed a dual combined real-time reverse transcription polymerase chain reaction (combo RT-qPCR) method for pan-lyssavirus detection. This method is based on two complementary technologies: a probe-based (TaqMan) RT-qPCR for detecting the RABV species (pan-RABV RT-qPCR) and a second reaction using an intercalating dye (SYBR Green) to detect other lyssavirus species (pan-lyssa RT-qPCR). The performance parameters of this combined assay were evaluated with a large panel of primary animal samples covering almost all the genetic variability encountered at the viral species level, and they extended to almost all lyssavirus species characterized to date. This method was also evaluated for the diagnosis of human rabies on 211 biological samples (positive n = 76 and negative n = 135) including saliva, skin and brain biopsies. It detected all 41 human cases of rabies tested and confirmed the sensitivity and the interest of skin biopsy (91.5%) and saliva (54%) samples for intra-vitam diagnosis of human rabies. Finally, this method was successfully implemented in two rabies reference laboratories in enzootic countries (Cambodia and Morocco). This combined RT-qPCR method constitutes a relevant, useful, validated tool for the diagnosis of rabies in both humans and animals, and represents a promising tool for lyssavirus surveillance.

Dual Combined Real-Time Reverse Transcription Polymerase Chain Reaction Assay for the Diagnosis of Lyssavirus Infection

PubMed Central

Lavenir, Rachel; Lepelletier, Anthony; Faouzi, Abdellah; Troupin, Cécile; Nourlil, Jalal; Buchy, Philippe; Bourhy, Herve

2016-01-01

The definitive diagnosis of lyssavirus infection (including rabies) in animals and humans is based on laboratory confirmation. The reference techniques for post-mortem rabies diagnosis are still based on direct immunofluorescence and virus isolation, but molecular techniques, such as polymerase chain reaction (PCR) based methods, are increasingly being used and now constitute the principal tools for diagnosing rabies in humans and for epidemiological analyses. However, it remains a key challenge to obtain relevant specificity and sensitivity with these techniques while ensuring that the genetic diversity of lyssaviruses does not compromise detection. We developed a dual combined real-time reverse transcription polymerase chain reaction (combo RT-qPCR) method for pan-lyssavirus detection. This method is based on two complementary technologies: a probe-based (TaqMan) RT-qPCR for detecting the RABV species (pan-RABV RT-qPCR) and a second reaction using an intercalating dye (SYBR Green) to detect other lyssavirus species (pan-lyssa RT-qPCR). The performance parameters of this combined assay were evaluated with a large panel of primary animal samples covering almost all the genetic variability encountered at the viral species level, and they extended to almost all lyssavirus species characterized to date. This method was also evaluated for the diagnosis of human rabies on 211 biological samples (positive n = 76 and negative n = 135) including saliva, skin and brain biopsies. It detected all 41 human cases of rabies tested and confirmed the sensitivity and the interest of skin biopsy (91.5%) and saliva (54%) samples for intra-vitam diagnosis of human rabies. Finally, this method was successfully implemented in two rabies reference laboratories in enzootic countries (Cambodia and Morocco). This combined RT-qPCR method constitutes a relevant, useful, validated tool for the diagnosis of rabies in both humans and animals, and represents a promising tool for lyssavirus surveillance. PMID:27380028

Raman spectroscopy as a tool in differentiating conjugated polyenes from synthetic and natural sources.

PubMed

Fernandes, Rafaella F; Maia, Lenize F; Couri, Mara R C; Costa, Luiz Antonio S; de Oliveira, Luiz Fernando C

2015-01-05

This work presents the Raman spectroscopic characterization of synthetic analogs of natural conjugated polyenals found in octocorals, focusing the unequivocal identification of the chemical species present in these systems. The synthetic material was produced by the autocondensation reaction of crotonaldehyde, generating a demethylated conjugated polyene containing 11 carbon-carbon double bonds, with just a methyl group on the end of the carbon chain. The resonance Raman spectra of such pigment has shown the existence of enhanced modes assigned to ν₁(CC) and ν₂(CC) modes of the main chain. For the resonance Raman spectra of natural pigments from octocorals collected in the Brazilian coast, besides the previously cited bands, it could be also observed the presence of the ν₄(CCH₃), related to the vibrational mode who describes the vibration of the methyl group of the central carbon chain of carotenoids. Other interesting point is the observation of overtones and combination bands, which for carotenoids involves the presence of the ν₄ mode, whereas for the synthetic polyene this band, besides be seen at a slightly different wavenumber position, does not appear as an enhanced mode and also as a combination, such as for the natural carotenoids. Theoretical molecular orbital analysis of polyenal-11 and lycopene has shown the structural differences which are also responsible for the resonance Raman data, based on the appearance of the (CH3) vibrational mode in the resonant transition only for lycopene. At last, the Raman band at ca. 1010 cm(-1), assigned to the (CH₃) vibrational mode, can be used for attributing the presence of each one of the conjugated polyenes: the resonance Raman spectrum containing the band at ca. 1010 cm(-1) refers to the carotenoid (in this case lycopene), and the absence of such band in resonance conditions refers to the polyenal (in this case the polyenal-11). Copyright © 2014 Elsevier B.V. All rights reserved.

Concurrent enterprise: a conceptual framework for enterprise supply-chain network activities

NASA Astrophysics Data System (ADS)

Addo-Tenkorang, Richard; Helo, Petri T.; Kantola, Jussi

2017-04-01

Supply-chain management (SCM) in manufacturing industries has evolved significantly over the years. Recently, a lot more relevant research has picked up on the development of integrated solutions. Thus, seeking a collaborative optimisation of geographical, just-in-time (JIT), quality (customer demand/satisfaction) and return-on-investment (profits), aspects of organisational management and planning through 'best practice' business-process management - concepts and application; employing system tools such as certain applications/aspects of enterprise resource planning (ERP) - SCM systems information technology (IT) enablers to enhance enterprise integrated product development/concurrent engineering principles. This article assumed three main organisation theory applications in positioning its assumptions. Thus, proposing a feasible industry-specific framework not currently included within the SCOR model's level four (4) implementation level, as well as other existing SCM integration reference models such as in the MIT process handbook's - Process Interchange Format (PIF), the TOVE project, etc. which could also be replicated in other SCs. However, the wider focus of this paper's contribution will be concentrated on a complimentary proposed framework to the SCC's SCOR reference model. Quantitative empirical closed-ended questionnaires in addition to the main data collected from a qualitative empirical real-life industrial-based pilot case study were used: To propose a conceptual concurrent enterprise framework for SCM network activities. This research adopts a design structure matrix simulation approach analysis to propose an optimal enterprise SCM-networked value-adding, customised master data-management platform/portal for efficient SCM network information exchange and an effective supply-chain (SC) network systems-design teams' structure. Furthermore, social network theory analysis will be employed in a triangulation approach with statistical correlation analysis to assess the scale/level of frequency, importance, level of collaborative-ness, mutual trust as well as roles and responsibility among the enterprise SCM network for systems product development (PD) design teams' technical communication network as well as extensive literature reviews.

Optimal clinical trial design based on a dichotomous Markov-chain mixed-effect sleep model.

PubMed

Steven Ernest, C; Nyberg, Joakim; Karlsson, Mats O; Hooker, Andrew C

2014-12-01

D-optimal designs for discrete-type responses have been derived using generalized linear mixed models, simulation based methods and analytical approximations for computing the fisher information matrix (FIM) of non-linear mixed effect models with homogeneous probabilities over time. In this work, D-optimal designs using an analytical approximation of the FIM for a dichotomous, non-homogeneous, Markov-chain phase advanced sleep non-linear mixed effect model was investigated. The non-linear mixed effect model consisted of transition probabilities of dichotomous sleep data estimated as logistic functions using piecewise linear functions. Theoretical linear and nonlinear dose effects were added to the transition probabilities to modify the probability of being in either sleep stage. D-optimal designs were computed by determining an analytical approximation the FIM for each Markov component (one where the previous state was awake and another where the previous state was asleep). Each Markov component FIM was weighted either equally or by the average probability of response being awake or asleep over the night and summed to derive the total FIM (FIM(total)). The reference designs were placebo, 0.1, 1-, 6-, 10- and 20-mg dosing for a 2- to 6-way crossover study in six dosing groups. Optimized design variables were dose and number of subjects in each dose group. The designs were validated using stochastic simulation/re-estimation (SSE). Contrary to expectations, the predicted parameter uncertainty obtained via FIM(total) was larger than the uncertainty in parameter estimates computed by SSE. Nevertheless, the D-optimal designs decreased the uncertainty of parameter estimates relative to the reference designs. Additionally, the improvement for the D-optimal designs were more pronounced using SSE than predicted via FIM(total). Through the use of an approximate analytic solution and weighting schemes, the FIM(total) for a non-homogeneous, dichotomous Markov-chain phase advanced sleep model was computed and provided more efficient trial designs and increased nonlinear mixed-effects modeling parameter precision.

Raman spectroscopy as a tool in differentiating conjugated polyenes from synthetic and natural sources

NASA Astrophysics Data System (ADS)

Fernandes, Rafaella F.; Maia, Lenize F.; Couri, Mara R. C.; Costa, Luiz Antonio S.; de Oliveira, Luiz Fernando C.

2015-01-01

This work presents the Raman spectroscopic characterization of synthetic analogs of natural conjugated polyenals found in octocorals, focusing the unequivocal identification of the chemical species present in these systems. The synthetic material was produced by the autocondensation reaction of crotonaldehyde, generating a demethylated conjugated polyene containing 11 carbon-carbon double bonds, with just a methyl group on the end of the carbon chain. The resonance Raman spectra of such pigment has shown the existence of enhanced modes assigned to ν1(Cdbnd C) and ν2(Csbnd C) modes of the main chain. For the resonance Raman spectra of natural pigments from octocorals collected in the Brazilian coast, besides the previously cited bands, it could be also observed the presence of the ν4(Csbnd CH3), related to the vibrational mode who describes the vibration of the methyl group of the central carbon chain of carotenoids. Other interesting point is the observation of overtones and combination bands, which for carotenoids involves the presence of the ν4 mode, whereas for the synthetic polyene this band, besides be seen at a slightly different wavenumber position, does not appear as an enhanced mode and also as a combination, such as for the natural carotenoids. Theoretical molecular orbital analysis of polyenal-11 and lycopene has shown the structural differences which are also responsible for the resonance Raman data, based on the appearance of the (sbnd CH3) vibrational mode in the resonant transition only for lycopene. At last, the Raman band at ca. 1010 cm-1, assigned to the (sbnd CH3) vibrational mode, can be used for attributing the presence of each one of the conjugated polyenes: the resonance Raman spectrum containing the band at ca. 1010 cm-1 refers to the carotenoid (in this case lycopene), and the absence of such band in resonance conditions refers to the polyenal (in this case the polyenal-11).

A unifying model for elongational flow of polymer melts and solutions based on the interchain tube pressure concept

NASA Astrophysics Data System (ADS)

Wagner, Manfred Hermann; Rolón-Garrido, Víctor Hugo

2015-04-01

An extended interchain tube pressure model for polymer melts and concentrated solutions is presented, based on the idea that the pressures exerted by a polymer chain on the walls of an anisotropic confinement are anisotropic (M. Doi and S. F. Edwards, The Theory of Polymer Dynamics, Oxford University Press, New York, 1986). In a tube model with variable tube diameter, chain stretch and tube diameter reduction are related, and at deformation rates larger than the inverse Rouse time τR, the chain is stretched and its confining tube becomes increasingly anisotropic. Tube diameter reduction leads to an interchain pressure in the lateral direction of the tube, which is proportional to the 3rd power of stretch (G. Marrucci and G. Ianniruberto. Macromolecules 37, 3934-3942, 2004). In the extended interchain tube pressure (EIP) model, it is assumed that chain stretch is balanced by interchain tube pressure in the lateral direction, and by a spring force in the longitudinal direction of the tube, which is linear in stretch. The scaling relations established for the relaxation modulus of concentrated solutions of polystyrene in oligomeric styrene (M. H. Wagner, Rheol. Acta 53, 765-777, 2014, M. H. Wagner, J. Non-Newtonian Fluid Mech. http://dx.doi.org/10.1016/j.jnnfm.2014.09.017, 2014) are applied to the solutions of polystyrene (PS) in diethyl phthalate (DEP) investigated by Bhattacharjee et al. (P. K. Bhattacharjee et al., Macromolecules 35, 10131-10148, 2002) and Acharya et al. (M. V. Acharya et al. AIP Conference Proceedings 1027, 391-393, 2008). The scaling relies on the difference ΔTg between the glass-transition temperatures of the melt and the glass-transition temperatures of the solutions. ΔTg can be inferred from the reported zero-shear viscosities, and the BSW spectra of the solutions are obtained from the BSW spectrum of the reference melt with good accuracy. Predictions of the EIP model are compared to the steady-state elongational viscosity data of PS/DEP solutions. Except for a possible influence of solvent quality, linear and nonlinear viscoelasticity of entangled polystyrene solutions can thus be obtained from the linear-viscoelastic characteristics of a reference polymer melt and the shift of the glass transition temperature between melt and solution.

Careful Selection of Reference Genes Is Required for Reliable Performance of RT-qPCR in Human Normal and Cancer Cell Lines

PubMed Central

Jacob, Francis; Guertler, Rea; Naim, Stephanie; Nixdorf, Sheri; Fedier, André; Hacker, Neville F.; Heinzelmann-Schwarz, Viola

2013-01-01

Reverse Transcription - quantitative Polymerase Chain Reaction (RT-qPCR) is a standard technique in most laboratories. The selection of reference genes is essential for data normalization and the selection of suitable reference genes remains critical. Our aim was to 1) review the literature since implementation of the MIQE guidelines in order to identify the degree of acceptance; 2) compare various algorithms in their expression stability; 3) identify a set of suitable and most reliable reference genes for a variety of human cancer cell lines. A PubMed database review was performed and publications since 2009 were selected. Twelve putative reference genes were profiled in normal and various cancer cell lines (n = 25) using 2-step RT-qPCR. Investigated reference genes were ranked according to their expression stability by five algorithms (geNorm, Normfinder, BestKeeper, comparative ΔCt, and RefFinder). Our review revealed 37 publications, with two thirds patient samples and one third cell lines. qPCR efficiency was given in 68.4% of all publications, but only 28.9% of all studies provided RNA/cDNA amount and standard curves. GeNorm and Normfinder algorithms were used in 60.5% in combination. In our selection of 25 cancer cell lines, we identified HSPCB, RRN18S, and RPS13 as the most stable expressed reference genes. In the subset of ovarian cancer cell lines, the reference genes were PPIA, RPS13 and SDHA, clearly demonstrating the necessity to select genes depending on the research focus. Moreover, a cohort of at least three suitable reference genes needs to be established in advance to the experiments, according to the guidelines. For establishing a set of reference genes for gene normalization we recommend the use of ideally three reference genes selected by at least three stability algorithms. The unfortunate lack of compliance to the MIQE guidelines reflects that these need to be further established in the research community. PMID:23554992

Boundary perimeter Bethe ansatz

NASA Astrophysics Data System (ADS)

Frassek, Rouven

2017-06-01

We study the partition function of the six-vertex model in the rational limit on arbitrary Baxter lattices with reflecting boundary. Every such lattice is interpreted as an invariant of the twisted Yangian. This identification allows us to relate the partition function of the vertex model to the Bethe wave function of an open spin chain. We obtain the partition function in terms of creation operators on a reference state from the algebraic Bethe ansatz and as a sum of permutations and reflections from the coordinate Bethe ansatz.

ATHLI16: the ATHens Lidar Intercomparison campaign

NASA Astrophysics Data System (ADS)

Amodeo, Aldo; D'Amico, Giuseppe; Giunta, Aldo; Papagiannopoulos, Nikolaos; Papayannis, Alex; Argyrouli, Athina; Mylonaki, Maria; Tsaknakis, Georgios; Kokkalis, Panos; Soupiona, Ourania; Tzanis, Chris

2018-04-01

The results of the ATHLI16 (ATHens Lidar Intercomparison) campaign, held in Athens from 26/09 to 07/10 2016 are presented. The campaign was performed within the Lidar Calibration Centre activities (EU H2020 ACTRIS-2 project) to assess the performance of the EOLE lidar system (NTUA, Athens, Greece), operating within EARLINET, by comparing against the EARLINET reference lidar system MUSA (CNR-IMAA, Potenza, Italy). For both lidars only products retrieved by the EARLINET Single Calculus Chain have been compared.

Exposure to Nickel, Chromium, or Cadmium Causes Distinct Changes in the Gene Expression Patterns of Rat Liver-Derived Cell Lines

DTIC Science & Technology

2010-05-22

member B8 Blue 1370939_at Acsl1 acyl-CoA synthetase long-chain family member 1 Yellow 1372006_at --- --- Blue 1372101_at Ppap2b phosphatidic acid ...Stress L-ascorbic Acid Binding Cation Binding Identical Protein Binding Protein Dimerization Activity Dioxygenase Activity Oxidoreductase...Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts, and proteins. Nucleic Acid Research. 35: D61-65. Ryter SW

Isolated central diabetes insipidus in a newborn with congenital toxoplasmosis.

PubMed

Karadag, Ahmet; Erdeve, Omer; Atasay, Begum; Arsan, Saadet; Deda, Gulhis; Ince, Erdal; Ocal, Gonul; Berberoglu, Merih

2006-02-01

We present a 5 day-old male newborn with isolated central diabetes insipidus due to congenital toxoplasmosis. This patient was referred to us for hydrocephalus. As we investigated the aetiology of the hydrocephalus, the patient's serum and cerebrospinal fluid tested positive for toxoplasmosis via ELISA and polymerase chain reaction. Computed tomography showed obstructive hydrocephalus and disseminated cranial calcifications. Central diabetes insipidus developed on the 10th day, apparently as a result of the toxoplasmosis infection, and was treated successfully with oral desmopressin.

Military Payloads Hosted on Commercial Satellites: How Can the Space and Missile Systems Center Increase the Number of Commercially Hosted Military Payload Contract Awards

DTIC Science & Technology

2015-12-01

commercial owner-operator’s opportunity to review the preliminary satellite design, raise concerns, and discuss needed modifications—is typically...concerns and raised those concerns through the chain of command. The division chief decided that the executive director of SMC (a two-star general...Indefinite Quantity (ID/ IQ ) contract for CHMPs, referred to as the HoPs (Hosted Payloads) ID/ IQ . The Federal Acquisition Regulation describes an ID

Ion Correlation Effects in Salt-Doped Block Copolymers

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; Seo, Youngmi; Hall, Lisa M.

2018-03-01

We apply classical density functional theory to study how salt changes the microphase morphology of diblock copolymers. Polymers are freely jointed and one monomer type favorably interacts with ions, to account for the selective solvation that arises from different dielectric constants of the microphases. By including correlations from liquid state theory of an unbound reference fluid, the theory can treat chain behavior, microphase separation, ion correlations, and preferential solvation, at the same coarse-grained level. We show good agreement with molecular dynamics simulations.

Predictive factors of life quality among packaging workers in Taiwan.

PubMed

Yang, Shang-Yu; Hsu, Der-Jen; Yen, Chun-Ming; Chang, Jer-Hao

2018-05-16

The semiconductor plants on the top of high-tech industrial chain hire many packaging workers to carry out miscellaneous packing tasks for various product orders from different companies and countries. Under tremendous workload the quality of life (QoL) of such packaging workers need to be concerned. The aim of this study was to explore factors influencing their QoL. This study recruited 247 packing workers (162 male and 85 female; mean age: 35.6 years old) in 2015 and 2016 from a semiconductor plant in Taiwan by convenience sampling. The questionnaire comprised four parts: demographics, the World Health Organization Quality of Life (WHOQOL-BREF), an occupational burnout inventory and the Nordic Musculoskeletal Questionnaire. The four domains of the WHOQOL-BREF were defined as outcome variables. Predictive factors included gender (reference: male), age (reference: ≤ 35), BMI (reference: ≤ 25), educational level (reference: below university), marital/partner status (reference: married/cohabiting), years of work (reference: ≤ 5), work shift (reference: day shift), personal burnout, work-related burnout, over-commitment to work and the number of body parts with discomfort (0-9). The findings showed that physical QoL was negatively correlated with night -shift work, personal burnout, and number of body parts with discomfort. Psychological QoL was negatively correlated with night shift work and personal burnout. Environment QoL was negatively correlated with being male, night shift work and personal burnout. The results showed that the QoL among the packaging workers could be improved by reducing musculoskeletal discomfort, personal burnout and by improving work schedules.

Toward Worldwide Hepcidin Assay Harmonization: Identification of a Commutable Secondary Reference Material.

PubMed

van der Vorm, Lisa N; Hendriks, Jan C M; Laarakkers, Coby M; Klaver, Siem; Armitage, Andrew E; Bamberg, Alison; Geurts-Moespot, Anneke J; Girelli, Domenico; Herkert, Matthias; Itkonen, Outi; Konrad, Robert J; Tomosugi, Naohisa; Westerman, Mark; Bansal, Sukhvinder S; Campostrini, Natascia; Drakesmith, Hal; Fillet, Marianne; Olbina, Gordana; Pasricha, Sant-Rayn; Pitts, Kelly R; Sloan, John H; Tagliaro, Franco; Weykamp, Cas W; Swinkels, Dorine W

2016-07-01

Absolute plasma hepcidin concentrations measured by various procedures differ substantially, complicating interpretation of results and rendering reference intervals method dependent. We investigated the degree of equivalence achievable by harmonization and the identification of a commutable secondary reference material to accomplish this goal. We applied technical procedures to achieve harmonization developed by the Consortium for Harmonization of Clinical Laboratory Results. Eleven plasma hepcidin measurement procedures (5 mass spectrometry based and 6 immunochemical based) quantified native individual plasma samples (n = 32) and native plasma pools (n = 8) to assess analytical performance and current and achievable equivalence. In addition, 8 types of candidate reference materials (3 concentrations each, n = 24) were assessed for their suitability, most notably in terms of commutability, to serve as secondary reference material. Absolute hepcidin values and reproducibility (intrameasurement procedure CVs 2.9%-8.7%) differed substantially between measurement procedures, but all were linear and correlated well. The current equivalence (intermeasurement procedure CV 28.6%) between the methods was mainly attributable to differences in calibration and could thus be improved by harmonization with a common calibrator. Linear regression analysis and standardized residuals showed that a candidate reference material consisting of native lyophilized plasma with cryolyoprotectant was commutable for all measurement procedures. Mathematically simulated harmonization with this calibrator resulted in a maximum achievable equivalence of 7.7%. The secondary reference material identified in this study has the potential to substantially improve equivalence between hepcidin measurement procedures and contributes to the establishment of a traceability chain that will ultimately allow standardization of hepcidin measurement results. © 2016 American Association for Clinical Chemistry.

Identifying optimal reference genes for the normalization of microRNA expression in cucumber under viral stress

PubMed Central

Liang, Chaoqiong; Hao, Jianjun; Meng, Yan; Luo, Laixin; Li, Jianqiang

2018-01-01

Cucumber green mottle mosaic virus (CGMMV) is an economically important pathogen and causes significant reduction of both yield and quality of cucumber (Cucumis sativus). Currently, there were no satisfied strategies for controlling the disease. A better understanding of microRNA (miRNA) expression related to the regulation of plant-virus interactions and virus resistance would be of great assistance when developing control strategies for CGMMV. However, accurate expression analysis is highly dependent on robust and reliable reference gene used as an internal control for normalization of miRNA expression. Most commonly used reference genes involved in CGMMV-infected cucumber are not universally expressed depending on tissue types and stages of plant development. It is therefore crucial to identify suitable reference genes in investigating the role of miRNA expression. In this study, seven reference genes, including Actin, Tubulin, EF-1α, 18S rRNA, Ubiquitin, GAPDH and Cyclophilin, were evaluated for the most accurate results in analyses using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Gene expression was assayed on cucumber leaves, stems and roots that were collected at different days post inoculation with CGMMV. The expression data were analyzed using algorithms including delta-Ct, geNorm, NormFinder, and BestKeeper as well as the comparative tool RefFinder. The reference genes were subsequently validated using miR159. The results showed that EF-1α and GAPDH were the most reliable reference genes for normalizing miRNA expression in leaf, root and stem samples, while Ubiquitin and EF-1α were the most suitable combination overall. PMID:29543906

[Report of the NEDO project "Research and development to promote the creation and utilization of an intellectual infrastructure: development of reference materials for laboratory medicine" "Development of pure substance-type certified reference materials"].

PubMed

Takatsu, Akiko

2009-06-01

There is an increasing demand to establish a metrological traceability system for in vitro diagnostics and medical devices. Pure substance-type reference materials are playing key roles in metrological traceability, because they form the basis for many traceability chains in chemistry. The National Metrology Institute of Japan (NMIJ), in the National Institute of Advanced Industrial Science and Technology (AIST), has been developing purity-certified reference materials (CRMs) in this field, such as cholesterol, creatinine, and urea. In the New Energy and Industrial Technology Development Organization (NEDO) project, entitled: "Research and Development to Promote the Creation and Utilization of an Intellectual Infrastructure: Development of Reference Materials for Laboratory Medicine", several pure substance-type CRMs were developed. For a pure protein solution CRM, amino acid analysis and nitrogen determination were chosen as the certification methods. The development and certification processes for the C-reactive protein (CRP) solution CRM were completed, with the recombinant human CRP solution as a candidate material. This CRP solution CRM is now available as NMIJ CRM. For cortisol CRM, a purified candidate material and highly pure primary reference material were prepared. Each impure compound in the materials was identified and quantified. The pure cortisol CRM will be available in 2009. These two CRMs provide a traceability link between routine clinical methods and the SI unit.

Selection of reference genes for microRNA analysis associated to early stress response to handling and confinement in Salmo salar.

PubMed

Zavala, Eduardo; Reyes, Daniela; Deerenberg, Robert; Vidal, Rodrigo

2017-05-11

MicroRNAs are key non-coding RNA molecules that play a relevant role in the regulation of gene expression through translational repression and/or transcript cleavage during normal development and physiological adaptation processes like stress. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become the approach normally used to determine the levels of microRNAs. However, this approach needs the use of endogenous reference. An improper selection of endogenous references can result in confusing interpretation of data. The aim of this study was to identify and validate appropriate endogenous reference miRNA genes for normalizing RT-qPCR survey of miRNAs expression in four different tissues of Atlantic salmon, under handling and confinement stress conditions associated to early or primary stress response. Nine candidate reference normalizers, including microRNAs and nuclear genes, normally used in vertebrate microRNA expression studies were selected from literature, validated by RT-qPCR and analyzed by the algorithms geNorm and NormFinder. The results revealed that the ssa-miR-99-5p gene was the most stable overall and that ssa-miR-99-5p and ssa-miR-23a-5p genes were the best combination. Moreover, the suitability of ssa-miR-99-5p and ssa-miR-23a-5p as endogeneuos reference genes was demostrated by the expression analysis of ssa-miR-193-5p gene.

Identification and evaluation of reference genes for qRT-PCR studies in Lentinula edodes

PubMed Central

Qin, Peng; He, Maolan; Yu, Xiumei; Zhao, Ke; Zhang, Xiaoping; Ma, Menggen; Chen, Qiang; Chen, Xiaoqiong; Zeng, Xianfu; Gu, Yunfu

2018-01-01

Lentinula edodes (shiitake mushroom) is a common edible mushroom with a number of potential therapeutic and nutritional applications. It contains various medically important molecules, such as polysaccharides, terpenoids, sterols, and lipids, were contained in this mushroom. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful tool to analyze the mechanisms underlying the biosynthetic pathways of these substances. qRT-PCR is used for accurate analyses of transcript levels owing to its rapidity, sensitivity, and reliability. However, its accuracy and reliability for the quantification of transcripts rely on the expression stability of the reference genes used for data normalization. To ensure the reliability of gene expression analyses using qRT-PCR in L. edodes molecular biology research, it is necessary to systematically evaluate reference genes. In the current study, ten potential reference genes were selected from L. edodes genomic data and their expression levels were measured by qRT-PCR using various samples. The expression stability of each candidate gene was analyzed by three commonly used software packages: geNorm, NormFinder, and BestKeeper. Base on the results, Rpl4 was the most stable reference gene across all experimental conditions, and Atu was the most stable gene among strains. 18S was found to be the best reference gene for different development stages, and Rpl4 was the most stably expressed gene under various nutrient conditions. The present work will contribute to qRT-PCR studies in L. edodes. PMID:29293626

Identification and evaluation of reference genes for qRT-PCR studies in Lentinula edodes.

PubMed

Xiang, Quanju; Li, Jin; Qin, Peng; He, Maolan; Yu, Xiumei; Zhao, Ke; Zhang, Xiaoping; Ma, Menggen; Chen, Qiang; Chen, Xiaoqiong; Zeng, Xianfu; Gu, Yunfu

2018-01-01

Lentinula edodes (shiitake mushroom) is a common edible mushroom with a number of potential therapeutic and nutritional applications. It contains various medically important molecules, such as polysaccharides, terpenoids, sterols, and lipids, were contained in this mushroom. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful tool to analyze the mechanisms underlying the biosynthetic pathways of these substances. qRT-PCR is used for accurate analyses of transcript levels owing to its rapidity, sensitivity, and reliability. However, its accuracy and reliability for the quantification of transcripts rely on the expression stability of the reference genes used for data normalization. To ensure the reliability of gene expression analyses using qRT-PCR in L. edodes molecular biology research, it is necessary to systematically evaluate reference genes. In the current study, ten potential reference genes were selected from L. edodes genomic data and their expression levels were measured by qRT-PCR using various samples. The expression stability of each candidate gene was analyzed by three commonly used software packages: geNorm, NormFinder, and BestKeeper. Base on the results, Rpl4 was the most stable reference gene across all experimental conditions, and Atu was the most stable gene among strains. 18S was found to be the best reference gene for different development stages, and Rpl4 was the most stably expressed gene under various nutrient conditions. The present work will contribute to qRT-PCR studies in L. edodes.

Evaluation of stability and validation of reference genes for RT-qPCR expression studies in rice plants under water deficit.

PubMed

Auler, Priscila Ariane; Benitez, Letícia Carvalho; do Amaral, Marcelo Nogueira; Vighi, Isabel Lopes; Dos Santos Rodrigues, Gabriela; da Maia, Luciano Carlos; Braga, Eugenia Jacira Bolacel

2017-05-01

Many studies use strategies that allow for the identification of a large number of genes expressed in response to different stress conditions to which the plant is subjected throughout its cycle. In order to obtain accurate and reliable results in gene expression studies, it is necessary to use reference genes, which must have uniform expression in the majority of cells in the organism studied. RNA isolation of leaves and expression analysis in real-time quantitative polymerase chain reaction (RT-qPCR) were carried out. In this study, nine candidate reference genes were tested, actin 11 (ACT11), ubiquitin conjugated to E2 enzyme (UBC-E2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta tubulin (β-tubulin), eukaryotic initiation factor 4α (eIF-4α), ubiquitin 10 (UBQ10), ubiquitin 5 (UBQ5), aquaporin TIP41 (TIP41-Like) and cyclophilin, in two genotypes of rice, AN Cambará and BRS Querência, with different levels of soil moisture (20%, 10% and recovery) in the vegetative (V5) and reproductive stages (period preceding flowering). Currently, there are different softwares that perform stability analyses and define the most suitable reference genes for a particular study. In this study, we used five different methods: geNorm, BestKeeper, ΔCt method, NormFinder and RefFinder. The results indicate that UBC-E2 and UBQ5 can be used as reference genes in all samples and softwares evaluated. The genes β-tubulin and eIF-4α, traditionally used as reference genes, along with GAPDH, presented lower stability values. The gene expression of basic leucine zipper (bZIP23 and bZIP72) was used to validate the selected reference genes, demonstrating that the use of an inappropriate reference can induce erroneous results.

Reference gene stability of a synanthropic fly, Chrysomya megacephala.

PubMed

Wang, Xiaoyun; Xiong, Mei; Wang, Jialu; Lei, Chaoliang; Zhu, Fen

2015-10-29

Stable reference genes are essential for accurate normalization in gene expression studies with reverse transcription quantitative polymerase chain reaction (qPCR). A synanthropic fly, Chrysomya megacephala, is a well known medical vector and forensic indicator. Unfortunately, previous studies did not look at the stability of reference genes used in C. megacephala. In this study, the expression level of Actin, ribosomal protein L8 (Rpl8), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1α (EF1), α-tubulin (α-TUB), β-tubulin (β-TUB), TATA binding box (TBP), 18S rRNA (18S) and ribosomal protein S7 (Rps7) were evaluated for their stability using online software RefFinder, which combines the normal software of the ΔCt method, BestKeeper, Normfinder, and geNorm. Moreover the number of suitable reference gene pairs was also suggested by Excel-based geNorm. The expression levels of these reference genes were evaluated under different experimental conditions with special perspectives of forensic applications: developmental stages (eggs, first, second and third instar larvae, pupae and adults); food sources of larvae (pork, fish and chicken); feeding larvae with drugs (untreated control, Estazolam and Marvelon); feeding larvae with heavy metals (untreated control, cadmium and zinc); tissues of adults (head, thorax, abdomen, legs and wings). According to RefFinder, EF1 was the most suitable reference gene of developmental stages, food and tissues; 18S and GAPDH were the most suitable reference genes for drugs and heavy metals, respectively, which could be widely used for quantification of target gene expression with qPCR in C. megacephala. Suitable reference gene pairs were also suggested by geNorm. This fundamental but vital work should facilitate the gene studies of related biological processes and deepen the understanding in physiology, toxicology, and especially medical and forensic entomology of C. megacephala.

Selection of Reliable Reference Genes for Gene Expression Studies on Rhododendron molle G. Don.

PubMed

Xiao, Zheng; Sun, Xiaobo; Liu, Xiaoqing; Li, Chang; He, Lisi; Chen, Shangping; Su, Jiale

2016-01-01

The quantitative real-time polymerase chain reaction (qRT-PCR) approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder, and BestKeeper. The results showed that EF1- α (elongation factor 1-alpha), 18S (18s ribosomal RNA), and RPL3 (ribosomal protein L3) were the most stable reference genes in developing rhododendron flowers and, thus, in all of the tested samples, while tublin ( TUB ) was the least stable. ACT5 (actin), RPL3 , 18S , and EF1- α were found to be the top four choices for different tissues, whereas TUB was not found to favor qRT-PCR normalization in these tissues. Three stable reference genes are recommended for the normalization of qRT-PCR data in R. molle . Furthermore, the expression profiles of RmPSY (phytoene synthase) and RmPDS (phytoene dehydrogenase) were assessed using EF1- α, 18S , ACT5 , RPL3 , and their combination as internals. Similar trends were found, but these trends varied when the least stable reference gene TUB was used. The results further prove that it is necessary to validate the stability of reference genes prior to their use for normalization under different experimental conditions. This study provides useful information for reliable qRT-PCR data normalization in gene studies of R. molle .

Performance assessment of a data processing chain for THz imaging

NASA Astrophysics Data System (ADS)

Catapano, Ilaria; Ludeno, Giovanni; Soldovieri, Francesco

2017-04-01

Nowadays, TeraHertz (THz) imaging is deserving huge attention as very high resolution diagnostic tool in many applicative fields, among which security, cultural heritage, material characterization and civil engineering diagnostics. This widespread use of THz waves is due to their non-ionizing nature, their capability of penetrating into non-metallic opaque materials, as well as to the technological advances, which have allowed the commercialization of compact, flexible and portable systems. However, the effectiveness of THz imaging depends strongly on the adopted data processing aimed at improving the imaging performance of the hardware device. In particular, data processing is required to mitigate detrimental and unavoidable effects like noise, signal attenuation, as well as to correct the sample surface topography. With respect to data processing, we have proposed recently a strategy involving three different steps aimed at reducing noise, filtering out undesired signal introduced by the adopted THz system and performing surface topography correction [1]. The first step regards noise filtering and exploits a procedure based on the Singular Value Decomposition (SVD) [2] of the data matrix, which does not require knowledge of noise level and it does not involve the use of a reference signal. The second step aims at removing the undesired signal that we have experienced to be introduced by the adopted Z-Omega Fiber-Coupled Terahertz Time Domain (FICO) system. Indeed, when the system works in a high-speed mode, an undesired low amplitude peak occurs always at the same time instant from the beginning of the observation time window and needs to be removed from the useful data matrix in order to avoid a wrong interpretation of the imaging results. The third step of the considered data processing chain is a topographic correction, which needs in order to image properly the samples surface and its inner structure. Such a procedure performs an automatic alignment of the first peak of the measured waveforms by exploiting the a-priori information on the focus distance at which the specimen under test must be located during the measurement phase. The usefulness of the proposed data processing chain has been widely assessed in the last few months by surveying several specimens made by different materials and representative of objects of interest for civil engineering and cultural heritage diagnostics. At the conference, we will show in detail the signal processing chain and present several achieved results. REFERENCES [1] I. Catapano, F. Soldovieri, "A Data Processing Chain for Terahertz Imaging and Its Use in Artwork Diagnostics". J Infrared Milli Terahz Waves, pp.13, Nov. 2016. [2] M. Bertero and P. Boccacci (1998), Introduction to Inverse Problems in Imaging, Bristol: Institute of Physics Publishing.

Fluorinated monomers useful for preparing fluorinated polyquinoline polymers

NASA Technical Reports Server (NTRS)

Hendricks, Neil H. (Inventor)

1994-01-01

A new class of polymers is provided, as well as the monomers used for their preparation. The polymers provided in accordance with practice of the present invention include repeating units comprising one or more quinoline groups, wherein at least a portion of the repeating units includes a hexafluoroisopropylidene (6F) group or a 1-aryl-2,2,2-trifluoroethylidene (3F) group, or both. The hexafluoroisopropylidene group is referred to herein as a 6F group and has the following structure: ##STR1## The 6F group includes a tetravalent carbon atom bound to two trifluoromethyl moieties, with its other two bonds forming linkages in the polymer chain. The 1-aryl-2,2,2-trifluoroethylidene group is referred to herein as a 3F group and has the following structure: ##STR2## wherein Ar' is an aryl group.

Validation of Reference Genes for Relative Quantitative Gene Expression Studies in Cassava (Manihot esculenta Crantz) by Using Quantitative Real-Time PCR

PubMed Central

Hu, Meizhen; Hu, Wenbin; Xia, Zhiqiang; Zhou, Xincheng; Wang, Wenquan

2016-01-01

Reverse transcription quantitative real-time polymerase chain reaction (real-time PCR, also referred to as quantitative RT-PCR or RT-qPCR) is a highly sensitive and high-throughput method used to study gene expression. Despite the numerous advantages of RT-qPCR, its accuracy is strongly influenced by the stability of internal reference genes used for normalizations. To date, few studies on the identification of reference genes have been performed on cassava (Manihot esculenta Crantz). Therefore, we selected 26 candidate reference genes mainly via the three following channels: reference genes used in previous studies on cassava, the orthologs of the most stable Arabidopsis genes, and the sequences obtained from 32 cassava transcriptome sequence data. Then, we employed ABI 7900 HT and SYBR Green PCR mix to assess the expression of these genes in 21 materials obtained from various cassava samples under different developmental and environmental conditions. The stability of gene expression was analyzed using two statistical algorithms, namely geNorm and NormFinder. geNorm software suggests the combination of cassava4.1_017977 and cassava4.1_006391 as sufficient reference genes for major cassava samples, the union of cassava4.1_014335 and cassava4.1_006884 as best choice for drought stressed samples, and the association of cassava4.1_012496 and cassava4.1_006391 as optimal choice for normally grown samples. NormFinder software recommends cassava4.1_006884 or cassava4.1_006776 as superior reference for qPCR analysis of different materials and organs of drought stressed or normally grown cassava, respectively. Results provide an important resource for cassava reference genes under specific conditions. The limitations of these findings were also discussed. Furthermore, we suggested some strategies that may be used to select candidate reference genes. PMID:27242878

Simulating the performance of a distance-3 surface code in a linear ion trap

NASA Astrophysics Data System (ADS)

Trout, Colin J.; Li, Muyuan; Gutiérrez, Mauricio; Wu, Yukai; Wang, Sheng-Tao; Duan, Luming; Brown, Kenneth R.

2018-04-01

We explore the feasibility of implementing a small surface code with 9 data qubits and 8 ancilla qubits, commonly referred to as surface-17, using a linear chain of 171Yb+ ions. Two-qubit gates can be performed between any two ions in the chain with gate time increasing linearly with ion distance. Measurement of the ion state by fluorescence requires that the ancilla qubits be physically separated from the data qubits to avoid errors on the data due to scattered photons. We minimize the time required to measure one round of stabilizers by optimizing the mapping of the two-dimensional surface code to the linear chain of ions. We develop a physically motivated Pauli error model that allows for fast simulation and captures the key sources of noise in an ion trap quantum computer including gate imperfections and ion heating. Our simulations showed a consistent requirement of a two-qubit gate fidelity of ≥99.9% for the logical memory to have a better fidelity than physical two-qubit operations. Finally, we perform an analysis of the error subsets from the importance sampling method used to bound the logical error rates to gain insight into which error sources are particularly detrimental to error correction.

Structure of Poly(dialkylsiloxane) Melts:  Comparisons of Wide-Angle X-ray Scattering, Molecular Dynamics Simulations, and Integral Equation Theory

DOE PAGES

Habenschuss, Anton; Tsige, Mesfin; Curro, John G.; ...

2007-08-21

Here, wide-angle X-ray scattering, molecular dynamics (MD) simulations, and integral equation theory are used to study the structure of poly(diethylsiloxane) (PDES), poly(ethylmethylsiloxane) (PEMS), and poly(dimethylsiloxane) (PDMS) melts. The structure functions of PDES, PEMS, and PDMS are similar, but systematic trends in the intermolecular packing are observed. The local intramolecular structure is extracted from the experimental structure functions. The bond distances and bond angles obtained, including the large Si-O-Si angle, are in good agreement with the explicit atom (EA) and united atom (UA) potentials used in the simulations and theory and from other sources. Very good agreement is found between themore » MD simulations using the EA potentials and the experimental scattering results. Good agreement is also found between the polymer reference interaction site model (PRISM theory) and the UA MD simulations. The intermolecular structure is examined experimentally using an appropriately weighted radial distribution function and with theory and simulation using intermolecular site/site pair correlation functions. Finally, experiment, simulation, and theory show systematic increases in the chain/chain packing distances in the siloxanes as the number of sites in the pendant side chains is increased.« less

Human and animal health risk assessments of chemicals in the food chain: Comparative aspects and future perspectives

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

Dorne, J.L.C.M., E-mail: jean-lou.dorne@efsa.europa.eu; Fink-Gremmels, J.

Chemicals from anthropogenic and natural origins enter animal feed, human food and water either as undesirable contaminants or as part of the components of a diet. Over the last five decades, considerable efforts and progress to develop methodologies to protect humans and animals against potential risks associated with exposure to such potentially toxic chemicals have been made. This special issue presents relevant methodological developments and examples of risk assessments of undesirable substances in the food chain integrating the animal health and the human health perspective and refers to recent Opinions of the Scientific Panel on Contaminants in the Food Chainmore » (CONTAM) of the European Food Safety Authority (EFSA). This introductory review aims to give a comparative account of the risk assessment steps used in human health and animal health risk assessments for chemicals in the food chain and provides a critical view of the data gaps and future perspectives for this cross-disciplinary field. - Highlights: ► Principles of human and animal health risk assessment. ► Data gaps for each step of animal health risk assessment. ► Implications of animal risk assessment on human risk assessment. ► Future perspectives on chemical risk assessment.« less

Symmetry Breaking in Side Chains Leading to Mixed Orientations and Improved Charge Transport in Isoindigo- alt -Bithiophene Based Polymer Thin Films

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

Xue, Guobiao; Zhao, Xikang; Qu, Ge

The selection of side chains is important in design of conjugated polymers. It not only affects their intrinsic physical properties, but also has an impact on thin film morphologies. Recent reports suggested that a face-on/edge-on bimodal orientation observed in polymer thin films may be responsible for a three-dimensional (3D) charge transport and leads to dramatically improved mobility in donor–acceptor based conjugated polymers. To achieve a bimodal orientation in thin films has been seldom explored from the aspect of molecular design. Here, we demonstrate a design strategy involving the use of asymmetric side chains that enables an isoindigo-based polymer to adoptmore » a distinct bimodal orientation, confirmed by the grazing incidence X-ray diffraction. As a result, the polymer presents an average high mobility of 3.8 ± 0.7 cm2 V–1 s–1 with a maximum value of 5.1 cm2 V–1 s–1, in comparison with 0.47 and 0.51 cm2 V–1 s–1 obtained from the two reference polymers. This study exemplifies a new strategy to develop the next generation polymers through understanding the property-structure relationship.« less

Novel class of potential therapeutics that target ricin retrograde translocation.

PubMed

Redmann, Veronika; Gardner, Thomas; Lau, Zerlina; Morohashi, Keita; Felsenfeld, Dan; Tortorella, Domenico

2013-12-23

Ricin toxin, an A-B toxin from Ricinus communis, induces cell death through the inhibition of protein synthesis. The toxin binds to the cell surface via its B chain (RTB) followed by its retrograde trafficking through intracellular compartments to the ER where the A chain (RTA) is transported across the membrane and into the cytosol. Ricin A chain is transported across the ER membrane utilizing cellular proteins involved in the disposal of aberrant ER proteins by a process referred to as retrograde translocation. Given the current lack of therapeutics against ricin intoxication, we developed a high-content screen using an enzymatically attenuated RTA chimera engineered with a carboxy-terminal enhanced green fluorescent protein (RTA(E177Q)egfp) to identify compounds that target RTA retrograde translocation. Stabilizing RTA(E177Q)egfp through the inclusion of proteasome inhibitor produced fluorescent peri-nuclear granules. Quantitative analysis of the fluorescent granules provided the basis to discover compounds from a small chemical library (2080 compounds) with known bioactive properties. Strikingly, the screen found compounds that stabilized RTA molecules within the cell and several compounds limited the ability of wild type RTA to suppress protein synthesis. Collectively, a robust high-content screen was developed to discover novel compounds that stabilize intracellular ricin and limit ricin intoxication.

Discovery, clinical development, and therapeutic uses of bisphosphonates.

PubMed

Licata, Angelo A

2005-04-01

To review the literature concerning the history, development, and therapeutic uses of bisphosphonates. English-language articles were identified through a search of MEDLINE (through December 2004) using the key word bisphosphonate. Reference lists of pivotal studies, reviews, and full prescribing information for the approved agents were also examined. Selected studies included those that discussed the discovery and initial applications of bisphosphonates, as well as their historical development, pharmacokinetic and pharmacodynamic properties, and current therapeutic uses. Bisphosphonates structurally resemble pyrophosphates (naturally occurring polyphosphates) and have demonstrated similar physicochemical effects to pyrophosphates. In addition, bisphosphonates reduce bone turnover and resist hydrolysis when administered orally. The information gained from initial work with etidronate generated a considerable scientific effort to design new and more effective bisphosphonates. The PCP moiety in the general bisphosphonate structure is essential for binding to hydroxyapatite and allows for a number of chemical variations by changing the 2 lateral side chains (designated R(1) and R(2)). The R(1) side chain determines binding affinity to hydroxyapatite, and the R(2) side chain determines antiresorptive potency. Accordingly, each bisphosphonate has its own characteristic profile of activity. The bisphosphonates reduce bone turnover, increase bone mass, and decrease fracture risk and therefore have a significant place in the management of skeletal disorders including osteoporosis, Paget's disease, bone metastases, osteogenesis imperfecta, and heterotopic ossification.

Resolution of an immunodiagnostic dilemma: heavy chain chimeric antibodies for species in which plasmocytomas are unknown.

PubMed

Butler, J E; Wertz, N; Sun, X-Z; Lunney, J K; Muyldermans, S

2013-01-01

The immunoglobulin (Ig) genes of many vertebrates have been characterized but IgG subclasses, IgD and IgE proteins are only available for three species in which plasmacytomas occur. This creates a major problem in the production and specificity verification of diagnostic anti-Ig reagents for the vast majority of mammals. We describe a novel solution using the swine system with its eleven different variants of IgG. It involves the in vitro synthesis of chimeric porcine-camelid heavy chain antibodies (HCAbs) that do not require light chains and therefore only a single transfection vector. The expressed chimeric HCAbs are comprised of the camelid VHH domain encoding specificity for lysozyme and the hinge, CH2 and CH3 domains of the various porcine IgGs. These HCAb retain their antigenic integrity and their ability to recognize lysozyme. The engineered specificity assures that these HCAb can be immobilized in native configuration when used for testing the specificity of anti-swine IgG antibodies. Comparative data to illustrate the importance of this point are provided. These are now available for use in hybridoma selection and as reference standards for evaluating the specificity of currently available anti-swine IgG antibodies. Copyright © 2012 Elsevier Ltd. All rights reserved.

Criticism of EFSA's scientific opinion on combinatorial effects of 'stacked' GM plants.

PubMed

Bøhn, Thomas

2018-01-01

Recent genetically modified plants tend to include both insect resistance and herbicide tolerance traits. Some of these 'stacked' GM plants have multiple Cry-toxins expressed as well as tolerance to several herbicides. This means that non-target organisms in the environment (biodiversity) will be co-exposed to multiple stressors simultaneously. A similar co-exposure may happen to consumers through chemical residues in the food chain. EFSA, the responsible unit for minimizing risk of harm in European food chains, has expressed its scientific interest in combinatorial effects. However, when new data showed how two Cry-toxins acted in combination (added toxicity), and that the same Cry-toxins showed combinatorial effects when co-exposed with Roundup (Bøhn et al., 2016), EFSA dismissed these new peer-reviewed results. In effect, EFSA claimed that combinatorial effects are not relevant for itself. EFSA was justifying this by referring to a policy question, and by making invalid assumptions, which could have been checked directly with the lead-author. With such approach, EFSA may miss the opportunity to improve its environmental and health risk assessment of toxins and pesticides in the food chain. Failure to follow its own published requests for combinatorial effects research, may also risk jeopardizing EFSA's scientific and public reputation. Copyright © 2017. Published by Elsevier Ltd.

Site-specific covalent modifications of human insulin by catechol estrogens: Reactivity and induced structural and functional changes

NASA Astrophysics Data System (ADS)

Ku, Ming-Chun; Fang, Chieh-Ming; Cheng, Juei-Tang; Liang, Huei-Chen; Wang, Tzu-Fan; Wu, Chih-Hsing; Chen, Chiao-Chen; Tai, Jung-Hsiang; Chen, Shu-Hui

2016-06-01

Proteins, covalently modified by catechol estrogens (CEs), were identified recently from the blood serum of diabetic patients and referred to as estrogenized proteins. Estrogenization of circulating insulin may occur and affect its molecular functioning. Here, the chemical reactivity of CEs towards specific amino acid residues of proteins and the structural and functional changes induced by the estrogenization of insulin were studied using cyclic voltammetry, liquid chromatography-mass spectrometry, circular dichroism spectroscopy, molecular modeling, and bioassays. Our results indicate that CEs, namely, 2- and 4-hydroxyl estrogens, were thermodynamically and kinetically more reactive than the catechol moiety. Upon co-incubation, intact insulin formed a substantial number of adducts with one or multiple CEs via covalent conjugation at its Cys 7 in the A or B chain, as well as at His10 or Lys29 in the B chain. Such conjugation was coupled with the cleavage of inter-chain disulfide linkages. Estrogenization on these sites may block the receptor-binding pockets of insulin. Insulin signaling and glucose uptake levels were lower in MCF-7 cells treated with modified insulin than in cells treated with native insulin. Taken together, our findings demonstrate that insulin molecules are susceptible to active estrogenization, and that such modification may alter the action of insulin.

Anti-knock quality of sugar derived levulinic esters and cyclic ethers

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

Tian, Miao; McCormick, Robert L.; Luecke, Jon

Here, the objective of this paper is to investigate the anti-knock quality of sugar-derived levulinic esters (methyl levulinate (ML) and ethyl levulinate (EL)) and cyclic ethers (furfuryl ethyl ether (FEE) and ethyl tetrahydrofurfuryl ether (ETE)). To this end, combustion experiments were carried out in both an engine and a constant volume autoignition device. The results from both apparati demonstrate that ML, EL and FEE have superior anti-knock quality than the reference Euro95 gasoline. ETE, conversely, performed markedly worse than the reference fuel on both setups and might therefore be a more appropriate fuel for compression ignition engines. The main reasonmore » of the distinctions in anti-knock quality can be found in the molecular structure of the neat biofuels. ML and EL are levulinic esters, with a ketone (C=O) functionality and an ester (C(=O)-O) group on the carbon chain. They can readily produce stable intermediates during the auto-ignition process, thereby slowing down the overall reaction rate. The unsaturated cyclic ether (FEE) has very strong ring C-H bonds. However, the saturated cyclic ether (ETE) has weak ring C-H bonds, which facilitate more readily ring opening reactions. Long side chains on the cyclic ethers further accelerate the reaction rate. Importantly for future research, our results suggest that IQT and engine experiments are interchangeable setups with respect to qualitative anti-knock quality evaluation of novel compounds.« less

Anti-knock quality of sugar derived levulinic esters and cyclic ethers

DOE PAGES

Tian, Miao; McCormick, Robert L.; Luecke, Jon; ...

2017-04-22

Here, the objective of this paper is to investigate the anti-knock quality of sugar-derived levulinic esters (methyl levulinate (ML) and ethyl levulinate (EL)) and cyclic ethers (furfuryl ethyl ether (FEE) and ethyl tetrahydrofurfuryl ether (ETE)). To this end, combustion experiments were carried out in both an engine and a constant volume autoignition device. The results from both apparati demonstrate that ML, EL and FEE have superior anti-knock quality than the reference Euro95 gasoline. ETE, conversely, performed markedly worse than the reference fuel on both setups and might therefore be a more appropriate fuel for compression ignition engines. The main reasonmore » of the distinctions in anti-knock quality can be found in the molecular structure of the neat biofuels. ML and EL are levulinic esters, with a ketone (C=O) functionality and an ester (C(=O)-O) group on the carbon chain. They can readily produce stable intermediates during the auto-ignition process, thereby slowing down the overall reaction rate. The unsaturated cyclic ether (FEE) has very strong ring C-H bonds. However, the saturated cyclic ether (ETE) has weak ring C-H bonds, which facilitate more readily ring opening reactions. Long side chains on the cyclic ethers further accelerate the reaction rate. Importantly for future research, our results suggest that IQT and engine experiments are interchangeable setups with respect to qualitative anti-knock quality evaluation of novel compounds.« less

Basic quantitative polymerase chain reaction using real-time fluorescence measurements.

PubMed

Ares, Manuel

2014-10-01

This protocol uses quantitative polymerase chain reaction (qPCR) to measure the number of DNA molecules containing a specific contiguous sequence in a sample of interest (e.g., genomic DNA or cDNA generated by reverse transcription). The sample is subjected to fluorescence-based PCR amplification and, theoretically, during each cycle, two new duplex DNA molecules are produced for each duplex DNA molecule present in the sample. The progress of the reaction during PCR is evaluated by measuring the fluorescence of dsDNA-dye complexes in real time. In the early cycles, DNA duplication is not detected because inadequate amounts of DNA are made. At a certain threshold cycle, DNA-dye complexes double each cycle for 8-10 cycles, until the DNA concentration becomes so high and the primer concentration so low that the reassociation of the product strands blocks efficient synthesis of new DNA and the reaction plateaus. There are two types of measurements: (1) the relative change of the target sequence compared to a reference sequence and (2) the determination of molecule number in the starting sample. The first requires a reference sequence, and the second requires a sample of the target sequence with known numbers of the molecules of sequence to generate a standard curve. By identifying the threshold cycle at which a sample first begins to accumulate DNA-dye complexes exponentially, an estimation of the numbers of starting molecules in the sample can be extrapolated. © 2014 Cold Spring Harbor Laboratory Press.

Dietary reference intakes for DHA and EPA.

PubMed

Kris-Etherton, Penny M; Grieger, Jessica A; Etherton, Terry D

2009-01-01

Various organizations worldwide have made dietary recommendations for eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and fish intake that are primarily for coronary disease risk reduction and triglyceride (TG) lowering. Recommendations also have been made for DHA intake for pregnant women, infants, and vegetarians/vegans. A Dietary Reference Intake (DRI), specifically, an Adequate Intake (AI), has been set for alpha-linolenic acid (ALA) by the Institute of Medicine (IOM) of The National Academies. This amount is based on an intake that supports normal growth and neural development and results in no nutrient deficiency. Although there is no DRI for EPA and DHA, the National Academies have recommended that approximately 10% of the Acceptable Macronutrient Distribution Range (AMDR) for ALA can be consumed as EPA and/or DHA. This recommendation represents current mean intake for EPA and DHA in the United States ( approximately 100mg/day), which is much lower than what many groups worldwide are currently recommending. Global recommendations for long-chain omega-3 fatty acids underscore the pressing need to establish DRIs for DHA and EPA because DRIs are recognized as the "official" standard by which federal agencies issue dietary guidance or policy directives for the health and well-being of individuals in the United States and Canada. Because of the many health benefits of DHA and EPA, it is important and timely that the National Academies establish DRIs for the individual long-chain (20 carbons or greater) omega-3 fatty acids.

Monte Carlo simulations in radiotherapy dosimetry.

PubMed

Andreo, Pedro

2018-06-27

The use of the Monte Carlo (MC) method in radiotherapy dosimetry has increased almost exponentially in the last decades. Its widespread use in the field has converted this computer simulation technique in a common tool for reference and treatment planning dosimetry calculations. This work reviews the different MC calculations made on dosimetric quantities, like stopping-power ratios and perturbation correction factors required for reference ionization chamber dosimetry, as well as the fully realistic MC simulations currently available on clinical accelerators, detectors and patient treatment planning. Issues are raised that include the necessity for consistency in the data throughout the entire dosimetry chain in reference dosimetry, and how Bragg-Gray theory breaks down for small photon fields. Both aspects are less critical for MC treatment planning applications, but there are important constraints like tissue characterization and its patient-to-patient variability, which together with the conversion between dose-to-water and dose-to-tissue, are analysed in detail. Although these constraints are common to all methods and algorithms used in different types of treatment planning systems, they make uncertainties involved in MC treatment planning to still remain "uncertain".

Analysis of the NMI01 marker for a population database of cannabis seeds.

PubMed

Shirley, Nicholas; Allgeier, Lindsay; Lanier, Tommy; Coyle, Heather Miller

2013-01-01

We have analyzed the distribution of genotypes at a single hexanucleotide short tandem repeat (STR) locus in a Cannabis sativa seed database along with seed-packaging information. This STR locus is defined by the polymerase chain reaction amplification primers CS1F and CS1R and is referred to as NMI01 (for National Marijuana Initiative) in our study. The population database consists of seed seizures of two categories: seed samples from labeled and unlabeled packages regarding seed bank source. Of a population database of 93 processed seeds including 12 labeled Cannabis varieties, the observed genotypes generated from single seeds exhibited between one and three peaks (potentially six alleles if in homozygous state). The total number of observed genotypes was 54 making this marker highly specific and highly individualizing even among seeds of common lineage. Cluster analysis associated many but not all of the handwritten labeled seed varieties tested to date as well as the National Park seizure to our known reference database containing Mr. Nice Seedbank and Sensi Seeds commercially packaged reference samples. © 2012 American Academy of Forensic Sciences.

Effects of cefonicid and other cephalosporin antibiotics on male sexual development in rats.

PubMed Central

Manson, J M; Zolna, L E; Kang, Y J; Johnson, C M

1987-01-01

The purpose of this study was to determine whether cefonicid, a cephalosporin antibiotic with a modified N-methylthiotetrazole (MTT) side chain, caused testicular toxicity when subcutaneously administered to Sprague-Dawley male rats from days 6 to 36 postpartum at doses of 50 to 1,000 mg/kg per day. Moxalactam (a cephamycin antibiotic which will be referred to as a cephalosporin for convenience throughout), which contains the MTT side chain, was used as a positive control and was administered at 100 to 1,000 mg/kg per day, and cephalothin, which lacks an MTT side chain, was used as the negative control at 1,000 mg/kg per day. Moxalactam caused a significant reduction in testicular and seminal vesicle weights in 37-day-old animals, and histological examination revealed bilateral multifocal atrophy of the seminiferous tubules at all dose levels. Animals reared to reproductive maturity had significant deficits in fertility, and histological examination revealed multifocal or diffuse atrophy of the seminiferous tubules at all doses with a severity greater than that observed in the 37-day-old animals. The histological findings were confirmed by marked reductions in testicular sperm production rates and cauda epididymal sperm numbers. Cephalothin and cefonicid had no treatment-related adverse effects on the sexual maturation of prepubertal, juvenile, or adult males. The absence (in cephalothin) or modification (in cefonicid) of the MTT side chain was not associated with adverse reproductive effects. The relevance of these findings to humans in prenatal and prepubertal stages of life cannot be determined at this time. Images PMID:3662478

A sensitive detection method for MPLW515L or MPLW515K mutation in chronic myeloproliferative disorders with locked nucleic acid-modified probes and real-time polymerase chain reaction.

PubMed

Pancrazzi, Alessandro; Guglielmelli, Paola; Ponziani, Vanessa; Bergamaschi, Gaetano; Bosi, Alberto; Barosi, Giovanni; Vannucchi, Alessandro M

2008-09-01

Acquired mutations in the juxtamembrane region of MPL (W515K or W515L), the receptor for thrombopoietin, have been described in patients with primary myelofibrosis or essential thrombocythemia, which are chronic myeloproliferative disorders. We have developed a real-time polymerase chain reaction assay for the detection and quantification of MPL mutations that is based on locked nucleic acid fluorescent probes. Mutational analysis was performed using DNA from granulocytes. Reference curves were obtained using cloned fragments of MPL containing either the wild-type or mutated sequence; the predicted sensitivity level was at least 0.1% mutant allele in a wild-type background. None of the 60 control subjects presented with a MPLW515L/K mutation. Of 217 patients with myelofibrosis, 19 (8.7%) harbored the MPLW515 mutation, 10 (52.6%) with the W515L allele. In one case, both the W515L and W515K alleles were detected by real-time polymerase chain reaction. By comparing results obtained with conventional sequencing, no erroneous genotype attribution using real-time polymerase chain reaction was found, whereas one patient considered wild type according to sequence analysis actually harbored a low W515L allele burden. This is a simple, sensitive, and cost-effective procedure for large-scale screening of the MPLW515L/K mutation in patients suspected to have a myeloproliferative disorder. It can also provide a quantitative estimate of mutant allele burden that might be useful for both patient prognosis and monitoring response to therapy.

Structural basis for ubiquitin-mediated antiviral signal activation by RIG-I.

PubMed

Peisley, Alys; Wu, Bin; Xu, Hui; Chen, Zhijian J; Hur, Sun

2014-05-01

Ubiquitin (Ub) has important roles in a wide range of intracellular signalling pathways. In the conventional view, ubiquitin alters the signalling activity of the target protein through covalent modification, but accumulating evidence points to the emerging role of non-covalent interaction between ubiquitin and the target. In the innate immune signalling pathway of a viral RNA sensor, RIG-I, both covalent and non-covalent interactions with K63-linked ubiquitin chains (K63-Ubn) were shown to occur in its signalling domain, a tandem caspase activation and recruitment domain (hereafter referred to as 2CARD). Non-covalent binding of K63-Ubn to 2CARD induces its tetramer formation, a requirement for downstream signal activation. Here we report the crystal structure of the tetramer of human RIG-I 2CARD bound by three chains of K63-Ub2. 2CARD assembles into a helical tetramer resembling a 'lock-washer', in which the tetrameric surface serves as a signalling platform for recruitment and activation of the downstream signalling molecule, MAVS. Ubiquitin chains are bound along the outer rim of the helical trajectory, bridging adjacent subunits of 2CARD and stabilizing the 2CARD tetramer. The combination of structural and functional analyses reveals that binding avidity dictates the K63-linkage and chain-length specificity of 2CARD, and that covalent ubiquitin conjugation of 2CARD further stabilizes the Ub-2CARD interaction and thus the 2CARD tetramer. Our work provides unique insights into the novel types of ubiquitin-mediated signal-activation mechanism, and previously unexpected synergism between the covalent and non-covalent ubiquitin interaction modes.

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization.

PubMed

Dong, Qian; Liang, Yuxue; Yan, Xinjian; Markey, Sanford P; Mirokhin, Yuri A; Tchekhovskoi, Dmitrii V; Bukhari, Tallat H; Stein, Stephen E

2018-04-01

We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1κ. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins.

Validation of amino-acids measurement in dried blood spot by FIA-MS/MS for PKU management.

PubMed

Bruno, C; Dufour-Rainfray, D; Patin, F; Vourc'h, P; Guilloteau, D; Maillot, F; Labarthe, F; Tardieu, M; Andres, C R; Emond, P; Blasco, H

2016-09-01

Phenylketonuria (PKU) is a metabolic disorder leading to high concentrations of phenylalanine (Phe) and low concentrations of tyrosine (Tyr) in blood and brain that may be neurotoxic. This disease requires a regular monitoring of plasma Phe and Tyr as well as branched-chain amino-acids concentrations to adapt the Phe-restricted diet and other therapy that may be prescribed in PKU. We validated a Flow Injection Analysis tandem Mass Spectrometry (FIA-MS/MS) to replace the enzymatic method routinely used for neonatal screening in order to monitor in parallel to Phe, Tyr and branched-chain amino-acids not detected by the enzymatic method. We ascertained the performances of the method: linearity, detection and quantification limits, contamination index, accuracy. We cross validated the FIA-MS/MS and enzymatic methods and we evaluated our own reference ranges to monitor Phe, Tyr, Leu, Val on 59 dried blood spots of normal controls. We also evaluated Tyr, Leu and Val concentrations in PKU patients to detect some potential abnormalities, not evaluated by the enzymatic method. We developed a rapid method with excellent performances including precision and accuracy <15%. We noted an excellent correlation of Phe concentrations between FIA-MS/MS and enzymatic methods (p<0.0001) based on our database which are similar to references ranges published. We observed that 50% of PKU patients had lower concentrations of Tyr, Leu and/or Val that could not be detected by the enzymatic method. Based on laboratory accreditation recommendations, we validated a robust, rapid and reliable FIA-MS/MS method to monitor plasma Phe concentrations but also Tyr, Leu and Val concentrations, suitable for PKU management. We evaluated our own reference ranges of concentration for a routine application of this method. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Comprehensive Assessment of Composition and Thermochemical Variability by High Resolution GC/QToF-MS and the Advanced Distillation-Curve Method as a Basis of Comparison for Reference Fuel Development.

PubMed

Lovestead, Tara M; Burger, Jessica L; Schneider, Nico; Bruno, Thomas J

2016-12-15

Commercial and military aviation is faced with challenges that include high fuel costs, undesirable emissions, and supply chain insecurity that result from the reliance on petroleum-based feedstocks. The development of alternative gas turbine fuels from renewable resources will likely be part of addressing these issues. The United States has established a target for one billion gallons of renewable fuels to enter the supply chain by 2018. These alternative fuels will have to be very similar in properties, chemistry, and composition to existing fuels. To further this goal, the National Jet Fuel Combustion Program (a collaboration of multiple U.S. agencies under the auspices of the Federal Aviation Administration, FAA) is coordinating measurements on three reference gas turbine fuels to be used as a basis of comparison. These fuels are reference fuels with certain properties that are at the limits of experience. These fuels include a low viscosity, low flash point, high hydrogen content "best case" JP-8 (POSF 10264) fuel, a relatively high viscosity, high flash point, low hydrogen content "worst case" JP-5 (POSF 10259) fuel, and a Jet-A (POSF 10325) fuel with relatively average properties. A comprehensive speciation of these fuels is provided in this paper by use of high resolution gas chromatography/quadrupole time-of-flight - mass spectrometry (GC/QToF-MS), which affords unprecedented resolution and exact molecular formula capabilities. The volatility information as derived from the measurement of the advanced distillation curve temperatures, T k and T h , provides an approximation of the vapor liquid equilibrium and examination of the composition channels provides detailed insight into thermochemical data. A comprehensive understanding of the compositional and thermophysical data of gas turbine fuels is required not only for comparison but also for modeling of such complex mixtures, which will, in turn, aid in the development of new fuels with the goals of diversified feedstocks, decreased pollution, and increased efficiency.

The NISTmAb tryptic peptide spectral library for monoclonal antibody characterization

PubMed Central

Dong, Qian; Liang, Yuxue; Yan, Xinjian; Markey, Sanford P.; Mirokhin, Yuri A.; Tchekhovskoi, Dmitrii V.; Bukhari, Tallat H.; Stein, Stephen E.

2018-01-01

ABSTRACT We describe the creation of a mass spectral library composed of all identifiable spectra derived from the tryptic digest of the NISTmAb IgG1κ. The library is a unique reference spectral collection developed from over six million peptide-spectrum matches acquired by liquid chromatography-mass spectrometry (LC-MS) over a wide range of collision energy. Conventional one-dimensional (1D) LC-MS was used for various digestion conditions and 20- and 24-fraction two-dimensional (2D) LC-MS studies permitted in-depth analyses of single digests. Computer methods were developed for automated analysis of LC-MS isotopic clusters to determine the attributes for all ions detected in the 1D and 2D studies. The library contains a selection of over 12,600 high-quality tandem spectra of more than 3,300 peptide ions identified and validated by accurate mass, differential elution pattern, and expected peptide classes in peptide map experiments. These include a variety of biologically modified peptide spectra involving glycosylated, oxidized, deamidated, glycated, and N/C-terminal modified peptides, as well as artifacts. A complete glycation profile was obtained for the NISTmAb with spectra for 58% and 100% of all possible glycation sites in the heavy and light chains, respectively. The site-specific quantification of methionine oxidation in the protein is described. The utility of this reference library is demonstrated by the analysis of a commercial monoclonal antibody (adalimumab, Humira®), where 691 peptide ion spectra are identifiable in the constant regions, accounting for 60% coverage for both heavy and light chains. The NIST reference library platform may be used as a tool for facile identification of the primary sequence and post-translational modifications, as well as the recognition of LC-MS method-induced artifacts for human and recombinant IgG antibodies. Its development also provides a general method for creating comprehensive peptide libraries of individual proteins. PMID:29425077

Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

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

Ghobadi, Ahmadreza F.; Elliott, J. Richard, E-mail: elliot1@uakron.edu

2014-07-14

In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-γ WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-γ refers to the particular form of “statistical associating fluid theory” that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A newmore » chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH{sub 2} and CH{sub 3} and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ∼2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ∼1% from simulation data while the theory reproduces the excess accumulation of ethane at the interface.« less

Implementation of standardization in clinical practice: not always an easy task.

PubMed

Panteghini, Mauro

2012-02-29

As soon as a new reference measurement system is adopted, clinical validation of correctly calibrated commercial methods should take place. Tracing back the calibration of routine assays to a reference system can actually modify the relation of analyte results to existing reference intervals and decision limits and this may invalidate some of the clinical decision-making criteria currently used. To maintain the accumulated clinical experience, the quantitative relationship to the previous calibration system should be established and, if necessary, the clinical decision-making criteria should be adjusted accordingly. The implementation of standardization should take place in a concerted action of laboratorians, manufacturers, external quality assessment scheme organizers and clinicians. Dedicated meetings with manufacturers should be organized to discuss the process of assay recalibration and studies should be performed to obtain convincing evidence that the standardization works, improving result comparability. Another important issue relates to the surveillance of the performance of standardized assays through the organization of appropriate analytical internal and external quality controls. Last but not least, uncertainty of measurement that fits for this purpose must be defined across the entire traceability chain, starting with the available reference materials, extending through the manufacturers and their processes for assignment of calibrator values and ultimately to the final result reported to clinicians by laboratories.

Identification and validation of reference genes for quantification of target gene expression with quantitative real-time PCR for tall fescue under four abiotic stresses.

PubMed

Yang, Zhimin; Chen, Yu; Hu, Baoyun; Tan, Zhiqun; Huang, Bingru

2015-01-01

Tall fescue (Festuca arundinacea Schreb.) is widely utilized as a major forage and turfgrass species in the temperate regions of the world and is a valuable plant material for studying molecular mechanisms of grass stress tolerance due to its superior drought and heat tolerance among cool-season species. Selection of suitable reference genes for quantification of target gene expression is important for the discovery of molecular mechanisms underlying improved growth traits and stress tolerance. The stability of nine potential reference genes (ACT, TUB, EF1a, GAPDH, SAND, CACS, F-box, PEPKR1 and TIP41) was evaluated using four programs, GeNorm, NormFinder, BestKeeper, and RefFinder. The combinations of SAND and TUB or TIP41 and TUB were most stably expressed in salt-treated roots or leaves. The combinations of GAPDH with TIP41 or TUB were stable in roots and leaves under drought stress. TIP41 and PEPKR1 exhibited stable expression in cold-treated roots, and the combination of F-box, TIP41 and TUB was also stable in cold-treated leaves. CACS and TUB were the two most stable reference genes in heat-stressed roots. TIP41 combined with TUB and ACT was stably expressed in heat-stressed leaves. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) assays of the target gene FaWRKY1 using the identified most stable reference genes confirmed the reliability of selected reference genes. The selection of suitable reference genes in tall fescue will allow for more accurate identification of stress-tolerance genes and molecular mechanisms conferring stress tolerance in this stress-tolerant species.

Identification of Appropriate Reference Genes for Normalization of miRNA Expression in Grafted Watermelon Plants under Different Nutrient Stresses

PubMed Central

Wu, Weifang; Deng, Qin; Shi, Pibiao; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

2016-01-01

Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy. The purpose of this study was to select appropriate reference genes in scion (watermelon) and rootstocks (squash and bottle gourd) of grafted watermelon plants under normal growth conditions and nutrient stresses (nitrogen and phosphorus starvation). Under nutrient starvation, geNorm identified miR167c and miR167f as two most stable genes in both watermelon leaves and squash roots. miR166b was recommended by both geNorm and NormFinder as the best reference in bottle gourd roots under nutrient limitation. Expression of a new Cucurbitaceae miRNA, miR85, was used to validate the reliability of candidate reference genes under nutrient starvation. Moreover, by comparing several target genes expression in qRT-PCR analysis with those in RNA-seq data, miR166b and miR167c were proved to be the most suitable reference genes to normalize miRNA expression under normal growth condition in scion and rootstock tissues, respectively. This study represents the first comprehensive survey of the stability of miRNA reference genes in Cucurbitaceae and provides valuable information for investigating more accurate miRNA expression involving grafted watermelon plants. PMID:27749935

Identification of Appropriate Reference Genes for Normalization of miRNA Expression in Grafted Watermelon Plants under Different Nutrient Stresses.

PubMed

Wu, Weifang; Deng, Qin; Shi, Pibiao; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

2016-01-01

Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy. The purpose of this study was to select appropriate reference genes in scion (watermelon) and rootstocks (squash and bottle gourd) of grafted watermelon plants under normal growth conditions and nutrient stresses (nitrogen and phosphorus starvation). Under nutrient starvation, geNorm identified miR167c and miR167f as two most stable genes in both watermelon leaves and squash roots. miR166b was recommended by both geNorm and NormFinder as the best reference in bottle gourd roots under nutrient limitation. Expression of a new Cucurbitaceae miRNA, miR85, was used to validate the reliability of candidate reference genes under nutrient starvation. Moreover, by comparing several target genes expression in qRT-PCR analysis with those in RNA-seq data, miR166b and miR167c were proved to be the most suitable reference genes to normalize miRNA expression under normal growth condition in scion and rootstock tissues, respectively. This study represents the first comprehensive survey of the stability of miRNA reference genes in Cucurbitaceae and provides valuable information for investigating more accurate miRNA expression involving grafted watermelon plants.

Reference Pricing, Consumer Cost-Sharing, and Insurer Spending for Advanced Imaging Tests.

PubMed

Robinson, James C; Whaley, Christopher; Brown, Timothy T

2016-12-01

Fees charged for similar imaging tests often vary dramatically within the same market, leading to wide variation in insurer spending and consumer cost-sharing. Reference pricing is an insurance design that offers good coverage to patients up to a defined contribution limit but requires the patients who select high-priced facilities to pay the remainder out of pocket. To measure the association between implementation of reference pricing and patient choice of facility, test prices, out-of-pocket spending, and insurer spending for advanced imaging (CT and MRI) procedures. Difference-in-differences multivariable analysis of insurance claims data. Study included 4751 employees of a national grocery chain (treatment group) and 23,428 enrollees in the nation's largest private insurance plan (comparison group) that used CT or MRI tests between 2010 and 2013. Patient choice of facility, price paid per test, patient out-of-pocket cost-sharing, and employer spending. Compared with trends in prices paid by insurance enrollees not subject to reference pricing, and after adjusting for characteristics of tests and patients, implementation of reference pricing was associated with a 12.5% (95% CI, -25.0%, 2.1%) reduction in average price paid per test by the end of the second full year of the program for CT scans and a 10.5% (95% CI, -16.9%, 3.6%) for MRIs. Out-of-pocket cost-sharing by patients declined by $71,508 (13.8%). The savings accruing to employees amounted to 45.5% of total savings from reference pricing, with the remainder accruing to the employer. Implementation of reference pricing led to reductions in payments by both employer and employees.

3D seismic structure of the Zhenbei-Huangyan seamount chain in the East sub-basin of the South China Sea and its mechanism of formation

NASA Astrophysics Data System (ADS)

Zhao, M.; Wang, J.; Qiu, X.; Sibuet, J. C.; He, E.; Zhang, J.

2015-12-01

The post-spreading volcanic ridge (PSVR) is oriented approximately E-W in its western part called the Zhenbei-Huangyan seamount chain. Where is the extinct spreading ridge (ESR) of the East Sub-basin located? beneath the PSVR (Li et al., 2014)? Or intersecting with the PSVR by N055° orientation (Sibuet et al., submitted)? A three-dimensional Ocean Bottom Seismometer (OBS) survey covered both the central extinct spreading ridge and the Zhenbei-Huangyan seamount chain, the IODP Site U1431 (Li et al., 2014) being located just north of the chain. The results of this experiment will provide the essential information to understand the emplacement of the PSVR within the previously formed oceanic crust. The comprehensive seismic record sections of 39 OBSs are of high quality and show clear and reliable P-wave seismic phases, such as Pg, Pn and PmP. These seismic arrivals provide strong constrains for modeling the detailed three-dimensional velocity structure. We will show that the crust is oceanic on each side of the Zhenbei-Huangyan seamount chain, where is the location of the ESR and what is the genetic relationship between the magma chambers and the overlying Zhenbei-Huangyan seamount chain. We suggest that the large thickness of the upper crust is possibly due to volcanic extrusions and the thickened lower crust to magmatic underplating. Combining previous geochemical study of PSVR outcropping samples, the formation mechanism of the seamount chain might be explained by a buoyancy decompression melting mechanism (Castillo et al., 2010). This research was granted by the Natural Science Foundation of China (91028002, 91428204, 41176053). ReferencesSibuet J.-C., Yeh Y.-C. and Lee C.-S., 2015 submitted. Geodynamics of the South China Sea: A review with emphasis on solved and unsolved questions. Tectonophysics. Li, C. F., et al. 2014. Ages and magnetic structures of the South China Sea constrained by deep tow magnetic surveys and IODP Expedition 349. Geochemistry, Geophysics, Geosystems, 15, 4958-4983. Castillo, P. R., Clague, D. A., Davis, A. S., Lonsdale, P. F., 2010. Petrogenesis of Davidson Seamount lavas and its implications for fossil spreading center and intraplate magmatism in the eastern Pacific. Geochemistry, Geophysics, Geosystems, 11, Q02005, doi:10.1029/2009GC002992.

Reconstruction of anthropogenic activities on the excavations of a fireplace sequence from the Krems-Wachtberg site (Austria) using molecular proxies

NASA Astrophysics Data System (ADS)

Wiesenberg, Guido; Hambach, Ulrich

2010-05-01

The well investigated Krems-Wachtberg excavation yielded a broad variety of anthropogenic artefacts and thus enables a proper reconstruction of an ancient settlement of Upper-Palaeolithic age. Despite these artefacts, some questions cannot be answered by sedimentologic and archaeologic approaches. Molecular fossils like lipids including aliphatic hydrocarbons are suitable to improve understanding of e.g. paleoclimatic, pedogenetic, and archaeologic contexts. Especially aliphatic hydrocarbons including straight-chain and branched alkanes yield potential to elucidate biogenic sources of soil and loess organic matter and to assess degradation conditions of primary organic matter. To improve understanding on the terms the fireplaces at the Krems-Wachtberg site are used, aliphatic hydrocarbons are investigated on a set of samples covering several horizons in the context of one fireplace, which was part of the excavation. Horizons above and below the fireplace as well as the fireplace itself were investigated for lipids. Additionally, reference loess samples from a similar age like the fireplace and a pit filling were investigated. Two replicates were available for most samples except for the pit filling. Two distinct fireplace series have been studies. All samples were extracted for lipids using Soxhlet extraction followed by column chromatography in order to separate the aliphatic hydrocarbon fraction from other lipids. Thereafter, aliphatic hydrocarbons were quantified using gas chromatography. The total amounts of extractable organic compounds in the whole sample set from the Krems-Wachtberg site were in the range of usual loess deposits and accounted for 30-80 mg kg-1 loess. The largest contents were observed in reference loess samples and decreased within the excavation from fireplaces > sediments covering fireplace > basement of fireplace > pit. The lower the extract yields, the stronger was the degradation of organic matter. In this context, the pit yielded either organic matter that was strongly degraded during rotting process of organic material after burial or incorporation of already strongly degraded organic matter like ash from fireplaces. The basement of the fireplace was exposed to high temperature for the whole usage of the place, resulting in a modification in the structure of the sediments and a degradation of organic matter within the sediments. The material from the fireplace itself probably was not completely burned and thus yielded comparatively large amounts of extractable components. The sediments covering the fireplace were potentially used to extinguish the fire and hence received a thermal alteration of the organic matter within the sediment under oxygen limiting conditions. Hence, the amount of extractable organic compounds can be used to reconstruct the firing process in the Krems-Wachtberg excavation. The amount of individual aliphatic hydrocarbons parallels the content of all extractable compounds and thus confirms the findings explained above. The aliphatic hydrocarbons reveal typical distribution patterns for grassland vegetation as indicated by a strong predomination of odd long chain alkanes and n-C31 as the most abundant homologue for most samples. Only sediments covering the fireplaces are dominated by n-C29 alkane. The different alkane distribution pattern for these sediments compared to all other samples including reference loess indicates a different biogenic source of the covering sediment than for all other samples. Probably, the covering sediments yield organic matter incorporated under forest or different grassland vegetation than the other sediments. In this study, several molecular markers have been tested for aliphatic hydrocarbons in order to elucidate their sources and to identify degradation effects responsible for the determined distribution patterns. The ratio of long chain vs. short chain alkanes enables the differentiation of plant-derived organic matter characterized by high ratios (>10) and organic matter derived from microbial biomass or degradation (<10). The reference loess samples were characterized by very high values (>50), which indicates plant biomass as the predominant source of loess organic matter. All other samples were characterized by low values (<10), which is due to degradation effects. Microbial alkanes as second potential source of short chain n-alkanes are not likely as odd homologues did not predominate over even homologues, which is typical for microbial alkanes. Furthermore even alkanes dominated in most samples, which can be related to thermal alteration of organic matter as common in fireplaces. Other degradation markers like n-alkanes vs. isoprenoid alkanes (n-C18/phytane) revealed values between 2-4.5. The fireplace samples were characterized by lowest values whereas the reference samples yielded highest values. Hence degradation increased from loess towards fireplace with an intermediate degradation of most other samples. Aliphatic hydrocarbon biomarkers like alkanes were found useful to reconstruct degradation intensity in ancient sediments and to elucidate anthropogenic activities like extinguishing of fire. Hence, organic geochemical investigations can be useful techniques to complement standard archaeological techniques.

Distribution and sources of aliphatic hydrocarbons and fatty acids in surface sediments of a tropical estuary south west coast of India (Cochin estuary).

PubMed

Gireeshkumar, T R; Deepulal, P M; Chandramohanakumar, N

2015-03-01

Surface sediments samples from the Cochin estuary were measured for elemental, stable isotopic and molecular biomarkers (aliphatic hydrocarbons and fatty acids) to study the sources and distribution of sedimentary organic matter. Concentrations of total organic carbon (TOC), total nitrogen (TN) and stable isotopic ratios of carbon (δ(13)C) ranged from 0.62 to 2.74 %, 0.09 to 0.25 % and -27.5 to 21.7 ‰, respectively. Sedimentary n-alkanes ranged from 6.03 to 43.23 μg g(-1) with an average of 16.79 μg g(-1), while total fatty acids varied from 22.55 to 440.69 μg g(-1). The TOC/TN ratios and δ(13)C suggest a mixture of marine- and terrestrial-derived organic matter in the surface sediments with increasing contributions from marine-derived organic matter towards the seaward side. Long-chain n-alkanes derived from higher plants predominated the inner part of the estuary, while short-chain n-alkanes derived from planktonic sources predominated the bar mouth region. The even carbon preference of the C12-C22 n-alkanes may refer to the direct biogenic contribution from bacteria, fungi and yeast species and to the potential direct petroleum inputs. The presence of odd mid-chain n-alkanes in the sediments indicates the organic matter inputs from submerged and floating macrophytes (water hyacinth). Various molecular indices such as carbon preference index, terrestrial to aquatic ratio, average chain length and the ratios of mid-chain n-alkanes support the aforementioned inferences. The high contribution of odd and branched chain fatty acids along with very low contribution of polyunsaturated fatty acids, suggest the effective utilisation of algae-derived organic matter by bacteria and the effective recycling of labile organic matter in whole settling and deposition processes. The distributional variability of n-alkanes and fatty acids reveals the preferential utilisation of marine-derived organic matter and the selective preservation of terrestrial-derived organic matter in surface sediments of the Cochin estuary.

An Evaluation of the Fixed Hotspot Hypothesis for the Pacific Plate

NASA Astrophysics Data System (ADS)

Wessel, P.; Kroenke, L. W.

2008-12-01

Using geometry and ages from 12 Pacific seamount chains, we recently constructed two new Pacific absolute plate motion models that extend our self-consistent and high-resolution models back to 145 Ma. The WK08-A model maps the full uncertainty in the age progressions into uncertainties in rotation opening angles, yielding a relatively smooth plate motion model. The WK08-G model relaxes the mapping of age uncertainties in order to better isolate secondary geometry changes seen along many co-registered chains. Both models have been used to assess the viability of the fixed hotspot hypothesis in the Pacific. In constructing these models, we found that only a small group of age samples had to be discarded on the grounds that they were discordant with the dominant trends. We were able to connect plate motions for pre- and post-Emperor age intervals by including the Ratak-Gilbert-Ellice, Liliuokalani and Musicians trails in our analysis. However, as no active hotspot locations exist for the older chains their inclusion adds additional model parameters. Both age and geometry misfits increase with age, reflecting the observed increase in age uncertainties and the broader and less distinct nature of the older trails. Paleomagnetic observations from the Emperor seamount chain have been interpreted to suggest that these seamounts must have formed at latitudes significantly more northerly than the present location of the Hawaii hotspot, implying a drifting mantle plume. At the same time, new estimates of the age of the Hawaii- Emperor bend places bend formation at a time of global plate reorganization. We will present a complete analysis of inter-chain distances between coeval radiometric samples from Pacific chains and compare these distances to the inter-hotspot distances at the present time. Significant departures from the current hotspot separations would be direct and unequivocal evidence of motion between the Pacific hotspot reference frame and the spin axis and as such complement the paleomagnetic analysis. Preliminary results suggest the Emperor segment data may indicate an increase in hotspot separation.

Mitigation of ammonia, nitrous oxide and methane emissions from manure management chains: a meta-analysis and integrated assessment.

PubMed

Hou, Yong; Velthof, Gerard L; Oenema, Oene

2015-03-01

Livestock manure contributes considerably to global emissions of ammonia (NH3 ) and greenhouse gases (GHG), especially methane (CH4 ) and nitrous oxide (N2 O). Various measures have been developed to mitigate these emissions, but most of these focus on one specific gas and/or emission source. Here, we present a meta-analysis and integrated assessment of the effects of mitigation measures on NH3 , CH4 and (direct and indirect) N2 O emissions from the whole manure management chain. We analysed the effects of mitigation technologies on NH3 , CH4 and N2 O emissions from individual sources statistically using results of 126 published studies. Whole-chain effects on NH3 and GHG emissions were assessed through scenario analysis. Significant NH3 reduction efficiencies were observed for (i) housing via lowering the dietary crude protein (CP) content (24-65%, compared to the reference situation), for (ii) external slurry storages via acidification (83%) and covers of straw (78%) or artificial films (98%), for (iii) solid manure storages via compaction and covering (61%, compared to composting), and for (iv) manure application through band spreading (55%, compared to surface application), incorporation (70%) and injection (80%). Acidification decreased CH4 emissions from stored slurry by 87%. Significant increases in N2 O emissions were found for straw-covered slurry storages (by two orders of magnitude) and manure injection (by 26-199%). These side-effects of straw covers and slurry injection on N2 O emission were relatively small when considering the total GHG emissions from the manure chain. Lowering the CP content of feed and acidifying slurry are strategies that consistently reduce NH3 and GHG emissions in the whole chain. Other strategies may reduce emissions of a specific gas or emissions source, by which there is a risk of unwanted trade-offs in the manure management chain. Proper farm-scale combinations of mitigation measures are important to minimize impacts of livestock production on global emissions of NH3 and GHG. © 2014 John Wiley & Sons Ltd.

Quality Control of Next-generation Sequencing-based In vitro Diagnostic Test for Onco-relevant Mutations Using Multiplex Reference Materials in Plasma.

PubMed

Liu, Donglai; Zhou, Haiwei; Shi, Dawei; Shen, Shu; Tian, Yabin; Wang, Lin; Lou, Jiatao; Cong, Rong; Lu, Juan; Zhang, Henghui; Zhao, Meiru; Zhu, Shida; Cao, Zhisheng; Jin, Ruilin; Wang, Yin; Zhang, Xiaoni; Yang, Guohua; Wang, Youchun; Zhang, Chuntao

2018-01-01

Background: Widespread clinical implementation of next-generation sequencing (NGS)-based cancer in vitro diagnostic tests (IVDs) highlighted the urgency to establish reference materials which could provide full control of the process from nucleic acid extraction to test report generation. The formalin-fixed, paraffin-embedded (FFPE) tissue and blood plasma containing circulating tumor deoxyribonucleic acid (ctDNA) were mostly used for clinically detecting onco-relevant mutations. Methods: We respectively developed multiplex FFPE and plasma reference materials covering three clinically onco-relevant mutations within the epidermal growth factor receptor ( EGFR ) gene at serial allelic frequencies. All reference materials were quantified and validated via droplet digital polymerase chain reaction (ddPCR), and then were distributed to eight domestic manufacturers for the collaborative evaluation of the performance of several domestic NGS-based cancer IVDs covering four major NGS platforms (NextSeq, HiSeq, Ion Proton and BGISEQ). Results: All expected mutations except one at extremely low allelic frequencies were detected, despite some differences in coefficient of variation (CV) which increased with the decrease of allelic frequency (CVs ranging from 18% to 106%). It was worth noting that the CV value seemed to correlate with a particular mutation as well. The repeatability of determination of different mutations was L858R>T790M>19del. Conclusions: The results indicated our reference materials would be pivotal for quality control of NGS-based cancer IVDs and would guide the further development of reference materials covering more onco-relevant mutations.

Genotyping of Indian antigenic, vaccine, and field Brucella spp. using multilocus sequence typing.

PubMed

Shome, Rajeswari; Krithiga, Natesan; Shankaranarayana, Padmashree B; Jegadesan, Sankarasubramanian; Udayakumar S, Vishnu; Shome, Bibek Ranjan; Saikia, Girin Kumar; Sharma, Narendra Kumar; Chauhan, Harshad; Chandel, Bharat Singh; Jeyaprakash, Rajendhran; Rahman, Habibur

2016-03-31

Brucellosis is one of the most important zoonotic diseases that affects multiple livestock species and causes great economic losses. The highly conserved genomes of Brucella, with > 90% homology among species, makes it important to study the genetic diversity circulating in the country. A total of 26 Brucella spp. (4 reference strains and 22 field isolates) and 1 B. melitensis draft genome sequence from India (B. melitensis Bm IND1) were included for sequence typing. The field isolates were identified by biochemical tests and confirmed by both conventional and quantitative polymerase chain reaction (qPCR) targeting bcsp 31Brucella genus-specific marker. Brucella speciation and biotyping was done by Bruce ladder, probe qPCR, and AMOS PCRs, respectively, and genotyping was done by multilocus sequence typing (MLST). The MLST typing of 27 Brucella spp. revealed five distinct sequence types (STs); the B. abortus S99 reference strain and 21 B. abortus field isolates belonged to ST1. On the other hand, the vaccine strain B. abortus S19 was genotyped as ST5. Similarly, B. melitensis 16M reference strain and one B. melitensis field isolate were grouped into ST7. Another B. melitensis field isolate belonged to ST8 (draft genome sequence from India), and only B. suis 1330 reference strain was found to be ST14. The sequences revealed genetic similarity of the Indian strains to the global reference and field strains. The study highlights the usefulness of MLST for typing of field isolates and validation of reference strains used for diagnosis and vaccination against brucellosis.

Characterization of reference genes for qPCR analysis in various tissues of the Fujian oyster Crassostrea angulata

NASA Astrophysics Data System (ADS)

Pu, Fei; Yang, Bingye; Ke, Caihuan

2015-07-01

Accurate quantification of transcripts using quantitative real-time polymerase chain reaction (qPCR) depends on the identification of reliable reference genes for normalization. This study aimed to identify and validate seven reference genes, including actin-2 ( ACT-2), elongation factor 1 alpha ( EF-1α), elongation factor 1 beta ( EF-1β), glyceraldehyde-3-phosphate dehydrogenase ( GAPDH), ubiquitin ( UBQ), β-tubulin ( β-TUB), and 18S ribosomal RNA, from Crassostrea angulata, a valuable marine bivalve cultured worldwide. Transcript levels of the candidate reference genes were examined using qPCR analysis and showed differential expression patterns in the mantle, gill, adductor muscle, labial palp, visceral mass, hemolymph and gonad tissues. Quantitative data were analyzed using the geNorm software to assess the expression stability of the candidate reference genes, revealing that β-TUB and UBQ were the most stable genes. The commonly used GAPDH and 18S rRNA showed low stability, making them unsuitable candidates in this system. The expression pattern of the G protein β-subunit gene ( Gβ) across tissue types was also examined and normalized to the expression of each or both of UBQ and β-TUB as internal controls. This revealed consistent trends with all three normalization approaches, thus validating the reliability of UBQ and β-TUB as optimal internal controls. The study provides the first validated reference genes for accurate data normalization in transcript profiling in Crassostrea angulata, which will be indispensable for further functional genomics studies in this economically valuable marine bivalve.

Development of a screening method for genetically modified soybean by plasmid-based quantitative competitive polymerase chain reaction.

PubMed

Shimizu, Eri; Kato, Hisashi; Nakagawa, Yuki; Kodama, Takashi; Futo, Satoshi; Minegishi, Yasutaka; Watanabe, Takahiro; Akiyama, Hiroshi; Teshima, Reiko; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

2008-07-23

A novel type of quantitative competitive polymerase chain reaction (QC-PCR) system for the detection and quantification of the Roundup Ready soybean (RRS) was developed. This system was designed based on the advantage of a fully validated real-time PCR method used for the quantification of RRS in Japan. A plasmid was constructed as a competitor plasmid for the detection and quantification of genetically modified soy, RRS. The plasmid contained the construct-specific sequence of RRS and the taxon-specific sequence of lectin1 (Le1), and both had 21 bp oligonucleotide insertion in the sequences. The plasmid DNA was used as a reference molecule instead of ground seeds, which enabled us to precisely and stably adjust the copy number of targets. The present study demonstrated that the novel plasmid-based QC-PCR method could be a simple and feasible alternative to the real-time PCR method used for the quantification of genetically modified organism contents.

Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals

PubMed Central

Ackerman, Paul J.; van de Lagemaat, Jao; Smalyukh, Ivan I.

2015-01-01

Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called ‘A-phase’ in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called ‘hopfions’, or ‘torons’ when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields. PMID:25607778

Determination of U, Th and K in bricks by gamma-ray spectrometry, X-ray fluorescence analysis and neutron activation analysis

NASA Astrophysics Data System (ADS)

Bártová, H.; Kučera, J.; Musílek, L.; Trojek, T.; Gregorová, E.

2017-11-01

Knowledge of the content of natural radionuclides in bricks can be important in some cases in dosimetry and application of ionizing radiation. Dosimetry of naturally occurring radionuclides in matter (NORM) in general is one of them, the other one, related to radiation protection, is radon exposure evaluation, and finally, it is needed for the thermoluminescence (TL) dating method. The internal dose rate inside bricks is caused mostly by contributions of the natural radionuclides 238U, 232Th, radionuclides of their decay chains, and 40K. The decay chain of 235U is usually much less important. The concentrations of 238U, 232Th and 40K were measured by various methods, namely by gamma-ray spectrometry, X-ray fluorescence analysis (XRF), and neutron activation analysis (NAA) which was used as a reference method. These methods were compared from the point of view of accuracy, limit of detection (LOD), amount of sample needed and sample handling, time demands, and instrument availability.

Rectal Lymphogranuloma Venereum in HIV-infected Patients Can Mimic Lymphoma.

PubMed

Crickx, Etienne; Meignin, Véronique; Gérard, Laurence; Plantier-Colcher, Isabelle; Walker-Combrouze, Francine; Boutboul, David; Galicier, Lionel; Fieschi, Claire; Oksenhendler, Eric

2016-01-01

An outbreak of rectal lymphogranuloma venereum (LGV) has been reported since 2003 in men who have sex with men, most of them being infected with human immunodeficiency virus. In these patients, unusual clinical presentations such as rectal tumor or intense lymphoproliferation on rectal biopsies may lead to an erroneous diagnosis of aggressive non-Hodgkin lymphoma. Three patients were referred to our center for the management of rectal B-cell non-Hodgkin lymphoma on the basis of a rectal pathologic specimen showing intense lymphoproliferation, the very suspect of lymphoma. Because of anamnesis of anal intercourses and venereal diseases, additional study revealed that all 3 had a positive Chlamydia trachomatis polymerase chain reaction on the rectal biopsy specimen. Rectal LGV was therefore considered and successfully treated with antibiotics. We propose that all patients presenting with a suspected rectal lymphoma should have a careful anamnesis of sexual behavior and a specific detection of C. trachomatis using polymerase chain reaction analysis on biopsy specimen to rule out the possibility of rectal LGV.

Mechanisms Linking the Gut Microbiome and Glucose Metabolism

PubMed Central

Kratz, Mario; Damman, Chris J.; Hullarg, Meredith

2016-01-01

Context: Type 2 diabetes mellitus is associated with gastrointestinal dysbiosis involving both compositional and functional changes in the gut microbiome. Changes in diet and supplementation with probiotics and prebiotics (ie, fermentable fibers) can induce favorable changes in gut bacterial species and improve glucose homeostasis. Objective: This paper will review the data supporting several potential mechanisms whereby gut dysbiosis contributes to metabolic dysfunction, including microbiota driven increases in systemic lipopolysaccharide concentrations, changes in bile acid metabolism, alterations in short chain fatty acid production, alterations in gut hormone secretion, and changes in circulating branched-chain amino acids. Methods: Data for this review were identified by searching English language references from PubMed and relevant articles. Conclusions: Understanding the mechanisms linking the gut microbiome to glucose metabolism, and the relevant compositional and functional characteristics of the gut microbiome, will help direct future research to develop more targeted approaches or novel compounds aimed at restoring a more healthy gut microbiome as a new approach to prevent and treat type 2 diabetes mellitus and related metabolic conditions. PMID:26938201

Comparative study of the antioxidant activities of some lipase-catalyzed alkyl dihydrocaffeates synthesized in ionic liquid.

PubMed

Gholivand, Somayeh; Lasekan, Ola; Tan, Chin Ping; Abas, Faridah; Wei, Leong Sze

2017-06-01

The solubility limitations of phenolic acids in many lipidic environments are now greatly improved by their enzymatic esterification in ionic liquids (ILs). Herein, four different ILs were tested for the esterification of dihydrocaffeic acid with hexanol and the best IL was selected for the synthesis of four other n-alkyl esters with different chain-lengths. The effect of alkyl chain length on the anti-oxidative properties of the resulted purified esters was investigated using β-carotene bleaching (BCB) and free radical scavenging method DPPH and compared with butylated hydroxytoluene (BHT) as reference compound. All four esters (methyl, hexyl, dodecyl and octadecyl dihydrocaffeates) exhibited relatively strong radical scavenging abilities. The scavenging activity of the test compounds was in the following order: methyl ester>hexyl ester⩾dodecyl ester>octadecyl ester>BHT while the order for the BCB anti-oxidative activity was; BHT>octadecyl ester>dodecyl ester>hexyl ester>methyl ester. Copyright © 2016 Elsevier Ltd. All rights reserved.

Submucosal hematoma is a highly suggestive finding for amyloid light-chain amyloidosis: Two case reports

PubMed Central

Yoshii, Shinji; Mabe, Katsuhiro; Nosho, Katsuhiko; Yamamoto, Hiroyuki; Yasui, Hiroshi; Okuda, Hiroyuki; Suzuki, Akira; Fujita, Masahiro; Sato, Toshihiro

2012-01-01

The clinical and endoscopic features of amyloid light-chain (AL) amyloidosis are diverse and mimic various other diseases. Endoscopically, few reports on submucosal hematomas of the gastrointestinal (GI) tract are available in the literature. Here, we report two cases of AL amyloidosis presenting as submucosal hematomas in the absence of clinical disease elsewhere in the body. The 2 cases were referred to our hospital because of hematochezia. The endoscopic findings in both cases were similar in submucosal hematoma formation. However, the clinical courses differed. In the first case, there was no evidence of systemic amyloidosis and the disease was conservatively managed. In the second case, the disease progressed to systemic amyloidosis and the patient died within a short time. We conclude that the endoscopic detection of a submucosal hematoma in the setting of GI bleeding should raise suspicion of AL amyloidosis. Referral to a hematologist should be done immediately for treatment while the involvement is limited to the GI tract. PMID:23125904

Structural and Immunological Activity Characterization of a Polysaccharide Isolated from Meretrix meretrix Linnaeus

PubMed Central

Li, Li; Li, Heng; Qian, Jianying; He, Yongfeng; Zheng, Jialin; Lu, Zhenming; Xu, Zhenghong; Shi, Jinsong

2015-01-01

Polysaccharides from marine clams perform various biological activities, whereas information on structure is scarce. Here, a water-soluble polysaccharide MMPX-B2 was isolated from Meretrix meretrix Linnaeus. The proposed structure was deduced through characterization and its immunological activity was investigated. MMPX-B2 consisted of d-glucose and d-galctose residues at a molar ratio of 3.51:1.00. The average molecular weight of MMPX-B2 was 510 kDa. This polysaccharide possessed a main chain of (1→4)-linked-α-d-glucopyranosyl residues, partially substituted at the C-6 position by a few terminal β-d-galactose residues or branched chains consisting of (1→3)-linked β-d-galactose residues. Preliminary immunological tests in vitro showed that MMPX-B2 could stimulate the murine macrophages to release various cytokines, and the structure-activity relationship was then established. The present study demonstrated the potential immunological activity of MMPX-B2, and provided references for studying the active ingredients in M. meretrix. PMID:26729136

Modeling and Computing of Stock Index Forecasting Based on Neural Network and Markov Chain

PubMed Central

Dai, Yonghui; Han, Dongmei; Dai, Weihui

2014-01-01

The stock index reflects the fluctuation of the stock market. For a long time, there have been a lot of researches on the forecast of stock index. However, the traditional method is limited to achieving an ideal precision in the dynamic market due to the influences of many factors such as the economic situation, policy changes, and emergency events. Therefore, the approach based on adaptive modeling and conditional probability transfer causes the new attention of researchers. This paper presents a new forecast method by the combination of improved back-propagation (BP) neural network and Markov chain, as well as its modeling and computing technology. This method includes initial forecasting by improved BP neural network, division of Markov state region, computing of the state transition probability matrix, and the prediction adjustment. Results of the empirical study show that this method can achieve high accuracy in the stock index prediction, and it could provide a good reference for the investment in stock market. PMID:24782659

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

Koch, D.; Fertitta, E.; Paulus, B.

Due to the importance of both static and dynamical correlation in the bond formation, low-dimensional beryllium systems constitute interesting case studies to test correlation methods. Aiming to describe the whole dissociation curve of extended Be systems we chose to apply the method of increments (MoI) in its multireference (MR) formalism. To gain insight into the main characteristics of the wave function, we started by focusing on the description of small Be chains using standard quantum chemical methods. In a next step we applied the MoI to larger beryllium systems, starting from the Be{sub 6} ring. The complete active space formalismmore » was employed and the results were used as reference for local MR calculations of the whole dissociation curve. Although this is a well-established approach for systems with limited multireference character, its application regarding the description of whole dissociation curves requires further testing. Subsequent to the discussion of the role of the basis set, the method was finally applied to larger rings and extrapolated to an infinite chain.« less