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Sample records for absolutely localized molecular

  1. Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design.

    PubMed

    Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

    2016-07-12

    We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.

  2. Probing non-covalent interactions with a second generation energy decomposition analysis using absolutely localized molecular orbitals.

    PubMed

    Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin

    2016-08-17

    An energy decomposition analysis (EDA) separates a calculated interaction energy into as many interpretable contributions as possible; for instance, permanent and induced electrostatics, Pauli repulsions, dispersion and charge transfer. The challenge is to construct satisfactory definitions of all terms in the chemically relevant regime where fragment densities overlap, rendering unique definitions impossible. Towards this goal, we present an improved EDA for Kohn-Sham density functional theory (DFT) with properties that have previously not been simultaneously attained. Building on the absolutely localized molecular orbital (ALMO)-EDA, this second generation ALMO-EDA is variational and employs valid antisymmetric electronic wavefunctions to produce all five contributions listed above. These contributions moreover all have non-trivial complete basis set limits. We apply the EDA to the water dimer, the T-shaped and parallel-displaced benzene dimer, the p-biphthalate dimer "anti-electrostatic" hydrogen bonding complex, the biologically relevant binding of adenine and thymine in stacked and hydrogen-bonded configurations, the triply hydrogen-bonded guanine-cytosine complex, the interaction of Cl(-) with s-triazine and with the 1,3-dimethyl imidazolium cation, which is relevant to the study of ionic liquids, and the water-formaldehyde-vinyl alcohol ter-molecular radical cationic complex formed in the dissociative photoionization of glycerol. PMID:27492057

  3. An energy decomposition analysis for second-order Møller–Plesset perturbation theory based on absolutely localized molecular orbitals

    SciTech Connect

    Thirman, Jonathan Head-Gordon, Martin

    2015-08-28

    An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller–Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond.

  4. An energy decomposition analysis for second-order Møller-Plesset perturbation theory based on absolutely localized molecular orbitals.

    PubMed

    Thirman, Jonathan; Head-Gordon, Martin

    2015-08-28

    An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller-Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond. PMID:26328835

  5. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C{sub s}-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  6. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level.

    PubMed

    Azar, R Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C(s)-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  7. Examination of the hydrogen-bonding networks in small water clusters (n = 2-5, 13, 17) using absolutely localized molecular orbital energy decomposition analysis.

    PubMed

    Cobar, Erika A; Horn, Paul R; Bergman, Robert G; Head-Gordon, Martin

    2012-11-28

    Using the ωB97X-D and B3LYP density functionals, the absolutely localized molecular orbital energy decomposition method (ALMO-EDA) is applied to the water dimer through pentamer, 13-mer and 17-mer clusters. Two-body, three-body, and total interaction energies are decomposed into their component energy terms: frozen density interaction energy, polarization energy, and charge transfer energy. Charge transfer, polarization, and frozen orbital interaction energies are all found to be significant contributors to the two-body and total interaction energies; the three-body interaction energies are dominated by polarization. Each component energy term for the two-body interactions is highly dependent on the associated hydrogen bond distance. The favorability of the three-body terms associated with the 13- and 17-mer structures depends on the hydrogen-donor or hydrogen-acceptor roles played by each of the three component waters. Only small errors arise from neglect of three-body interactions without two adjacent water molecules, or beyond three-body interactions. Interesting linear correlations are identified between the contributions of charge-transfer and polarization terms to the two and three-body interactions, which permits elimination of explicit calculation of charge transfer to a good approximation.

  8. Molecular iodine absolute frequencies. Final report

    SciTech Connect

    Sansonetti, C.J.

    1990-06-25

    Fifty specified lines of {sup 127}I{sub 2} were studied by Doppler-free frequency modulation spectroscopy. For each line the classification of the molecular transition was determined, hyperfine components were identified, and one well-resolved component was selected for precise determination of its absolute frequency. In 3 cases, a nearby alternate line was selected for measurement because no well-resolved component was found for the specified line. Absolute frequency determinations were made with an estimated uncertainty of 1.1 MHz by locking a dye laser to the selected hyperfine component and measuring its wave number with a high-precision Fabry-Perot wavemeter. For each line results of the absolute measurement, the line classification, and a Doppler-free spectrum are given.

  9. Absolute determination of local tropospheric OH concentrations

    NASA Technical Reports Server (NTRS)

    Armerding, Wolfgang; Comes, Franz-Josef

    1994-01-01

    Long path absorption (LPA) according to Lambert Beer's law is a method to determine absolute concentrations of trace gases such as tropospheric OH. We have developed a LPA instrument which is based on a rapid tuning of the light source which is a frequency doubled dye laser. The laser is tuned across two or three OH absorption features around 308 nm with a scanning speed of 0.07 cm(exp -1)/microsecond and a repetition rate of 1.3 kHz. This high scanning speed greatly reduces the fluctuation of the light intensity caused by the atmosphere. To obtain the required high sensitivity the laser output power is additionally made constant and stabilized by an electro-optical modulator. The present sensitivity is of the order of a few times 10(exp 5) OH per cm(exp 3) for an acquisition time of a minute and an absorption path length of only 1200 meters so that a folding of the optical path in a multireflection cell was possible leading to a lateral dimension of the cell of a few meters. This allows local measurements to be made. Tropospheric measurements have been carried out in 1991 resulting in the determination of OH diurnal variation at specific days in late summer. Comparison with model calculations have been made. Interferences are mainly due to SO2 absorption. The problem of OH self generation in the multireflection cell is of minor extent. This could be shown by using different experimental methods. The minimum-maximum signal to noise ratio is about 8 x 10(exp -4) for a single scan. Due to the small size of the absorption cell the realization of an open air laboratory is possible in which by use of an additional UV light source or by additional fluxes of trace gases the chemistry can be changed under controlled conditions allowing kinetic studies of tropospheric photochemistry to be made in open air.

  10. Molecular structure and absolute configuration of the diterpene lactone, praelolide.

    PubMed

    Dai, J B; Wan, Z L; Rao, Z H; Liang, D C; Fang, Z; Luo, Y K; Long, K H

    1985-11-01

    Praelolide is a new compound which was isolated out from the gorgonian, Menella praelonga (Ridley), collected from the South Sea of China at Zhanjiang, Guangdong. The molecular formula is C28H35O12Cl. The research result by X-ray diffraction method on the crystal structure is presented. The compound is orthorhombic with space group P2(1)2(1)2, cell dimensions a = 16.936, b = 16.709, c = 10.333 A, and Z = 4. The structure has been solved by direct method and refined to R = 0.055 for 2257 unique observable reflexions by least-squares. The molecule is composed of the major conformational isomer in which the three main rings (a six-membered ring, an eight-membered ring, a six-membered ring) take separately the form of chair-chairboat-chair, a five-membered actone ring, a C1 substitution, 4 acetate groups, and a three-membered epoxide ring. The absolute configuration of the molecule has also been determined by statistics (R factor ratio R = 1.012) and Bijvoet pairs observation. For 30 pairs of the greatest anomalous contributions the residuals are R'(+) = 0.057 for the first enantiomorph and R'(-) = 0.005 for the second one, so the latter should unambiguously correspond to the absolute configuration of the molecule.

  11. Photoinduced absolute negative current in a symmetric molecular electronic bridge

    SciTech Connect

    Prociuk, Alexander; Dunietz, Barry D

    2010-09-28

    The study of current induced by photoradiating a molecular-based device under bias is of fundamental importance to the improvement of photoconductors and photovoltaics. In this technology, electron pumps generate an uphill current that opposes a potential drop and thereby recharges a fuel cell. While the modeled molecular electron pump is completely symmetric, the sign of the photocurrent is solely determined by the existing bias and the nature of photoinduced electronic excitations. The photoradiation induces nonequilibrium population of the electrode-coupled system. The dependence of the photocurrent on electrode coupling, photoradiation field strength, and applied bias are studied at a basic model level.

  12. Hole localization in molecular crystals from hybrid density functional theory.

    PubMed

    Sai, Na; Barbara, Paul F; Leung, Kevin

    2011-06-01

    We use first-principles computational methods to examine hole trapping in organic molecular crystals. We present a computational scheme based on the tuning of the fraction of exact exchange in hybrid density functional theory to eliminate the many-electron self-interaction error. With small organic molecules, we show that this scheme gives accurate descriptions of ionization and dimer dissociation. We demonstrate that the excess hole in perfect molecular crystals forms self-trapped molecular polarons. The predicted absolute ionization potentials of both localized and delocalized holes are consistent with experimental values.

  13. First Absolutely Calibrated Localized Measurements of Ion Velocity in the MST in Locked and Rotating Plasmas

    NASA Astrophysics Data System (ADS)

    Baltzer, M.; Craig, D.; den Hartog, D. J.; Nornberg, M. D.; Munaretto, S.

    2015-11-01

    An Ion Doppler Spectrometer (IDS) is used on MST for high time-resolution passive and active measurements of impurity ion emission. Absolutely calibrated measurements of flow are difficult because the spectrometer records data within 0.3 nm of the C+5 line of interest, and commercial calibration lamps do not produce lines in this narrow range . A novel optical system was designed to absolutely calibrate the IDS. The device uses an UV LED to produce a broad emission curve in the desired region. A Fabry-Perot etalon filters this light, cutting transmittance peaks into the pattern of the LED emission. An optical train of fused silica lenses focuses the light into the IDS with f/4. A holographic diffuser blurs the light cone to increase homogeneity. Using this light source, the absolute Doppler shift of ion emissions can be measured in MST plasmas. In combination with charge exchange recombination spectroscopy, localized ion velocities can now be measured. Previously, a time-averaged measurement along the chord bisecting the poloidal plane was used to calibrate the IDS; the quality of these central chord calibrations can be characterized with our absolute calibration. Calibration errors may also be quantified and minimized by optimizing the curve-fitting process. Preliminary measurements of toroidal velocity in locked and rotating plasmas will be shown. This work has been supported by the US DOE.

  14. Multiscale Reactive Molecular Dynamics for Absolute pK a Predictions and Amino Acid Deprotonation.

    PubMed

    Nelson, J Gard; Peng, Yuxing; Silverstein, Daniel W; Swanson, Jessica M J

    2014-07-01

    Accurately calculating a weak acid's pK a from simulations remains a challenging task. We report a multiscale theoretical approach to calculate the free energy profile for acid ionization, resulting in accurate absolute pK a values in addition to insights into the underlying mechanism. Importantly, our approach minimizes empiricism by mapping electronic structure data (QM/MM forces) into a reactive molecular dynamics model capable of extensive sampling. Consequently, the bulk property of interest (the absolute pK a) is the natural consequence of the model, not a parameter used to fit it. This approach is applied to create reactive models of aspartic and glutamic acids. We show that these models predict the correct pK a values and provide ample statistics to probe the molecular mechanism of dissociation. This analysis shows changes in the solvation structure and Zundel-dominated transitions between the protonated acid, contact ion pair, and bulk solvated excess proton. PMID:25061442

  15. Dynamical Localization in Molecular Systems.

    NASA Astrophysics Data System (ADS)

    Wang, Xidi

    In the first four chapters of this thesis we concentrate on the Davydov model which describes the vibrational energy quanta of Amide I bonds (C=O bonds on the alpha -helix) coupled to the acoustic phonon modes of the alpha-helix backbone in the form of a Frohlich Hamiltonian. Following a brief introduction in chapter one, in chapter two we formulate the dynamics of vibrational quanta at finite temperature by using coherent state products. The fluctuation-dissipation relation is derived. At zero temperature, in the continuum limit, we recover the original results of Davydov. We also achieve good agreement with numerical simulations. In chapter three, the net contraction of the lattice is calculated exactly at any temperature, and its relation to the so -call "topological stability" of the Davydov soliton is discussed. In the second section of the chapter three we calculate the overtone spectra of crystalline acetanilide (according to some opinions ACN provides experimental evidence for the existence of Davydov solitons). Good agreement with experimental data has been obtained. In chapter four we study the self-trapped vibrational excitations by the Quantum Monte Carlo technique. For a single excitation, the temperature dependence of different physical observables is calculated. The quasi-particle which resembles the Davydov soliton has been found to be fairly narrow using the most commonly used data for the alpha -helix; at temperatures above a few Kelvin, the quasi-particle reaches its smallest limit (extends over three sites), which implies diffusive motion of the small polaron-like quasi-particle at high temperatures. For the multi-excitation case, bound pairs and clusters of excitations are found at low temperatures; they gradually dissociate when the temperature of the system is increased as calculated from the density-density correlation function. In the last chapter of this thesis, we study a more general model of dynamical local modes in molecular systems

  16. Local Molecular Orbitals from a Projection onto Localized Centers.

    PubMed

    Heßelmann, Andreas

    2016-06-14

    A localization method for molecular orbitals is presented which exploits the locality of the eigenfunctions associated with the largest eigenvalues of the matrix representation of spatially localized functions. Local molecular orbitals are obtained by a projection of the canonical orbitals onto the set of the eigenvectors which correspond to the largest eigenvalues of these matrices. Two different types of spatially localized functions were chosen in this work, a two-parameter smooth-step-type function and the weight functions determined by a Hirshfeld partitioning of the molecular volume. It is shown that the method can provide fairly local occupied molecular orbitals if the positions of the set of local functions are set to the molecular bond centers. The method can also yield reasonably well-localized virtual molecular orbitals, but here, a sensible choice of the positions of the functions are the atomic sites and the locality then depends more strongly on the shape of the set of local functions. The method is tested for a range of polypeptide molecules in two different conformations, namely, a helical and a β-sheet conformation. Futhermore, it is shown that an adequate locality of the occupied and virtual orbitals can also be obtained for highly delocalized systems. PMID:27164445

  17. The Question of Absolute Space and Time Directions in Relation to Molecular Chirality, Parity Violation, and Biomolecular Homochirality

    SciTech Connect

    Quack, Martin

    2001-03-21

    The questions of the absolute directions of space and time or the “observability” of absolute time direction as well as absolute handedness-left or right- are related to the fundamental symmetries of physics C, P, T as well as their combinations, in particular CPT, and their violations, such as parity violation. At the same time there is a relation to certain still open questions in chemistry concerning the fundamental physical- chemical principles of molecular chirality and in biochemistry concerning the selection of homochirality in evolution. In the lecture we shall introduce the concepts and then report new theoretical results from our work on parity violation in chiral molecules, showing order of magnitude increases with respect to previously accepted values. We discus as well our current experimental efforts. We shall briefly mention the construction of an absolute molecular clock.

  18. The Question of Absolute Space and Time Directions in Relation to Molecular Chirality, Parity Violation, and Biomolecular Homochirality

    SciTech Connect

    Quack, Martin

    2001-03-21

    The questions of the absolute directions of space and time or the 'observability' of absolute time direction as well as absolute handedness - left or right - are related to the fundamental symmetries of physics C, P, T as well as their combinations, in particular CPT, and their violations, such as parity violation. At the same time there is a relation to certain still open questions in chemistry concerning the fundamental physical-chemical principles of molecular chirality and in biochemistry concerning the selection of homochirality in evolution. In the lecture we shall introduce the concepts and then report new theoretical results from our work on parity violation in chiral molecules, showing order of magnitude increases with respect to previously accepted values. We discuss as well our current experimental efforts. We shall briefly mention the construction of an absolute molecular clock.

  19. Absolute molecular transition frequencies measured by three cavity-enhanced spectroscopy techniques

    NASA Astrophysics Data System (ADS)

    Cygan, A.; Wójtewicz, S.; Kowzan, G.; Zaborowski, M.; Wcisło, P.; Nawrocki, J.; Krehlik, P.; Śliwczyński, Ł.; Lipiński, M.; Masłowski, P.; Ciuryło, R.; Lisak, D.

    2016-06-01

    Absolute frequencies of unperturbed 12C16O transitions from the near-infrared (3-0) band were measured with uncertainties five-fold lower than previously available data. The frequency axis of spectra was linked to the primary frequency standard. Three different cavity enhanced absorption and dispersion spectroscopic methods and various approaches to data analysis were used to estimate potential systematic instrumental errors. Except for a well established frequency-stabilized cavity ring-down spectroscopy, we applied the cavity mode-width spectroscopy and the one-dimensional cavity mode-dispersion spectroscopy for measurement of absorption and dispersion spectra, respectively. We demonstrated the highest quality of the dispersion line shape measured in optical spectroscopy so far. We obtained line positions of the Doppler-broadened R24 and R28 transitions with relative uncertainties at the level of 10-10. The pressure shifting coefficients were measured and the influence of the line asymmetry on unperturbed line positions was analyzed. Our dispersion spectra are the first demonstration of molecular spectroscopy with both axes of the spectra directly linked to the primary frequency standard, which is particularly desirable for the future reference-grade measurements of molecular spectra.

  20. Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials

    PubMed Central

    Wang, Jiyao; Deng, Yuqing; Roux, Benoît

    2006-01-01

    The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned “on” and “off.” Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from ∼25,000 to 2500. The computations are very efficient and the statistical error is small (∼1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within ∼2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining

  1. Dynamic localization and negative absolute conductance in terahertz driven semiconductor superlattices

    SciTech Connect

    Keay, B.J.; Allen, S.J.; Campman, K.L.

    1995-12-31

    We report the first observation of Negative Absolute Conductance (NAC), dynamic localization and multiphoton stimulated emission assisted tunneling in terahertz driven semiconductor superlattices. Theories predicting NAC in semiconductor superlattices subjected to AC electric fields have existed for twenty years, but have never been verified experimentally. Most theories are based upon semiclassical arguments and are only valid for superlattices in the miniband or coherent tunneling regime. We are not aware of models predicting NAC in superlattices in the sequential tunneling regime, although there has been recent theoretical work on double-barrier structures. Perhaps the most remarkable result is found in the power dependence of the current-voltage (I-V) characteristics near zero DC bias. As the laser power is increased the current decreases towards zero and then becomes negative. This result implies that the electrons are absorbing energy from the laser field, producing a net current in the direction opposite to the applied voltage. NAC around zero DC bias is a particularly surprising observation considering photon-assisted tunneling is not expected to be observable between the ground states of neighboring quantum wells in a semiconductor superlattice. Contrary to this believe our results are most readily attributable to photon absorption and multiphoton emission between ground states of neighboring wells. The I-V characteristics measured in the presence of terahertz radiation at low DC bias also contain steps and plateaus analogous to photon-assisted steps observed in superconducting junctions. As many as three steps have been clearly resolved corresponding to stimulated emission into the terahertz field by a three-photon process.

  2. Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.

    PubMed

    Fun, Hoong-Kun; Chantrapromma, Suchada; Salae, Abdul Wahab; Razak, Ibrahim Abdul; Karalai, Chatchanok

    2011-05-01

    The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ▶). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H⋯O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions. The packing also features C⋯O [3.131 (3) Å] short contacts.

  3. Design, validation, and absolute sensitivity of a novel test for the molecular detection of avian pneumovirus.

    PubMed

    Cecchinato, Mattia; Catelli, Elena; Savage, Carol E; Jones, Richard C; Naylor, Clive J

    2004-11-01

    This study describes attempts to increase and measure sensitivity of molecular tests to detect avian pneumovirus (APV). Polymerase chain reaction (PCR) diagnostic tests were designed for the detection of nucleic acid from an A-type APV genome. The objective was selection of PCR oligonucleotide combinations, which would provide the greatest test sensitivity and thereby enable optimal detection when used for later testing of field materials. Relative and absolute test sensitivities could be determined because of laboratory access to known quantities of purified full-length DNA copies of APV genome derived from the same A-type virus. Four new nested PCR tests were designed in the fusion (F) protein (2 tests), small hydrophobic (SH) protein (1 test), and nucleocapsid (N) protein (1 test) genes and compared with an established test in the attachment (G) protein gene. Known amounts of full-length APV genome were serially diluted 10-fold, and these dilutions were used as templates for the different tests. Sensitivities were found to differ between the tests, the most sensitive being the established G test, which proved able to detect 6,000 copies of the G gene. The G test contained predominantly pyrimidine residues at its 3' termini, and because of this, oligonucleotides for the most sensitive F test were modified to incorporate the same residue types at their 3' termini. This was found to increase sensitivity, so that after full 3' pyrimidine substitutions, the F test became able to detect 600 copies of the F gene.

  4. Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.

    PubMed

    Fun, Hoong-Kun; Chantrapromma, Suchada; Salae, Abdul Wahab; Razak, Ibrahim Abdul; Karalai, Chatchanok

    2011-05-01

    The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ▶). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H⋯O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions. The packing also features C⋯O [3.131 (3) Å] short contacts. PMID:21754362

  5. Absolute cross sections for molecular photoabsorption, partial photoionization, and ionic photofragmentation process

    SciTech Connect

    Gallagher, J.W.; Brion, C.E.; Samson, J.A.R.; Langhoff, P.W.

    1988-01-01

    A compilation is provided of absolute total photoabsorption and partial-channel photoionization cross sections for the valence shells of selected molecules, including diatomics (H2, N2, O2, CO, NO) and triatomics (CO2, N2O), simple hydrides (H2O, NH3, CH4), hydrogen halides (HF, HCl, HBr, HI), sulfur compounds (H2S, CS2, OCS, SO2, SF6),and chlorine compounds (Cl2, CCl4). The partial-channel cross sections presented refer to production of the individual electronic states of molecular ions and also to production of parent and specific fragment ions, as functions of incident photon energy, typically from approximately 20 to 100 eV. Photoelectron anisotropy factors, which together with electronic partial cross sections provide cross sections differential in photon energy and in ejection angle, are also reported. There is generally good agreement between cross sections measured by the physically distinct optical and dipole electron-impact methods. The cross sections and anisotropy factors also compare favorably with selection ab initio and model potential (X-alpha) calculations which provide a basis for interpretation of the measurements.

  6. Atom-chip based quantum gravimetry for the precise determination of absolute local gravity

    NASA Astrophysics Data System (ADS)

    Abend, S.

    2015-12-01

    We present a novel technique for the precise measurement of absolute local gravity based on cold atom interferometry. Atom interferometry utilizes the interference of matter waves interrogated by laser light to read out inertial forces. Today's generation of these devices typically operate with test mass samples, that consists of ensembles of laser cooled atoms. Their performance is limited by the velocity spread and finite-size of the test masses that impose systematic uncertainties at the level of a few μGal. Rather than laser cooled atoms we employ quantum degenerate ensembles, so called Bose-Einstein condensates, as ultra-sensitive probes for gravity. These sources offer unique properties in temperature as well as in ensemble size that will allow to overcome the current limitations with the next generation of sensors. Furthermore, atom-chip technologies offer the possibility to generate Bose-Einstein condensates in a fast and reliable way. We show a lab-based prototype that uses the atom-chip itself to retro-reflect the interrogation laser and thus serving as inertial reference inside the vacuum. With this setup it is possible to demonstrate all necessary steps to measure gravity, including the preparation of the source, spanning an interferometer as well as the detection of the output signal, within an area of 1 cm3 right below the atom-chip and to analyze relevant systematic effects. In the framework of the center of excellence geoQ a next generation device is under construction at the Institut für Quantenoptik, that will allow for in-field measurements. This device will feature a state-of-the-art atom-chip source with a high-flux of ultra-cold atoms at a repetition rate of 1-2 Hz. In cooperation with the Müller group at the Institut für Erdmessung the sensor will be characterized in the laboratory first, to be ultimately employed in campaigns to measure the Fennoscandian uplift at the level of 1 μGal. The presented work is part of the center of

  7. Local Refinements in Classical Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Fackeldey, Konstantin; Weber, Marcus

    2014-03-01

    Quantum mechanics provide a detailed description of the physical and chemical behavior of molecules. However, with increasing size of the system the complexity rises exponentially, which is prohibitive for efficient dynamical simulation. In contrast, classical molecular dynamics procure a coarser description by using less degrees of freedom. Thus, it seems natural to seek for an adequate trade-off between accurateness and computational feasibility in the simulation of molecules. Here, we propose a novel method, which combines classical molecular simulations with quantum mechanics for molecular systems. For this we decompose the state space of the respective molecule into subsets, by employing a meshfree partition of unity. We show, that this partition allows us to localize an empirical force field and to run locally constrained classical trajectories. Within each subset, we compute the energy on the quantum level for a fixed number of spatial states (ab initio points). With these energy values from the ab initio points we have a local scattered data problem, which can be solved by the moving least squares method.

  8. Easy Absolute Values? Absolutely

    ERIC Educational Resources Information Center

    Taylor, Sharon E.; Mittag, Kathleen Cage

    2015-01-01

    The authors teach a problem-solving course for preservice middle-grades education majors that includes concepts dealing with absolute-value computations, equations, and inequalities. Many of these students like mathematics and plan to teach it, so they are adept at symbolic manipulations. Getting them to think differently about a concept that they…

  9. Absolute vacuum ultraviolet photoabsorption cross section studies of atomic and molecular species: Techniques and observational data

    NASA Technical Reports Server (NTRS)

    Judge, D. L.; Wu, C. Y. R.

    1990-01-01

    Absorption of a high energy photon (greater than 6 eV) by an isolated molecule results in the formation of highly excited quasi-discrete or continuum states which evolve through a wide range of direct and indirect photochemical processes. These are: photoionization and autoionization, photodissociation and predissociation, and fluorescence. The ultimate goal is to understand the dynamics of the excitation and decay processes and to quantitatively measure the absolute partial cross sections for all processes which occur in photoabsorption. Typical experimental techniques and the status of observational results of particular interest to solar system observations are presented.

  10. Saddle point localization of molecular wavefunctions

    NASA Astrophysics Data System (ADS)

    Mellau, Georg Ch.; Kyuberis, Alexandra A.; Polyansky, Oleg L.; Zobov, Nikolai; Field, Robert W.

    2016-09-01

    The quantum mechanical description of isomerization is based on bound eigenstates of the molecular potential energy surface. For the near-minimum regions there is a textbook-based relationship between the potential and eigenenergies. Here we show how the saddle point region that connects the two minima is encoded in the eigenstates of the model quartic potential and in the energy levels of the [H, C, N] potential energy surface. We model the spacing of the eigenenergies with the energy dependent classical oscillation frequency decreasing to zero at the saddle point. The eigenstates with the smallest spacing are localized at the saddle point. The analysis of the HCN ↔ HNC isomerization states shows that the eigenstates with small energy spacing relative to the effective (v1, v3, ℓ) bending potentials are highly localized in the bending coordinate at the transition state. These spectroscopically detectable states represent a chemical marker of the transition state in the eigenenergy spectrum. The method developed here provides a basis for modeling characteristic patterns in the eigenenergy spectrum of bound states.

  11. Saddle point localization of molecular wavefunctions

    PubMed Central

    Mellau, Georg Ch.; Kyuberis, Alexandra A.; Polyansky, Oleg L.; Zobov, Nikolai; Field, Robert W.

    2016-01-01

    The quantum mechanical description of isomerization is based on bound eigenstates of the molecular potential energy surface. For the near-minimum regions there is a textbook-based relationship between the potential and eigenenergies. Here we show how the saddle point region that connects the two minima is encoded in the eigenstates of the model quartic potential and in the energy levels of the [H, C, N] potential energy surface. We model the spacing of the eigenenergies with the energy dependent classical oscillation frequency decreasing to zero at the saddle point. The eigenstates with the smallest spacing are localized at the saddle point. The analysis of the HCN ↔ HNC isomerization states shows that the eigenstates with small energy spacing relative to the effective (v1, v3, ℓ) bending potentials are highly localized in the bending coordinate at the transition state. These spectroscopically detectable states represent a chemical marker of the transition state in the eigenenergy spectrum. The method developed here provides a basis for modeling characteristic patterns in the eigenenergy spectrum of bound states. PMID:27629262

  12. Saddle point localization of molecular wavefunctions.

    PubMed

    Mellau, Georg Ch; Kyuberis, Alexandra A; Polyansky, Oleg L; Zobov, Nikolai; Field, Robert W

    2016-01-01

    The quantum mechanical description of isomerization is based on bound eigenstates of the molecular potential energy surface. For the near-minimum regions there is a textbook-based relationship between the potential and eigenenergies. Here we show how the saddle point region that connects the two minima is encoded in the eigenstates of the model quartic potential and in the energy levels of the [H, C, N] potential energy surface. We model the spacing of the eigenenergies with the energy dependent classical oscillation frequency decreasing to zero at the saddle point. The eigenstates with the smallest spacing are localized at the saddle point. The analysis of the HCN ↔ HNC isomerization states shows that the eigenstates with small energy spacing relative to the effective (v1, v3, ℓ) bending potentials are highly localized in the bending coordinate at the transition state. These spectroscopically detectable states represent a chemical marker of the transition state in the eigenenergy spectrum. The method developed here provides a basis for modeling characteristic patterns in the eigenenergy spectrum of bound states. PMID:27629262

  13. Alignment of absolute and relative molecular size specifications for a polyvalent pneumococcal polysaccharide vaccine (PNEUMOVAX 23).

    PubMed

    MacNair, John E; Desai, Tejal; Teyral, Jennifer; Abeygunawardana, Chitrananda; Hennessey, John P

    2005-03-01

    An approach was developed to align release and end-expiry specifications for molecular size for the polyvalent pneumococcal polysaccharide vaccine (PNEUMOVAX 23). Each of the 23 polysaccharide components of the vaccine was separately subjected to ultrasonication to produce a series of preparations of decreasing weight-average molecular mass (Mw). These size-reduced polysaccharides were analysed as monovalent solutions by high-performance size exclusion chromatography (HPSEC) with multi-angle laser light scattering (MALLS) and refractive index (RI) detection to measure their Mw. These samples were also analysed by HPSEC with rate nephelometry (RN) detection to measure their relative molecular size (r-MS). The data from the two molecular size measurements established a correlation between Mw and r-MS. For each polysaccharide component of the vaccine, this correlation permits the direct alignment of the r-MS specification in the final formulated product with the Mw specification for the monovalent polysaccharide preparation. The alignment of specifications provides a high level of assurance that the quality control of the final vaccine product is consistent with that of the polysaccharide starting materials.

  14. Absolute frequency measurement for the emission transitions of molecular iodine in the 982 - 985 nm range

    SciTech Connect

    Matyugin, Yu A; Ignatovich, S M; Kuznetsov, Sergei A; Nesterenko, M I; Okhapkin, M V; Pivtsov, V S; Skvortsov, Mikhail N; Bagaev, Sergei N

    2012-03-31

    We report high-precision frequency measurements of the separate hyperfine structure (HFS) components of the emission B - X system transitions of {sup 127}I{sub 2} molecules in the 982 - 985 nm range. To resolve the HFS of the emission lines, advantage was taken of the method of three-level laser spectroscopy. The function of exciting radiation was fulfilled by the second harmonic of a cw Nd : YAG laser, and the probe radiation in the 968 - 998 nm range was generated by an external-cavity diode laser. The output Nd : YAG laser frequency was locked to an HFS component of the absorption transition and the probing laser radiation to the emission transition component. When both frequencies were locked to HFS components with a common upper level, the output diode laser frequency was precisely equal to the emission transition frequency. The output frequency of the thus stabilised diode laser was measured with the help of a femtosecond optical frequency synthesiser based on a Ti : sapphire laser. We present the results of the absolute frequency measurements of 20 HFS components belonging to six vibrational - rotational transitions of the B - X system of iodine [R56(32 - 48)a1, P58(32 - 48)a1, P85(33 - 48)a1, R87(33 - 48a1, R88(33 - 48)a10] and all 15 components of the R86(33 - 48) line. The relative measurement uncertainty is equal to 7 Multiplication-Sign 10{sup -10} and is determined by the frequency instability of the diode laser radiation.

  15. Quantitative Vapor-phase IR Intensities and DFT Computations to Predict Absolute IR Spectra based on Molecular Structure: I. Alkanes

    SciTech Connect

    Williams, Stephen D.; Johnson, Timothy J.; Sharpe, Steven W.; Yavelak, Veronica; Oats, R. P.; Brauer, Carolyn S.

    2013-11-13

    Recently recorded quantitative IR spectra of a variety of gas-phase alkanes are shown to have integrated intensities in both the C-H stretching and C-H bending regions that depend linearly on the molecular size, i.e. the number of C-H bonds. This result is well predicted from CH4 to C15H32 by DFT computations of IR spectra at the B3LYP/6-31+G(d,p) level of DFT theory. A simple model predicting the absolute IR band intensities of alkanes based only on structural formula is proposed: For the C-H stretching band near 2930 cm-1 this is given by (in km/mol): CH¬_str = (34±3)*CH – (41±60) where CH is number of C-H bonds in the alkane. The linearity is explained in terms of coordinated motion of methylene groups rather than the summed intensities of autonomous -CH2- units. The effect of alkyl chain length on the intensity of a C-H bending mode is explored and interpreted in terms of conformer distribution. The relative intensity contribution of a methyl mode compared to the total C-H stretch intensity is shown to be linear in the number of terminal methyl groups in the alkane, and can be used to predict quantitative spectra a priori based on structure alone.

  16. Controlling local currents in molecular junctions

    NASA Astrophysics Data System (ADS)

    Yadalam, Hari Kumar; Harbola, Upendra

    2016-09-01

    The effects of nonequilibrium constraints and dephasing on the circulating currents in molecular junctions are analyzed. Circulating currents are manifestations of quantum effects and can be induced either by externally applied bias or an external magnetic field through the molecular system. In a symmetric Aharonov-Bohm ring, bond currents have two contributions, bias driven and magnetic field driven. We analyze the competition between these two contributions and show that, as a consequence, current through one of the branches can be completely suppressed. We then study the effect of asymmetry (as a result of chemical substitution) on the current pathways inside the molecule and study asymmetry-induced circulating currents (without magnetic field) by tuning the coupling strength of the substituent (at finite bias).

  17. Localization of energy on the molecular scale

    SciTech Connect

    Lindenberg, K.; Brown, D.W.

    1997-12-31

    We discuss the spontaneous localization of vibrational energy in translationally invariant anharmonic chains at finite temperatures. In addition to the familiar energy-driven coherent mechanisms, which are rapidly degraded by thermal fluctuations, we identify the entropy-driven phenomenon we call {open_quotes}stochastic localization{close_quotes}, within which we include a number of characteristics of soft anharmonic oscillators in thermal equilibrium. Principal among these are a tendency for soft oscillators to spend more time at higher energies than comparable harmonic oscillators, and for high-energy fluctuations in soft oscillators to persist for longer times than lower-energy fluctuations, leading to a tendency for energy fluctuations to be organized into {open_quotes}bursts{close_quotes} separated by intervals of relative quiet. We illustrate the effects of stochastic localization on a bistable impurity embedded in a chain of soft oscillators by comparing it to an impurity embedded in a harmonic chain. Effects on transition rates at a given system energy can be quite dramatic.

  18. On the absolute thermodynamics of water from computer simulations: A comparison of first-principles molecular dynamics, reactive and empirical force fields

    NASA Astrophysics Data System (ADS)

    Pascal, Tod A.; Schärf, Daniel; Jung, Yousung; Kühne, Thomas D.

    2012-12-01

    We present the absolute enthalpy, entropy, heat capacity, and free energy of liquid water at ambient conditions calculated by the two-phase thermodynamic method applied to ab initio, reactive and classical molecular dynamics simulations. We find that the absolute entropy and heat capacity of liquid water from ab initio molecular dynamics (AIMD) is underestimated, but falls within the range of the flexible empirical as well as the reactive force fields. The origin of the low absolute entropy of liquid water from AIMD simulations is due to an underestimation of the translational entropy by 20% and the rotational entropy by 40% compared to the TIP3P classical water model, consistent with previous studies that reports low diffusivity and increased ordering of liquid water from AIMD simulations. Classical MD simulations with rigid water models tend to be in better agreement with experiment (in particular TIP3P yielding the best agreement), although the TIP4P-ice water model, the only empirical force field that reproduces the experimental melting temperature, has the lowest entropy, perhaps expectedly. This reiterates the limitations of existing empirical water models in simultaneously capturing the thermodynamics of solid and liquid phases. We find that the quantum corrections to heat capacity of water can be as large as 60%. Although certain water models are computed to yield good absolute free energies of water compared to experiments, they are often due to the fortuitous enthalpy-entropy cancellation, but not necessarily due to the correct descriptions of enthalpy and entropy separately.

  19. Estimates of absolute flux and radiance factor of localized regions on Mars in the 2-4 micron wavelength region

    NASA Technical Reports Server (NTRS)

    Roush, Ted L.; Roush, Eileen A.; Singer, Robert B.; Lucey, Paul G.

    1992-01-01

    IRTF spectrophotometric observations of Mars obtained during the 1986 opposition are the bases for the present estimates of 2.0-4.15 micron absolute flux and radiance factor values. The bright/dark ratios obtained show a wavelength dependence similar to that observed by Bell and Crisp (1991) in 1990, but the spectral contrast for 1986 is lower than in those observations; this difference could be due to changes in the location, sample are size, and/or suspended atmospheric dust.

  20. Quantum Localization in Laser-Driven Molecular Rotation

    NASA Astrophysics Data System (ADS)

    Averbukh, Ilya

    2016-05-01

    Recently we predicted that several celebrated solid state quantum localization phenomena - Anderson localization, Bloch oscillations, and Tamm-Shockley surface states - may manifest themselves in the rotational dynamics of laser-kicked molecules. In this talk, I will present these new rotational effects in a gas of linear molecules subject to a moderately long periodic train of femtosecond laser pulses. A small detuning of the train period from the rotational revival time causes Anderson localization in the angular momentum space above some critical value of J - the Anderson wall. This wall marks an impenetrable border stopping any further rotational excitation. Below the Anderson wall, the rotational excitation oscillates with the number of pulses due to a mechanism similar to Bloch oscillations in crystalline solids. I will present the results of the first experimental observation of the laser-induced rotational Bloch oscillations in molecular nitrogen at ambient conditions (Stanford & Weizmann, 2015). We will also discuss the prospects of observing the rotational analogues of the Tamm surface states in a similar experimental setup. Our results offer laser-driven molecular rotation as a new platform for studies on the localization phenomena in quantum transport. These effects are important for many processes involving highly excited rotational states, including coherent optical manipulations in molecular mixtures, and propagation of powerful laser pulses in atmosphere.

  1. Local reactivity descriptors from degenerate frontier molecular orbitals

    NASA Astrophysics Data System (ADS)

    Martínez, Jorge

    2009-08-01

    Conceptual Density Functional Theory (DFT) has proposed a set of local descriptors to measure the reactivity on specific sites of a molecule, as an example dual descriptor has been successfully used in analyzing interesting systems to understand their local reactivity, however under the frozen orbital approximation (FOA), it is defined from non-degenerate frontier molecular orbitals (FMOs). In this work, the degeneration is taken into account to propose approximated expressions to obtain the dual descriptor, nucleophilic and electrophilic Fukui functions in closed-shell systems. The proposed expressions have been tested on molecules presenting degenerate FMOs.

  2. Absolute localization of ground robots by matching LiDAR and image data in dense forested environments

    NASA Astrophysics Data System (ADS)

    Hussein, Marwan; Renner, Matthew; Iagnemma, Karl

    2014-06-01

    A method for the autonomous geolocation of ground vehicles in forest environments is discussed. The method provides an estimate of the global horizontal position of a vehicle strictly based on finding a geometric match between a map of observed tree stems, scanned in 3D by Light Detection and Ranging (LiDAR) sensors onboard the vehicle, to another stem map generated from the structure of tree crowns analyzed from high resolution aerial orthoimagery of the forest canopy. Extraction of stems from 3D data is achieved by using Support Vector Machine (SVM) classifiers and height above ground filters that separate ground points from vertical stem features. Identification of stems from overhead imagery is achieved by finding the centroids of tree crowns extracted using a watershed segmentation algorithm. Matching of the two maps is achieved by using a robust Iterative Closest Point (ICP) algorithm that determines the rotation and translation vectors to align the datasets. The alignment is used to calculate the absolute horizontal location of the vehicle. The method has been tested with real-world data and has been able to estimate vehicle geoposition with an average error of less than 2 m. It is noted that the algorithm's accuracy performance is currently limited by the accuracy and resolution of aerial orthoimagery used. The method can be used in real-time as a complement to the Global Positioning System (GPS) in areas where signal coverage is inadequate due to attenuation by the forest canopy, or due to intentional denied access. The method has two key properties that are significant: i) It does not require a priori knowledge of the area surrounding the robot. ii) Uses the geometry of detected tree stems as the only input to determine horizontal geoposition.

  3. Mapping the microvascular and the associated absolute values of oxy-hemoglobin concentration through turbid media via local off-set diffuse optical imaging

    NASA Astrophysics Data System (ADS)

    Chen, Chen; Klämpfl, Florian; Stelzle, Florian; Schmidt, Michael

    2014-11-01

    An imging resolution of micron-scale has not yet been discovered by diffuse optical imaging (DOI), while a superficial response was eliminated. In this work, we report on a new approach of DOI with a local off-set alignment to subvert the common boundary conditions of the modified Beer-Lambert Law (MBLL). It can resolve a superficial target in micron scale under a turbid media. To validate both major breakthroughs, this system was used to recover a subsurface microvascular mimicking structure under an skin equivalent phantom. This microvascular was included with oxy-hemoglobin solution in variant concentrations to distiguish the absolute values of CtRHb and CtHbO2 . Experimental results confirmed the feasibility of recovering the target vascular of 50 µm in diameter, and graded the values of the concentrations of oxy-hemoglobin from 10 g/L to 50 g/L absolutely. Ultimately, this approach could evolve into a non-invasive imaging system to map the microvascular pattern and the associated oximetry under a human skin in-vivo.

  4. Absolute Summ

    NASA Astrophysics Data System (ADS)

    Phillips, Alfred, Jr.

    Summ means the entirety of the multiverse. It seems clear, from the inflation theories of A. Guth and others, that the creation of many universes is plausible. We argue that Absolute cosmological ideas, not unlike those of I. Newton, may be consistent with dynamic multiverse creations. As suggested in W. Heisenberg's uncertainty principle, and with the Anthropic Principle defended by S. Hawking, et al., human consciousness, buttressed by findings of neuroscience, may have to be considered in our models. Predictability, as A. Einstein realized with Invariants and General Relativity, may be required for new ideas to be part of physics. We present here a two postulate model geared to an Absolute Summ. The seedbed of this work is part of Akhnaton's philosophy (see S. Freud, Moses and Monotheism). Most important, however, is that the structure of human consciousness, manifest in Kenya's Rift Valley 200,000 years ago as Homo sapiens, who were the culmination of the six million year co-creation process of Hominins and Nature in Africa, allows us to do the physics that we do. .

  5. The warm and cold neutral phase in the local interstellar medium at absolute value of B greater than or equal to 10 deg

    NASA Astrophysics Data System (ADS)

    Poppel, W. G. L.; Marronetti, P.; Benaglia, P.

    1994-07-01

    We made a systematic separation of both the neutral phases using the atlases of 21-cm profiles of Heiles & Habing (1974) and Colomb et al. (1980), complemented with other data. First, we fitted the emission of the warm neutral medium (WNM) by means of a broad Gaussian curve (velocity dispersion sigma approximately 10-14 km/s). We derived maps of the column densities NWH and the radial velocities VW of the WNM. Its overall distribution appears to be very inhomogeneous with a large hole in the range b greater than or equal to +50 deg. However, if the hole is excluded, the mean latitude-profiles admit a rough cosec absolute value of b-fit common to both hemispheres. A kinematical analysis of VW for the range 10 deg less than or equal to absolute value of b less than or equal to 40 deg indicates a mean differential rotation with a small nodal deviation. At absolute value of b greater than 50 deg VW is negative, with larger values and discontinuities in the north. On the mean, sigma increases for absolute value of b decreasing, as is expected from differential rotation. From a statistical study of the peaks of the residual profiles we derived some characteristics of the cold neutral medium (CNM). The latter is generally characterized by a single component of sigma approximately 2-6 km/s. Additionally we derived the sky-distribution of the column densities NCH and the radial velocities VC of the CNM within bins of 1.2 deg sec b x 1 deg in l, b. Furthermore, we focused on the characteristics of Linblad's feature A of cool gas by considering the narrow ridge of local H I, which appears in the b-V contour maps at fixed l (e.g. Schoeber 1976). The ridge appears to be the main component of the CNM. We suggest a scenario for the formulation and evolution of the Gould belt system of stars and gas on the basis of an explosive event within a shingle of cold dense gas tilted to the galactic plane. The scenario appears to be consistent with the results found for both the neutral

  6. Molecular mechanisms of nerve block by local anesthetics.

    PubMed

    Strichartz, G

    1976-10-01

    block increases with the frequency of nerve impulses. When impulses occur at higher frequencies more sodium channels are open over a period of time comparable to the time necessary for the anesthetic binding reaction, thus more channels are blocked. In addition the changes of the inactivation function result in a longer refractory period and, thus, a decrease of impulse height at higher frequencies. Charged anesthetic molecules may bind in the pore of the sodium channel. Their binding can be modulated by the electrical field in the membrane. The channel has a higher affinity for larger anesthetic molecules, but this may result from their greater hydrophobicity as well as from their size. The binding site favors molecules that contain more polar linkages between the amine group and the aromatic residue. Binding of amine anesthetics is weakly stereospecific and, surprisingly, shows no absolute requirement for the terminal alkyl ammonium moiety present in most local anesthetics...

  7. Possibilities of modelling of local and global hydrological changes from high-resolution Global Hydrological Model in the absolute gravity observations - the case of Józefosław Observatory

    NASA Astrophysics Data System (ADS)

    Olszak, Tomasz; Barlik, Marcin; Pachuta, Andrzej; Próchniewicz, Dominik

    2014-05-01

    Geodynamical use of epoch gravimetric relative and absolute observations requires the elimination of one from the most significant effect related to local and global changes of hydrological conditions. It is understood that hydrological effect is associated with changes in groundwater levels and soil moisture around the gravimetric station. In Poland, the quasi - permanent observations of gravity changes by absolute method carried out since 2005 on gravity station located in the Astronomical - Geodetic Observatory in Józefosław. In the poster will be shortly described measurement strategy of absolute observations and different approaches to the elimination of the local and global effects associated with changes in hydrology. This paper will discuss the results of the analysis of tidal observations relevant to the development of absolute observations - seasonal changes in barometric correction factor and differences in the locally designated tidal corrections model. Analysis of the possibility of elimination the impact of global hydrological influence is based on the model GLDAS a spatial resolution of 0.25 degree independently on a local scale and global. Józefosław Observatory is equipped with additional sensors linked to the monitoring of local hydrological conditions. It gives a possibility to verify the quality of modeling of hydrological changes using global models in local and global scale.

  8. Nuclear Localization Signal Peptides Induce Molecular Delivery along Microtubules

    PubMed Central

    Salman, Hanna; Abu-Arish, Asmahan; Oliel, Shachar; Loyter, Avraham; Klafter, Joseph; Granek, Rony; Elbaum, Michael

    2005-01-01

    Many essential processes in eukaryotic cells depend on regulated molecular exchange between its two major compartments, the cytoplasm and the nucleus. In general, nuclear import of macromolecular complexes is dependent on specific peptide signals and their recognition by receptors that mediate translocation through the nuclear pores. Here we address the question of how protein products bearing such nuclear localization signals arrive at the nuclear membrane before import, i.e., by simple diffusion or perhaps with assistance of cytoskeletal elements or cytoskeleton-associated motor proteins. Using direct single-particle tracking and detailed statistical analysis, we show that the presence of nuclear localization signals invokes active transport along microtubules in a cell-free Xenopus egg extract. Chemical and antibody inhibition of minus-end directed cytoplasmic dynein blocks this active movement. In the intact cell, where microtubules project radially from the centrosome, such an interaction would effectively deliver nuclear-targeted cargo to the nuclear envelope in preparation for import. PMID:16040740

  9. Molecular designs for controlling the local environments around metal ions.

    PubMed

    Cook, Sarah A; Borovik, A S

    2015-08-18

    The functions of metal complexes are directly linked to the local environment in which they are housed; modifications to the local environment (or secondary coordination sphere) are known to produce changes in key properties of the metal centers that can affect reactivity. Noncovalent interactions are the most common and influential forces that regulate the properties of secondary coordination spheres, which leads to complexities in structure that are often difficult to achieve in synthetic systems. Using key architectural features from the active sites of metalloproteins as inspiration, we have developed molecular systems that enforce intramolecular hydrogen bonds (H-bonds) around a metal center via incorporation of H-bond donors and acceptors into rigid ligand scaffolds. We have utilized these molecular species to probe mechanistic aspects of biological dioxygen activation and water oxidation. This Account describes the stabilization and characterization of unusual M-oxo and heterobimetallic complexes. These types of species have been implicated in a range of oxidative processes in biology but are often difficult to study because of their inherent reactivity. Our H-bonding ligand systems allowed us to prepare an Fe(III)-oxo species directly from the activation of O2 that was subsequently oxidized to form a monomeric Fe(IV)-oxo species with an S = 2 spin state, similar to those species proposed as key intermediates in non-heme monooxygenases. We also demonstrated that a single Mn(III)-oxo center that was prepared from water could be converted to a high-spin Mn(V)-oxo species via stepwise oxidation, a process that mimics the oxidative charging of the oxygen-evolving complex (OEC) of photosystem II. Current mechanisms for photosynthetic O-O bond formation invoke a Mn(IV)-oxyl species rather than the isoelectronic Mn(V)-oxo system as the key oxidant based on computational studies. However, there is no experimental information to support the existence of a Mn

  10. Teaching Absolute Value Meaningfully

    ERIC Educational Resources Information Center

    Wade, Angela

    2012-01-01

    What is the meaning of absolute value? And why do teachers teach students how to solve absolute value equations? Absolute value is a concept introduced in first-year algebra and then reinforced in later courses. Various authors have suggested instructional methods for teaching absolute value to high school students (Wei 2005; Stallings-Roberts…

  11. Localized excitations in hydrogen-bonded molecular crystals

    NASA Astrophysics Data System (ADS)

    Alexander, D. M.; Krumhansl, J. A.

    1986-05-01

    Localized excitations analogous to the small Holstein polaron, to localized modes in alkali halides, and to localized excitonic states, are postulated for a set of internal vibrational modes in crystalline acetanilide. The theoretical framework in which one can describe the characteristics of the ir and Raman spectroscopy peaks associated with these localized states is adequately provided by the Davydov model (formally equivalent to the Holstein polaron model). The possible low-lying excitations arising from this model are determined using a variational approach. Hence, the contribution to the spectral function due to each type of excitation can be calculated. The internal modes of chief concern here are the amide-I (CO stretch) and the N-H stretch modes for which we demonstrate consistency of the theoretical model with the available ir data. Past theoretical approaches will be discussed and reasons why one should prefer one description over another will be examined.

  12. Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

    SciTech Connect

    Bresme, F.; Armstrong, J.

    2014-01-07

    We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation.

  13. Eosinophil count - absolute

    MedlinePlus

    Eosinophils; Absolute eosinophil count ... the white blood cell count to give the absolute eosinophil count. ... than 500 cells per microliter (cells/mcL). Normal value ranges may vary slightly among different laboratories. Talk ...

  14. Analyzing the molecular mechanism of lipoprotein localization in Brucella.

    PubMed

    Goolab, Shivani; Roth, Robyn L; van Heerden, Henriette; Crampton, Michael C

    2015-01-01

    Bacterial lipoproteins possess diverse structure and functionality, ranging from bacterial physiology to pathogenic processes. As such many lipoproteins, originating from Brucella are exploited as potential vaccines to countermeasure brucellosis infection in the host. These membrane proteins are translocated from the cytoplasm to the cell membrane where they are anchored peripherally by a multifaceted targeting mechanism. Although much research has focused on the identification and classification of Brucella lipoproteins and their potential use as vaccine candidates for the treatment of Brucellosis, the underlying route for the translocation of these lipoproteins to the outer surface of the Brucella (and other pathogens) outer membrane (OM) remains mostly unknown. This is partly due to the complexity of the organism and evasive tactics used to escape the host immune system, the variation in biological structure and activity of lipoproteins, combined with the complex nature of the translocation machinery. The biosynthetic pathway of Brucella lipoproteins involves a distinct secretion system aiding translocation from the cytoplasm, where they are modified by lipidation, sorted by the lipoprotein localization machinery pathway and thereafter equipped for export to the OM. Surface localized lipoproteins in Brucella may employ a lipoprotein flippase or the β-barrel assembly complex for translocation. This review provides an overview of the characterized Brucella OM proteins that form part of the OM, including a handful of other characterized bacterial lipoproteins and their mechanisms of translocation. Lipoprotein localization pathways in gram negative bacteria will be used as a model to identify gaps in Brucella lipoprotein localization and infer a potential pathway. Of particular interest are the dual topology lipoproteins identified in Escherichia coli and Haemophilus influenza. The localization and topology of these lipoproteins from other gram negative bacteria

  15. Analyzing the molecular mechanism of lipoprotein localization in Brucella

    PubMed Central

    Goolab, Shivani; Roth, Robyn L.; van Heerden, Henriette; Crampton, Michael C.

    2015-01-01

    Bacterial lipoproteins possess diverse structure and functionality, ranging from bacterial physiology to pathogenic processes. As such many lipoproteins, originating from Brucella are exploited as potential vaccines to countermeasure brucellosis infection in the host. These membrane proteins are translocated from the cytoplasm to the cell membrane where they are anchored peripherally by a multifaceted targeting mechanism. Although much research has focused on the identification and classification of Brucella lipoproteins and their potential use as vaccine candidates for the treatment of Brucellosis, the underlying route for the translocation of these lipoproteins to the outer surface of the Brucella (and other pathogens) outer membrane (OM) remains mostly unknown. This is partly due to the complexity of the organism and evasive tactics used to escape the host immune system, the variation in biological structure and activity of lipoproteins, combined with the complex nature of the translocation machinery. The biosynthetic pathway of Brucella lipoproteins involves a distinct secretion system aiding translocation from the cytoplasm, where they are modified by lipidation, sorted by the lipoprotein localization machinery pathway and thereafter equipped for export to the OM. Surface localized lipoproteins in Brucella may employ a lipoprotein flippase or the β-barrel assembly complex for translocation. This review provides an overview of the characterized Brucella OM proteins that form part of the OM, including a handful of other characterized bacterial lipoproteins and their mechanisms of translocation. Lipoprotein localization pathways in gram negative bacteria will be used as a model to identify gaps in Brucella lipoprotein localization and infer a potential pathway. Of particular interest are the dual topology lipoproteins identified in Escherichia coli and Haemophilus influenza. The localization and topology of these lipoproteins from other gram negative bacteria

  16. Quantitative analysis of localized surface plasmons based on molecular probing.

    PubMed

    Deeb, Claire; Bachelot, Renaud; Plain, Jérôme; Baudrion, Anne-Laure; Jradi, Safi; Bouhelier, Alexandre; Soppera, Olivier; Jain, Prashant K; Huang, Libai; Ecoffet, Carole; Balan, Lavinia; Royer, Pascal

    2010-08-24

    We report on the quantitative characterization of the plasmonic optical near-field of a single silver nanoparticle. Our approach relies on nanoscale molecular molding of the confined electromagnetic field by photoactivated molecules. We were able to directly image the dipolar profile of the near-field distribution with a resolution better than 10 nm and to quantify the near-field depth and its enhancement factor. A single nanoparticle spectral signature was also assessed. This quantitative characterization constitutes a prerequisite for developing nanophotonic applications.

  17. Absolute nuclear material assay

    DOEpatents

    Prasad, Manoj K.; Snyderman, Neal J.; Rowland, Mark S.

    2012-05-15

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  18. Absolute nuclear material assay

    DOEpatents

    Prasad, Manoj K.; Snyderman, Neal J.; Rowland, Mark S.

    2010-07-13

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  19. Absolute instability of the Gaussian wake profile

    NASA Technical Reports Server (NTRS)

    Hultgren, Lennart S.; Aggarwal, Arun K.

    1987-01-01

    Linear parallel-flow stability theory has been used to investigate the effect of viscosity on the local absolute instability of a family of wake profiles with a Gaussian velocity distribution. The type of local instability, i.e., convective or absolute, is determined by the location of a branch-point singularity with zero group velocity of the complex dispersion relation for the instability waves. The effects of viscosity were found to be weak for values of the wake Reynolds number, based on the center-line velocity defect and the wake half-width, larger than about 400. Absolute instability occurs only for sufficiently large values of the center-line wake defect. The critical value of this parameter increases with decreasing wake Reynolds number, thereby indicating a shrinking region of absolute instability with decreasing wake Reynolds number. If backflow is not allowed, absolute instability does not occur for wake Reynolds numbers smaller than about 38.

  20. New molecular descriptors based on local properties at the molecular surface and a boiling-point model derived from them.

    PubMed

    Ehresmann, Bernd; de Groot, Marcel J; Alex, Alexander; Clark, Timothy

    2004-01-01

    New molecular descriptors based on statistical descriptions of the local ionization potential, local electron affinity, and the local polarizability at the surface of the molecule are proposed. The significance of these descriptors has been tested by calculating them for the Maybridge database in addition to our set of 26 descriptors reported previously. The new descriptors show little correlation with those already in use. Furthermore, the principal components of the extended set of descriptors for the Maybridge data show that especially the descriptors based on the local electron affinity extend the variance in our set of descriptors, which we have previously shown to be relevant to physical properties. The first nine principal components are shown to be most significant. As an example of the usefulness of the new descriptors, we have set up a QSPR model for boiling points using both the old and new descriptors.

  1. CONNECTING LOCAL STRUCTURE TO INTERFACE FORMATION: A Molecular Scale van der Waals Theory of Nonuniform Liquids

    NASA Astrophysics Data System (ADS)

    Weeks, John D.

    2002-10-01

    This article reviews a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. The method optimally combines two standard approximations, molecular (mean) field theory to describe interface formation and linear response (or Gaussian fluctuation) theory to describe local structure. Accurate results have been found in many different applications in nonuniform simple fluids and these ideas may have important implications for the theory of hydrophobic interactions in water.

  2. Absolute biological needs.

    PubMed

    McLeod, Stephen

    2014-07-01

    Absolute needs (as against instrumental needs) are independent of the ends, goals and purposes of personal agents. Against the view that the only needs are instrumental needs, David Wiggins and Garrett Thomson have defended absolute needs on the grounds that the verb 'need' has instrumental and absolute senses. While remaining neutral about it, this article does not adopt that approach. Instead, it suggests that there are absolute biological needs. The absolute nature of these needs is defended by appeal to: their objectivity (as against mind-dependence); the universality of the phenomenon of needing across the plant and animal kingdoms; the impossibility that biological needs depend wholly upon the exercise of the abilities characteristic of personal agency; the contention that the possession of biological needs is prior to the possession of the abilities characteristic of personal agency. Finally, three philosophical usages of 'normative' are distinguished. On two of these, to describe a phenomenon or claim as 'normative' is to describe it as value-dependent. A description of a phenomenon or claim as 'normative' in the third sense does not entail such value-dependency, though it leaves open the possibility that value depends upon the phenomenon or upon the truth of the claim. It is argued that while survival needs (or claims about them) may well be normative in this third sense, they are normative in neither of the first two. Thus, the idea of absolute need is not inherently normative in either of the first two senses. PMID:23586876

  3. Absolute biological needs.

    PubMed

    McLeod, Stephen

    2014-07-01

    Absolute needs (as against instrumental needs) are independent of the ends, goals and purposes of personal agents. Against the view that the only needs are instrumental needs, David Wiggins and Garrett Thomson have defended absolute needs on the grounds that the verb 'need' has instrumental and absolute senses. While remaining neutral about it, this article does not adopt that approach. Instead, it suggests that there are absolute biological needs. The absolute nature of these needs is defended by appeal to: their objectivity (as against mind-dependence); the universality of the phenomenon of needing across the plant and animal kingdoms; the impossibility that biological needs depend wholly upon the exercise of the abilities characteristic of personal agency; the contention that the possession of biological needs is prior to the possession of the abilities characteristic of personal agency. Finally, three philosophical usages of 'normative' are distinguished. On two of these, to describe a phenomenon or claim as 'normative' is to describe it as value-dependent. A description of a phenomenon or claim as 'normative' in the third sense does not entail such value-dependency, though it leaves open the possibility that value depends upon the phenomenon or upon the truth of the claim. It is argued that while survival needs (or claims about them) may well be normative in this third sense, they are normative in neither of the first two. Thus, the idea of absolute need is not inherently normative in either of the first two senses.

  4. Quantitative Structure-Cytotoxicity Relationship of Bioactive Heterocycles by the Semi-empirical Molecular Orbital Method with the Concept of Absolute Hardness

    NASA Astrophysics Data System (ADS)

    Ishihara, Mariko; Sakagami, Hiroshi; Kawase, Masami; Motohashi, Noboru

    The relationship between the cytotoxicity of N-heterocycles (13 4-trifluoromethylimidazole, 15 phenoxazine and 12 5-trifluoromethyloxazole derivatives), O-heterocycles (11 3-formylchromone and 20 coumarin derivatives) and seven vitamin K2 derivatives against eight tumor cell lines (HSC-2, HSC-3, HSC-4, T98G, HSG, HepG2, HL-60, MT-4) and a maximum of 15 chemical descriptors was investigated using CAChe Worksystem 4.9 project reader. After determination of the conformation of these compounds and approximation to the molecular form present in vivo (biomimetic) by CONFLEX5, the most stable structure was determined by CAChe Worksystem 4.9 MOPAC (PM3). The present study demonstrates the best relationship between the cytotoxic activity and molecular shape or molecular weight of these compounds. Their biological activities can be estimated by hardness and softness, and by using η-χ activity diagrams.

  5. Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy.

    PubMed

    Gao, Xian; Wei, Zhipeng; Zhao, Fenghuan; Yang, Yahui; Chen, Rui; Fang, Xuan; Tang, Jilong; Fang, Dan; Wang, Dengkui; Li, Ruixue; Ge, Xiaotian; Ma, Xiaohui; Wang, Xiaohua

    2016-01-01

    We report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration.

  6. Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy

    NASA Astrophysics Data System (ADS)

    Gao, Xian; Wei, Zhipeng; Zhao, Fenghuan; Yang, Yahui; Chen, Rui; Fang, Xuan; Tang, Jilong; Fang, Dan; Wang, Dengkui; Li, Ruixue; Ge, Xiaotian; Ma, Xiaohui; Wang, Xiaohua

    2016-07-01

    We report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration.

  7. Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy

    PubMed Central

    Gao, Xian; Wei, Zhipeng; Zhao, Fenghuan; Yang, Yahui; Chen, Rui; Fang, Xuan; Tang, Jilong; Fang, Dan; Wang, Dengkui; Li, Ruixue; Ge, Xiaotian; Ma, Xiaohui; Wang, Xiaohua

    2016-01-01

    We report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration. PMID:27381641

  8. Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy.

    PubMed

    Gao, Xian; Wei, Zhipeng; Zhao, Fenghuan; Yang, Yahui; Chen, Rui; Fang, Xuan; Tang, Jilong; Fang, Dan; Wang, Dengkui; Li, Ruixue; Ge, Xiaotian; Ma, Xiaohui; Wang, Xiaohua

    2016-01-01

    We report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration. PMID:27381641

  9. Long-range orientational order, local-field anisotropy, and mean molecular polarizability in liquid crystals

    SciTech Connect

    Aver'yanov, E. M.

    2009-01-15

    The problems on the relation of the mean effective molecular polarizability {gamma}-bar to the long-range orientational order of molecules (the optical anisotropy of the medium) in uniaxial and biaxial liquid crystals, the local anisotropy on mesoscopic scales, and the anisotropy of the Lorentz tensor L and the local-field tensor f are formulated and solved. It is demonstrated that the presence of the long-range orientational order of molecules in liquid crystals imposes limitations from below on the molecular polarizability {gamma}-bar, which differs for uniaxial and biaxial liquid crystals. The relation between the local anisotropy and the molecular polarizability {gamma}-bar is investigated for calamitic and discotic uniaxial liquid crystals consisting of lath- and disk-shaped molecules. These liquid crystals with identical macroscopic symmetry differ in the local anisotropy and the relationships between the components L{sub parallel} < L{sub perpendicular} , f{sub parallel} < f{sub perpendicular} (calamitic) and L{sub parallel} > L{sub perpendicular} , f{sub parallel} > f{sub perpendicular} (discotic) for an electric field oriented parallel and perpendicular to the director. The limitations from below and above on the molecular polarizability {gamma}-bar due to the anisotropy of the tensors L and f are established for liquid crystals of both types. These limitations indicate that the molecular polarizability {gamma}-bar depends on the phase state and the temperature. The factors responsible for the nonphysical consequences of the local-field models based on the approximation {gamma}-bar = const are revealed. The theoretical inferences are confirmed by the experimental data for a number of calamitic nematic liquid crystals with different values of birefringence and the discotic liquid crystal Col{sub ho}.

  10. MolLoc: a web tool for the local structural alignment of molecular surfaces.

    PubMed

    Angaran, Stefano; Bock, Mary Ellen; Garutti, Claudio; Guerra, Concettina

    2009-07-01

    MolLoc stands for Molecular Local surface comparison, and is a web server for the structural comparison of molecular surfaces. Given two structures in PDB format, the user can compare their binding sites, cavities or any arbitrary residue selection. Moreover, the web server allows the comparison of a query structure with a list of structures. Each comparison produces a structural alignment that maximizes the extension of the superimposition of the surfaces, and returns the pairs of atoms with similar physicochemical properties that are close in space after the superimposition. Based on this subset of atoms sharing similar physicochemical properties a new rototranslation is derived that best superimposes them. MolLoc approach is both local and surface-oriented, and therefore it can be particularly useful when testing if molecules with different sequences and folds share any local surface similarity. The MolLoc web server is available at http://bcb.dei.unipd.it/MolLoc.

  11. Absolute shielding scale for 31P from gas-phase NMR studies

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; De Dios, Angel; Keith Jameson, A.

    1990-04-01

    Differences in the 31P nuclear shielding in the zero-pressure limit have been measured in seven compounds. An absolute 31P shielding scale based on the PH 3 molecular beam data is established and the absolute shielding of the standard liquid reference (85% aqueous H 3PO 4) is found to be 328.35 ppm, based on PH 3 being 594.45 ± 0.63 ppm. Comparisons with ab initio calculations show that calculations using local origins (the IGLO method) are in good agreement with experiment.

  12. Molecular Gas and Star Formation in Local Early-type Galaxies

    NASA Astrophysics Data System (ADS)

    Bureau, M.; Davis, T. A.; Alatalo, K.; Crocker, A. F.; Blitz, L.; Young, L. M.; Combes, F.; Bois, M.; Bournaud, F.; Cappellari, M.; Davies, R. L.; de Zeeuw, P. T.; Duc, P.-A.; Emsellem, E.; Khochfar, S.; Krajnović, D.; Kuntschner, H.; Lablanche, P.-Y.; McDermid, R. M.; Morganti, R.; Naab, T.; Oosterloo, T.; Sarzi, M.; Scott, N.; Serra, P.; Weijmans, A.

    2011-12-01

    The molecular gas content of local early-type galaxies is constrained and discussed in relation to their evolution. First, as part of the ATLAS3D survey, we present the first complete, large (260 objects), volume-limited single-dish survey of CO in normal local early-type galaxies. We find a surprisingly high detection rate of 22%, independent of luminosity and at best weakly dependent on environment. Second, the extent of the molecular gas is constrained with CO synthesis imaging, and a variety of morphologies is revealed. The kinematics of the molecular gas and stars are often misaligned, implying an external gas origin in over a third of the systems, although this behaviour is drastically diffferent between field and cluster environments. Third, many objects appear to be in the process of forming regular kpc-size decoupled disks, and a star formation sequence can be sketched by piecing together multi-wavelength information on the molecular gas, current star formation, and young stars. Last, early-type galaxies do not seem to systematically obey all our usual prejudices regarding star formation, following the standard Schmidt-Kennicutt law but not the far infrared-radio correlation. This may suggest a greater diversity in star formation processes than observed in disk galaxies. Using multiple molecular tracers, we are thus starting to probe the physical conditions of the cold gas in early-types.

  13. The absolute path command

    2012-05-11

    The ap command traveres all symlinks in a given file, directory, or executable name to identify the final absolute path. It can print just the final path, each intermediate link along with the symlink chan, and the permissions and ownership of each directory component in the final path. It has functionality similar to "which", except that it shows the final path instead of the first path. It is also similar to "pwd", but it canmore » provide the absolute path to a relative directory from the current working directory.« less

  14. The absolute path command

    SciTech Connect

    Moody, A.

    2012-05-11

    The ap command traveres all symlinks in a given file, directory, or executable name to identify the final absolute path. It can print just the final path, each intermediate link along with the symlink chan, and the permissions and ownership of each directory component in the final path. It has functionality similar to "which", except that it shows the final path instead of the first path. It is also similar to "pwd", but it can provide the absolute path to a relative directory from the current working directory.

  15. Edge localized mode characteristics during edge localized mode mitigation by supersonic molecular beam injection in Korea Superconducting Tokamak Advanced Research

    NASA Astrophysics Data System (ADS)

    Lee, H. Y.; Hahn, S. H.; Ghim, Y.-C.; Bak, J. G.; Lee, J. H.; Ko, W. H.; Lee, K. D.; Lee, S. H.; Lee, H. H.; Juhn, J.-W.; Kim, H. S.; Yoon, S. W.; Han, H.; Hong, J. H.; Jang, J. H.; Park, J. S.; Choe, Wonho

    2015-12-01

    It has been reported that supersonic molecular beam injection (SMBI) is an effective means of edge localized mode (ELM) mitigation. This paper newly reports the changes in the ELM, plasma profiles, and fluctuation characteristics during ELM mitigation by SMBI in Korea Superconducting Tokamak Advanced Research. During the mitigated ELM phase, the ELM frequency increased by a factor of 2-3 and the ELM size, which was estimated from the Dα amplitude, the fractional changes in the plasma-stored energy and the line-averaged electron density, and divertor heat flux during an ELM burst, decreased by a factor of 0.34-0.43. Reductions in the electron and ion temperatures rather than in the electron density were observed during the mitigated ELM phase. In the natural ELM phase, frequency chirping of the plasma fluctuations was observed before the ELM bursts; however, the ELM bursts occurred without changes in the plasma fluctuation frequency in the mitigated ELM phase.

  16. Weak links between fast mobility and local structure in molecular and atomic liquids

    SciTech Connect

    Bernini, S.; Puosi, F.; Leporini, D.

    2015-03-28

    We investigate by molecular-dynamics simulations, the fast mobility—the rattling amplitude of the particles temporarily trapped by the cage of the neighbors—in mildly supercooled states of dense molecular (linear trimers) and atomic (binary mixtures) liquids. The mixture particles interact by the Lennard-Jones potential. The non-bonded particles of the molecular system are coupled by the more general Mie potential with variable repulsive and attractive exponents in a range which is a characteristic of small n-alkanes and n-alcohols. Possible links between the fast mobility and the geometry of the cage (size and shape) are searched. The correlations on a per-particle basis are rather weak. Instead, if one groups either the particles in fast-mobility subsets or the cages in geometric subsets, the increase of the fast mobility with both the size and the asphericity of the cage is revealed. The observed correlations are weak and differ in states with equal relaxation time. Local forces between a tagged particle and the first-neighbour shell do not correlate with the fast mobility in the molecular liquid. It is concluded that the cage geometry alone is unable to provide a microscopic interpretation of the known, universal link between the fast mobility and the slow structural relaxation. We suggest that the particle fast dynamics is affected by regions beyond the first neighbours, thus supporting the presence of collective, extended fast modes.

  17. General theory of electronic transport in molecular crystals. I. Local linear electron-phonon coupling

    NASA Astrophysics Data System (ADS)

    Silbey, R.; Munn, R. W.

    1980-02-01

    An improved general theory of electronic transport in molecular crystals with local linear electron-phonon coupling is presented. It is valid for arbitrary electronic and phonon bandwidths and for arbitrary electron-phonon coupling strength, yielding small-polaron theory for narrow electronic bands and strong coupling, and semiconductor theory for wide electronic bands and weak coupling. Detailed results are derived for electronic excitations fully clothed with phonons and having a bandwidth no larger than the phonon frequency; the electronic and phonon densities of states are taken as Gaussian for simplicity. The dependence of the diffusion coefficient on temperature and on the other parameters is analyzed thoroughly. The calculated behavior provides a rational interpretation of observed trends in the magnitude and temperature dependence of charge-carrier drift mobilities in molecular crystals.

  18. Edge localized mode characteristics during edge localized mode mitigation by supersonic molecular beam injection in Korea Superconducting Tokamak Advanced Research

    SciTech Connect

    Lee, H. Y.; Hong, J. H.; Jang, J. H.; Park, J. S.; Choe, Wonho; Hahn, S. H.; Bak, J. G.; Lee, J. H.; Ko, W. H.; Lee, K. D.; Lee, S. H.; Lee, H. H.; Juhn, J.-W.; Kim, H. S.; Yoon, S. W.; Han, H.; Ghim, Y.-C.

    2015-12-15

    It has been reported that supersonic molecular beam injection (SMBI) is an effective means of edge localized mode (ELM) mitigation. This paper newly reports the changes in the ELM, plasma profiles, and fluctuation characteristics during ELM mitigation by SMBI in Korea Superconducting Tokamak Advanced Research. During the mitigated ELM phase, the ELM frequency increased by a factor of 2–3 and the ELM size, which was estimated from the D{sub α} amplitude, the fractional changes in the plasma-stored energy and the line-averaged electron density, and divertor heat flux during an ELM burst, decreased by a factor of 0.34–0.43. Reductions in the electron and ion temperatures rather than in the electron density were observed during the mitigated ELM phase. In the natural ELM phase, frequency chirping of the plasma fluctuations was observed before the ELM bursts; however, the ELM bursts occurred without changes in the plasma fluctuation frequency in the mitigated ELM phase.

  19. The effects of flow-inhomogeneities on molecular cloud formation: Local versus global collapse

    SciTech Connect

    Carroll-Nellenback, Jonathan J.; Frank, Adam; Heitsch, Fabian

    2014-07-20

    Observational evidence from local star-forming regions mandates that star formation occurs shortly after, or even during, molecular cloud formation. Models of molecular cloud formation in large-scale converging flows have identified the physical mechanisms driving the necessary rapid fragmentation. They also point to global gravitational collapse driving supersonic turbulence in molecular clouds. Previous cloud formation models have focused on turbulence generation, gravitational collapse, magnetic fields, and feedback. Here, we explore the effect of structure in the flow on the resulting clouds and the ensuing gravitational collapse. We compare two extreme cases, one with a collision between two smooth streams, and one with streams containing small clumps. We find that structured converging flows lead to a delay of local gravitational collapse ({sup c}ore formation{sup )}. Hence, the cloud has more time to accumulate mass, eventually leading to a strong global collapse, and thus to a high core formation rate. Uniform converging flows fragment hydrodynamically early on, leading to the rapid onset of local gravitational collapse and an overall low core formation rate. This is also mirrored in the core mass distribution: the uniform initial conditions lead to more low-mass cores than the clumpy initial conditions. Kinetic (E{sub k} ) and gravitational energy (E{sub g} ) budgets suggest that collapse is only prevented for E{sub k} >> E{sub g} , which occurs for large scales in the smooth flow, and for small scales for the clumpy flow. Whenever E{sub k} ≈ E{sub g} , we observe gravitational collapse on those scales. Signatures of chemical abundance variations evolve differently for the gas phase and for the stellar population. For smooth flows, the forming cloud is well mixed, while its stellar population retains more information about the initial metallicities. For clumpy flows, the gas phase is less well mixed, while the stellar population has lost most of the

  20. OT1_nlu_1: Herschel Spectroscopic Survey of Warm Molecular Gas in Local Luminous Infrared Galaxies

    NASA Astrophysics Data System (ADS)

    Lu, N.

    2010-07-01

    We propose to survey CO spectral line energy distribution (SLED), from J=4-3 up to J=13-12, on 93 local luminous infrared galaxies (LIRGs; L_{IR} > 1.0E11 L_{sun}) with Herschel SPIRE FTS spectrometer. These galaxies, plus 32 additional LIRGs that will have similar data from existing Herschel programs (mainly the HerCULES project), form a flux-limited subset of the Great Observatories All-Sky LIRGs Survey (GOALS) sample. Our proposal is built on the legacy of GOALS and extends beyond the existing Herschel HerCULES program, which emphasizes more on ULIRGs, to a much needed sample coverage of the more numerous and diverse population of less luminous LIRGs. The data from the proposed observations will not only provide much needed local LIRG templates for future ALMA studies of high-redshift counterparts, but also lend us a powerful diagnostic tool to probe the warm and dense molecular gas that are more closely related to the starburst or AGN activity in the nuclei of LIRGs. The data from this proposal will provide important statistical clues to the interplay between the cold and warm molecular gas, IR luminosity, star formation rate and efficiency, and the diverse properties of LIRGs. Specifically, using the homogeneous CO SLED data from this proposal, together with ground-base, low-order CO line data (mainly J=1-0) and other data that have been compiled for the GOALS sample, we will address the following questions: (1) What is the dominant nuclear power source in individual sample galaxy: starburst or AGN? (2) What are the typical physical properties of warm molecular gas in the nuclei of LIRGs? (3) How do the nuclear warm gas components correlate to the cold gas component, star formation rate and efficiency, dust temperature, etc? and (4) How does molecular gas excitation change along a merger sequence?

  1. Non-linear non-local molecular electrodynamics with nano-optical fields.

    PubMed

    Chernyak, Vladimir Y; Saurabh, Prasoon; Mukamel, Shaul

    2015-10-28

    The interaction of optical fields sculpted on the nano-scale with matter may not be described by the dipole approximation since the fields may vary appreciably across the molecular length scale. Rather than incrementally adding higher multipoles, it is advantageous and more physically transparent to describe the optical process using non-local response functions that intrinsically include all multipoles. We present a semi-classical approach for calculating non-local response functions based on the minimal coupling Hamiltonian. The first, second, and third order response functions are expressed in terms of correlation functions of the charge and the current densities. This approach is based on the gauge invariant current rather than the polarization, and on the vector potential rather than the electric and magnetic fields.

  2. Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity.

    PubMed

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

    Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

  3. Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.

    PubMed

    Feig, Michael

    2016-07-25

    A method for the local refinement of protein structures that targets improvements in local stereochemistry while preserving the overall fold is presented. The method uses force field-based minimization and sampling via molecular dynamics simulations with a modified force field to bring bonds, angles, and torsion angles into an acceptable range for high-resolution protein structures. The method is implemented in the locPREFMD web server and was tested on computational models submitted to CASP11. Using MolProbity scores as the main assessment criterion, the locPREFMD method significantly improves the stereochemical quality of given input models close to the quality expected for experimental structures while maintaining the Cα coordinates of the initial model.

  4. Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.

    PubMed

    Feig, Michael

    2016-07-25

    A method for the local refinement of protein structures that targets improvements in local stereochemistry while preserving the overall fold is presented. The method uses force field-based minimization and sampling via molecular dynamics simulations with a modified force field to bring bonds, angles, and torsion angles into an acceptable range for high-resolution protein structures. The method is implemented in the locPREFMD web server and was tested on computational models submitted to CASP11. Using MolProbity scores as the main assessment criterion, the locPREFMD method significantly improves the stereochemical quality of given input models close to the quality expected for experimental structures while maintaining the Cα coordinates of the initial model. PMID:27380201

  5. Non-linear non-local molecular electrodynamics with nano-optical fields.

    PubMed

    Chernyak, Vladimir Y; Saurabh, Prasoon; Mukamel, Shaul

    2015-10-28

    The interaction of optical fields sculpted on the nano-scale with matter may not be described by the dipole approximation since the fields may vary appreciably across the molecular length scale. Rather than incrementally adding higher multipoles, it is advantageous and more physically transparent to describe the optical process using non-local response functions that intrinsically include all multipoles. We present a semi-classical approach for calculating non-local response functions based on the minimal coupling Hamiltonian. The first, second, and third order response functions are expressed in terms of correlation functions of the charge and the current densities. This approach is based on the gauge invariant current rather than the polarization, and on the vector potential rather than the electric and magnetic fields. PMID:26520498

  6. Photoluminescence of localized excitons in ZnCdO thin films grown by molecular beam epitaxy

    NASA Astrophysics Data System (ADS)

    Wu, T. Y.; Huang, Y. S.; Hu, S. Y.; Lee, Y. C.; Tiong, K. K.; Chang, C. C.; Shen, J. L.; Chou, W. C.

    2016-07-01

    We have investigated the luminescence characteristics of Zn1-xCdxO thin films with different Cd contents grown by molecular beam epitaxy system. The temperature-dependent photoluminescence (PL) and excitation power-dependent PL spectra were measured to clarify the luminescence mechanisms of the Zn1-xCdxO thin films. The peak energy of the Zn1-xCdxO thin films with increasing the Cd concentration is observed as redshift and can be fitted by the quadratic function of alloy content. The broadened full-width at half-maximum (FWHM) estimated from the 15 K PL spectra as a function of Cd content shows a larger deviation between the experimental values and theoretical curve, which indicates that experimental FWHM values are affected not only by alloy compositional disorder but also by localized excitons occupying states in the tail of the density of states. The Urbach energy determined from an analysis of the lineshape of the low-energy side of the PL spectrum and the degree of localization effect estimated from the temperature-induced S-shaped PL peak position described an increasing mean exciton-localization effects in ZnCdO films with increasing the Cd content. In addition, the PL intensity and peak position as a function of excitation power are carried out to clarify the types of radiative recombination and the effects of localized exciton in the ZnCdO films with different Cd contents.

  7. ABSOLUTE POLARIMETRY AT RHIC.

    SciTech Connect

    OKADA; BRAVAR, A.; BUNCE, G.; GILL, R.; HUANG, H.; MAKDISI, Y.; NASS, A.; WOOD, J.; ZELENSKI, Z.; ET AL.

    2007-09-10

    Precise and absolute beam polarization measurements are critical for the RHIC spin physics program. Because all experimental spin-dependent results are normalized by beam polarization, the normalization uncertainty contributes directly to final physics uncertainties. We aimed to perform the beam polarization measurement to an accuracy Of {Delta}P{sub beam}/P{sub beam} < 5%. The absolute polarimeter consists of Polarized Atomic Hydrogen Gas Jet Target and left-right pairs of silicon strip detectors and was installed in the RHIC-ring in 2004. This system features proton-proton elastic scattering in the Coulomb nuclear interference (CNI) region. Precise measurements of the analyzing power A{sub N} of this process has allowed us to achieve {Delta}P{sub beam}/P{sub beam} = 4.2% in 2005 for the first long spin-physics run. In this report, we describe the entire set up and performance of the system. The procedure of beam polarization measurement and analysis results from 2004-2005 are described. Physics topics of AN in the CNI region (four-momentum transfer squared 0.001 < -t < 0.032 (GeV/c){sup 2}) are also discussed. We point out the current issues and expected optimum accuracy in 2006 and the future.

  8. Structural effects of the local anesthetic bupivacaine hydrochloride on the human erythrocyte membrane and molecular models.

    PubMed

    Suwalsky, Mario; Schneider, Carlos; Villena, Fernando; Norris, Beryl; Cárdenas, Hernán; Cuevas, Francisco; Sotomayor, Carlos P

    2002-01-01

    The interaction of the local anesthetic bupivacaine with the human erythrocyte membrane and molecular models is described. The latter consisted of isolated unsealed human erythrocyte membranes (IUM), large unilamellar vesicles (LUV) of dimyristoylphosphatidylcholine (DMPC), and phospholipid multilayers built-up of DMPC and dimyristoylphosphatidylethanolamine (DMPE), representatives of phospholipid classes located in the outer and inner monolayers of the human erythrocyte membrane, respectively. Optical and scanning electron microscopy revealed that bupivacaine induced erythrocyte spheroechinocytosis. According to the bilayer couple hypothesis, this result implied that bupivacaine inserted in the outer monolayer of the erythrocyte membrane. Experiments performed on IUM and DMPC LUV by fluorescence spectroscopy and X-ray diffraction on DMPC and DMPE multilayers confirmed this result. Changes in the molecular organization of membranes alter lipid-protein interactions and induce functional perturbation of membrane proteins such as Na(+) channels. Since local anesthetics may control the influx of Na(+) into the human erythrocyte, in order to relate the structural perturbations induced by bupivacaine in these systems to Na(+) transport, the interaction of this anesthetic with isolated toad skin was also studied. Electrophysiological measurements indicated a significant decrease in the potential difference and in the short-circuit current of the skin after the application of the anesthetic, reflecting inhibition of the active transport of ions. These results suggest that bupivacaine-induced conformational changes of the lipid molecules alter the lipid-protein boundaries of the outer moiety of the erythrocyte membrane, thus interfering with the function of neighboring sodium channels. PMID:12482399

  9. Comparative study of local structure of two cyanobiphenyl liquid crystals by molecular dynamics method

    SciTech Connect

    Gerts, Egor D. Komolkin, Andrei V.; Burmistrov, Vladimir A.; Alexandriysky, Victor V.; Dvinskikh, Sergey V.

    2014-08-21

    Fully-atomistic molecular dynamics simulations were carried out on two similar cyanobiphenyl nematogens, HO-6OCB and 7OCB, in order to study effects of hydrogen bonds on local structure of liquid crystals. Comparable length of these two molecules provides more evident results on the effects of hydrogen bonding. The analysis of radial and cylindrical distribution functions clearly shows the differences in local structure of two mesogens. The simulations showed that anti-parallel alignment is preferable for the HO-6OCB. Hydrogen bonds between OH-groups are observed for 51% of HO-6OCB molecules, while hydrogen bonding between CN- and OH-groups occurs only for 16% of molecules. The lifetimes of H-bonds differ due to different mobility of molecular fragments (50 ps for N⋅⋅⋅H–O and 41 ps for O⋅⋅⋅H–O). Although the standard Optimized Potentials for Liquid Simulations - All-Atom force field cannot reproduce some experimental parameters quantitatively (order parameters are overestimated, diffusion coefficients are not reproduced well), the comparison of relative simulated results for the pair of mesogens is nevertheless consistent with the same relative experimental parameters. Thus, the comparative study of simulated and experimental results for the pair of similar liquid crystals still can be assumed plausible.

  10. A localized momentum constraint for non-equilibrium molecular dynamics simulations.

    PubMed

    Smith, E R; Heyes, D M; Dini, D; Zaki, T A

    2015-02-21

    A method which controls momentum evolution in a sub-region within a molecular dynamics simulation is derived from Gauss's principle of least constraint. The technique for localization is founded on the equations by Irving and Kirkwood [J. Chem. Phys. 18, 817 (1950)] expressed in a weak form according to the control volume (CV) procedure derived by Smith et al. [Phys. Rev. E. 85, 056705 (2012)]. A term for the advection of molecules appears in the derived constraint and is shown to be essential in order to exactly control the time evolution of momentum in the subvolume. The numerical procedure converges the total momentum in the CV to the target value to within machine precision in an iterative manner. The localized momentum constraint can prescribe essentially arbitrary flow fields in non-equilibrium molecular dynamics simulations. The methodology also forms a rigorous mathematical framework for introducing coupling constraints at the boundary between continuum and discrete systems. This functionality is demonstrated with a boundary-driven flow test case.

  11. Local Elastic Constants for Epoxy-Nanotube Composites from Molecular Dynamics Simulation

    NASA Technical Reports Server (NTRS)

    Frankland, S. J. V.; Gates, T. S.

    2007-01-01

    A method from molecular dynamics simulation is developed for determining local elastic constants of an epoxy/nanotube composite. The local values of C11, C33, K12, and K13 elastic constants are calculated for an epoxy/nanotube composite as a function of radial distance from the nanotube. While the results possess a significant amount of statistical uncertainty resulting from both the numerical analysis and the molecular fluctuations during the simulation, the following observations can be made. If the size of the region around the nanotube is increased from shells of 1 to 6 in thickness, then the scatter in the data reduces enough to observe trends. All the elastic constants determined are at a minimum 20 from the center of the nanotube. The C11, C33, and K12 follow similar trends as a function of radial distance from the nanotube. The K13 decreases greater distances from the nanotube and becomes negative which may be a symptom of the statistical averaging.

  12. Basis set effects on frontier molecular orbital energies and energy gaps: a comparative study between plane waves and localized basis functions in molecular systems.

    PubMed

    Matus, Myrna H; Garza, Jorge; Galván, Marcelo

    2004-06-01

    In order to study the Kohn-Sham frontier molecular orbital energies in the complete basis limit, a comparative study between localized functions and plane waves, obtained with the local density approximation exchange-correlation functional is made. The analyzed systems are ethylene and butadiene, since they are theoretical and experimentally well characterized. The localized basis sets used are those developed by Dunning. For the plane-waves method, the pseudopotential approximation is employed. The results obtained by the localized basis sets suggest that it is possible to get an estimation of the orbital energies in the limit of the complete basis set, when the basis set size is large. It is shown that the frontier molecular orbital energies and the energy gaps obtained with plane waves are similar to those obtained with a large localized basis set, when the size of the supercell and the plane-wave expansion have been appropriately calibrated.

  13. Molecular adsorbates as probes of the local properties of doped graphene

    PubMed Central

    Pham, Van Dong; Joucken, Frédéric; Repain, Vincent; Chacon, Cyril; Bellec, Amandine; Girard, Yann; Rousset, Sylvie; Sporken, Robert; Santos, Maria Cristina dos; Lagoute, Jérôme

    2016-01-01

    Graphene-based sensors are among the most promising of graphene’s applications. The ability to signal the presence of molecular species adsorbed on this atomically thin substrate has been explored from electric measurements to light scattering. Here we show that the adsorbed molecules can be used to sense graphene properties. The interaction of porphyrin molecules with nitrogen-doped graphene has been investigated using scanning tunneling microscopy and ab initio calculations. Molecular manipulation was used to reveal the surface below the adsorbed molecules allowing to achieve an atomic-scale measure of the interaction of molecules with doped graphene. The adsorbate’s frontier electronic states are downshifted in energy as the molecule approaches the doping site, with largest effect when the molecule sits over the nitrogen dopant. Theoretical calculations showed that, due to graphene’s high polarizability, the adsorption of porphyrin induces a charge rearrangement on the substrate similar to the image charges on a metal. This charge polarization is enhanced around nitrogen site, leading to an increased interaction of molecules with their image charges on graphene. Consequently, the molecular states are stabilized and shift to lower energies. These findings reveal the local variation of polarizability induced by nitrogen dopant opening new routes towards the electronic tuning of graphene. PMID:27097555

  14. Molecular organization, localization and orientation of antifungal antibiotic amphotericin B in a single lipid bilayer

    PubMed Central

    Grudzinski, Wojciech; Sagan, Joanna; Welc, Renata; Luchowski, Rafal; Gruszecki, Wieslaw I.

    2016-01-01

    Amphotericin B is a popular antifungal antibiotic, a gold standard in treatment of systemic mycotic infections, due to its high effectiveness. On the other hand, applicability of the drug is limited by its considerable toxicity to patients. Biomembranes are a primary target of physiological activity of amphotericin B and both the pharmacologically desired and toxic side effects of the drug relay on its molecular organization in the lipid phase. In the present work, molecular organization, localization and orientation of amphotericin B, in a single lipid bilayer system, was analysed simultaneously, thanks to application of a confocal fluorescence lifetime imaging microscopy of giant unilamellar vesicles. The results show that the presence of sterols, in the lipid phase, promotes formation of supramolecular structures of amphotericin B and their penetration into the membrane hydrophobic core. The fact that such an effect is substantially less pronounced in the case of cholesterol than ergosterol, the sterol of fungal membranes, provides molecular insight into the selectivity of the drug. PMID:27620838

  15. Molecular organization, localization and orientation of antifungal antibiotic amphotericin B in a single lipid bilayer.

    PubMed

    Grudzinski, Wojciech; Sagan, Joanna; Welc, Renata; Luchowski, Rafal; Gruszecki, Wieslaw I

    2016-01-01

    Amphotericin B is a popular antifungal antibiotic, a gold standard in treatment of systemic mycotic infections, due to its high effectiveness. On the other hand, applicability of the drug is limited by its considerable toxicity to patients. Biomembranes are a primary target of physiological activity of amphotericin B and both the pharmacologically desired and toxic side effects of the drug relay on its molecular organization in the lipid phase. In the present work, molecular organization, localization and orientation of amphotericin B, in a single lipid bilayer system, was analysed simultaneously, thanks to application of a confocal fluorescence lifetime imaging microscopy of giant unilamellar vesicles. The results show that the presence of sterols, in the lipid phase, promotes formation of supramolecular structures of amphotericin B and their penetration into the membrane hydrophobic core. The fact that such an effect is substantially less pronounced in the case of cholesterol than ergosterol, the sterol of fungal membranes, provides molecular insight into the selectivity of the drug. PMID:27620838

  16. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    PubMed

    Genoni, Alessandro

    2013-07-01

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  17. Radiative interactions in molecular gases under local and nonlocal thermodynamic equilibrium conditions

    NASA Technical Reports Server (NTRS)

    Tiwari, S. N.; Jha, M. K.

    1993-01-01

    Basic formulations, analyses, and numerical procedures are presented to investigate radiative heat interactions in diatomic and polyatomic gases under local and nonlocal thermodynamic equilibrium conditions. Essential governing equations are presented for both gray and nongray gases. Information is provided on absorption models, relaxation times, and transfer equations. Radiative flux equations are developed which are applicable under local and nonlocal thermodynamic equilibrium conditions. The problem is solved for fully developed laminar incompressible flows between two parallel plates under the boundary condition of a uniform surface heat flux. For specific applications, three diatomic and three polyatomic gases are considered. The results are obtained numerically by employing the method of variation of parameters. The results are compared under local and nonlocal thermodynamic equilibrium conditions at different temperature and pressure conditions. Both gray and nongray studies are conducted extensively for all molecular gases considered. The particular gases selected for this investigation are CO, NO, OH, CO2, H2O, and CH4. The temperature and pressure range considered are 300-2000 K and 0.1-10 atmosphere, respectively. In general, results demonstrate that the gray gas approximation overestimates the effect of radiative interaction for all conditions. The conditions of NLTE, however, result in underestimation of radiative interactions. The method developed for this study can be extended to solve complex problems of radiative heat transfer involving nonequilibrium phenomena.

  18. Molecular dynamics simulations of the local structures and transport coefficients of molten alkali chlorides.

    PubMed

    Wang, Jia; Sun, Ze; Lu, Guimin; Yu, Jianguo

    2014-08-28

    Systematic results from molecular dynamics simulations of molten alkali chlorides (ACl) serials are presented in detail in this paper. The effects of temperature and cationic size on the structures and transport properties of molten salts have been investigated and analyzed. The local structures of molten ACl have been studied via the analysis of radial distribution functions and angular distribution functions. The coordination number of ACl decreases when ACl melts from solid and increases as cationic radius increases. Molten LiCl takes a distorted tetrahedral complex as the microconfiguration, while other melts have the tendency to keep the original local structure of the corresponding crystal. Temperature has no significant effect on the local structures of molten ACls. The results also show that the Tosi-Fumi potential predicts positive temperature dependences for self-diffusion coefficients and ionic conductivity, and negative temperature dependences for both viscosity and thermal conductivity of molten ACls. Ionic diffusivity decreases as cationic radius increases from LiCl to CsCl. The simulation results are in agreement with the experimental data available in the literature.

  19. Absolute Equilibrium Entropy

    NASA Technical Reports Server (NTRS)

    Shebalin, John V.

    1997-01-01

    The entropy associated with absolute equilibrium ensemble theories of ideal, homogeneous, fluid and magneto-fluid turbulence is discussed and the three-dimensional fluid case is examined in detail. A sigma-function is defined, whose minimum value with respect to global parameters is the entropy. A comparison is made between the use of global functions sigma and phase functions H (associated with the development of various H-theorems of ideal turbulence). It is shown that the two approaches are complimentary though conceptually different: H-theorems show that an isolated system tends to equilibrium while sigma-functions allow the demonstration that entropy never decreases when two previously isolated systems are combined. This provides a more complete picture of entropy in the statistical mechanics of ideal fluids.

  20. Local Platinum Environments in a Solid Analogue of the Molecular Periana Catalyst

    DOE PAGES

    Soorholtz, Mario; Jones, Louis C.; Samuelis, Dominik; Weidenthaler, Claudia; White, Robin J.; Titirici, Maria-Magdalena; Cullen, David A.; Zimmermann, Tobias; Antonietti, Markus; Maier, Joachim; et al

    2016-02-16

    Combining advantages of homogeneous and heterogeneous catalysis by incorporating active species on a solid support is often an effective strategy for improving overall catalyst performance, although the influences of the support are generally challenging to establish, especially at a molecular level. In this paper, we report the local compositions, and structures of platinum species incorporated into covalent triazine framework (Pt-CTF) materials, a solid analogue of the molecular Periana catalyst, Pt(bpym)Cl2, both of which are active for the selective oxidation of methane in the presence of concentrated sulfuric acid. By using a combination of solid-state 195Pt nuclear magnetic resonance (NMR) spectroscopy,more » aberration-corrected scanning transmission electron microscopy (AC-STEM), X-ray photoelectron spectroscopy (XPS), and X-ray absorption spectroscopy (XAS), important similarities and differences are observed between the Pt-CTF and Periana catalysts, which are likely related to their respective macroscopic reaction properties. In particular, wide-line solid-state 195Pt NMR spectra enable direct measurement, identification, and quantification of distinct platinum species in as-synthesized and used Pt-CTF catalysts. The results indicate that locally ordered and disordered Pt sites are present in as-synthesized Pt-CTF, with the former being similar to one of the two crystallographically distinct Pt sites in crystalline Pt(bpym)Cl2. A distribution of relatively disordered Pt moieties is also present in the used catalyst, among which are the principal active sites. Similarly XAS shows good agreement between the measured data of Pt-CTF and a theoretical model based on Pt(bpym)Cl2. Analyses of the absorption spectra of Pt-CTF used for methane oxidation suggests ligand exchange, as predicted for the molecular catalyst. XPS analyses of Pt(bpym)Cl2, Pt-CTF, as well as the unmodified ligands, further corroborate platinum coordination by pyridinic N atoms

  1. Combination of cross-sectional and molecular imaging studies in the localization of gastroenteropancreatic neuroendocrine tumors.

    PubMed

    Toumpanakis, Christos; Kim, Michelle K; Rinke, Anja; Bergestuen, Deidi S; Thirlwell, Christina; Khan, Mohid S; Salazar, Ramon; Oberg, Kjell

    2014-01-01

    Molecular imaging modalities exploit aspects of neuroendocrine tumors (NET) pathophysiology for both diagnostic imaging and therapeutic purposes. The characteristic metabolic pathways of NET determine which tracers are useful for their visualization. In this review, we summarize the diagnostic value of all available molecular imaging studies, present data about their use in daily practice in NET centers globally, and finally make recommendations about the appropriate use of those modalities in specific clinical scenarios. Somatostatin receptor scintigraphy (SRS) continues to have a central role in the diagnostic workup of patients with NET, as it is also widely available. However, and despite the lack of prospective randomized studies, many NET experts predict that Gallium-68 ((68)Ga)-DOTA positron emission tomography (PET) techniques may replace SRS in the future, not only because of their technical advantages, but also because they are superior in patients with small-volume disease, in patients with skeletal metastases, and in those with occult primary tumors. Carbon-11 ((11)C)-5-hydroxy-L-tryptophan (5-HTP) PET and (18)F-dihydroxyphenylalanine ((18)F-DOPA) PET are new molecular imaging techniques of limited availability, and based on retrospective data, their sensitivities seem to be inferior to that of (68)Ga-DOTA PET. Glucagon-like-peptide-1 (GLP-1) receptor imaging seems promising for localization of the primary in benign insulinomas, but is currently available only in a few centers. Fluorine-18 ((18)F)-fluorodeoxyglucose ((18)F-FDG) PET was initially thought to be of limited value in NET, due to their usually slow-growing nature. However, according to subsequent data, (18)F-FDG PET is particularly helpful for visualizing the more aggressive NET, such as poorly differentiated neuroendocrine carcinomas, and well-differentiated tumors with Ki67 values >10%. According to limited data, (18)F-FDG-avid tumor lesions, even in slow-growing NET, may indicate a more

  2. Molecular basis of cellular localization of poly C binding protein 1 in neuronal cells

    SciTech Connect

    Berry, Andrea M.; Flock, Kelly E.; Loh, Horace H.; Ko, Jane L. . E-mail: kojane@shu.edu

    2006-11-03

    Poly C binding protein 1 (PCBP) is involved in the transcriptional regulation of neuronal mu-opioid receptor gene. In this study, we examined the molecular basis of PCBP cellular/nuclear localization in neuronal cells using EGFP fusion protein. PCBP, containing three KH domains and a variable domain, distributed in cytoplasm and nucleus with a preferential nuclear expression. Domain-deletional analyses suggested the requirement of variable and KH3 domains for strong PCBP nuclear expression. Within the nucleus, a low nucleolar PCBP expression was observed, and PCBP variable domain contributed to this restricted nucleolar expression. Furthermore, the punctate nuclear pattern of PCBP was correlated to its single-stranded (ss) DNA binding ability, with both requiring cooperativity of at least three sequential domains. Collectively, certain PCBP domains thus govern its nuclear distribution and transcriptional regulatory activity in the nucleus of neurons, whereas the low nucleolar expression implicates the disengagement of PCBP in the ribosomal RNA synthesis.

  3. Effects of the local anesthetic benzocaine on the human erythrocyte membrane and molecular models.

    PubMed

    Suwalsky, Mario; Schneider, Carlos; Villena, Fernando; Norris, Beryl; Cárdenas, Hernán; Cuevas, Francisco; Sotomayor, Carlos P

    2004-04-01

    The interaction of the local anesthetic benzocaine with the human erythrocyte membrane and molecular models is described. The latter consisted of isolated unsealed human erythrocyte membranes (IUM), large unilamellar vesicles (LUV) of dimyristoylphospatidylcholine (DMPC), and phospholipid multilayers of DMPC and dimyristoylphospatidyletanolamine (DMPE), representatives of phospholipid classes located in the outer and inner monolayers of the human erythrocyte membrane, respectively. Optical and scanning electron microscopy of human erythrocytes revealed that benzocaine induced the formation of echinocytes. Experiments performed on IUM and DMPC LUV by fluorescence spectroscopy showed that benzocaine interacted with the phospholipid bilayer polar groups and hydrophobic acyl chains. X-ray diffraction analysis of DMPC confirmed these results and showed that benzocaine had no effects on DMPE. The effect on sodium transport was also studied using the isolated toad skin. Electrophysiological measurements indicated a significant decrease in the potential difference (PD) and in the short-circuit current (Isc) after the application of benzocaine, reflecting inhibition of active ion transport. PMID:15059670

  4. Human phenol sulfotransferase STP2 gene: Molecular cloning, structural characterization, and chromosomal localization

    SciTech Connect

    Her, C.; Raftogianis, R.; Weinshilboum, R.M.

    1996-05-01

    Sulfonation is an important pathway in the biotransformation of many drugs, xenobiotics, neurotransmitters, and steroid hormones. The thermostable (TS) form of phenol sulfotransferase (PST) preferentially catalyzes the sulfonation of {open_quotes}simple{close_quotes} planar phenols, and levels of activity of TS PST in human tissues are controlled by inheritance. Two different human liver TS PST cDNAs have been cloned that encode proteins with amino acid sequences that are 96% identical. We have determined the structure and chromosomal localization of the gene for one of these two cDNAs, STP2, as a step toward understanding molecular genetic mechanisms involved in the regulation of this enzyme activity in humans. STP2 spans approximately 5.1 kb and contains nine exons that range in length from 74 to 347 bp. The locations of most STP2 exon-intron splice junctions are identical to those of a gene for the thermolabile form of PST in humans, STM; a rat PST gene; a human estrogen ST (EST) gene, STE; and a guinea pig EST gene. The two initial STP2 exons, IA and IB, were identified by performing 5{prime}-rapid amplification of cDNA ends with human liver cDNA as template. Exons IA and IB are noncoding and represent two different human liver TS PST cDNA 5{prime}untranslated region sequences. The two apparent 5{prime}-ons IA and IB, contain no canonical TATA boxes, but do contain CCAAT elements. STP2 was localized to human chromosome 16 by performing the PCR with DNA from NIGMS human/rodent somatic cell hybrids as template. Structural characterization of STP2 will make it possible to begin to study molecular genetic mechanisms involved in the regulation of TS PST activity in human tissues. 63 refs., 7 figs., 1 tab.

  5. Localized surface plasmon resonances in nanostructures to enhance nonlinear vibrational spectroscopies: towards an astonishing molecular sensitivity

    PubMed Central

    2014-01-01

    Summary Vibrational transitions contain some of the richest fingerprints of molecules and materials, providing considerable physicochemical information. Vibrational transitions can be characterized by different spectroscopies, and alternatively by several imaging techniques enabling to reach sub-microscopic spatial resolution. In a quest to always push forward the detection limit and to lower the number of needed vibrational oscillators to get a reliable signal or imaging contrast, surface plasmon resonances (SPR) are extensively used to increase the local field close to the oscillators. Another approach is based on maximizing the collective response of the excited vibrational oscillators through molecular coherence. Both features are often naturally combined in vibrational nonlinear optical techniques. In this frame, this paper reviews the main achievements of the two most common vibrational nonlinear optical spectroscopies, namely surface-enhanced sum-frequency generation (SE-SFG) and surface-enhanced coherent anti-Stokes Raman scattering (SE-CARS). They can be considered as the nonlinear counterpart and/or combination of the linear surface-enhanced infrared absorption (SEIRA) and surface-enhanced Raman scattering (SERS) techniques, respectively, which are themselves a branching of the conventional IR and spontaneous Raman spectroscopies. Compared to their linear equivalent, those nonlinear vibrational spectroscopies have proved to reach higher sensitivity down to the single molecule level, opening the way to astonishing perspectives for molecular analysis. PMID:25551056

  6. The Search for Molecular Outflows in Local Volume AGNs with Herschel-PACS

    NASA Astrophysics Data System (ADS)

    Stone, M.; Veilleux, S.; Meléndez, M.; Sturm, E.; Graciá-Carpio, J.; González-Alfonso, E.

    2016-08-01

    We present the results from a systematic search for galactic-scale, molecular (OH 119 μm) outflows in a sample of 52 Local Volume (d\\lt 50 Mpc) Burst Alert Telescope detected active galactic nuclei (BAT AGNs) with Herschel-PACS. We combine the results from our analysis of the BAT AGNs with the published Herschel/PACS data of 43 nearby (z\\lt 0.3) galaxy mergers, mostly ultra-luminous infrared galaxies (ULIRGs) and QSOs. The objects in our sample of BAT AGNs have, on average, ˜ 10{--}100 times lower AGN luminosities, star formation rates, and stellar masses than those of the ULIRG and QSO samples. OH 119 μm is detected in 42 of our BAT AGN targets. Evidence for molecular outflows (i.e., OH absorption profiles with median velocities more blueshifted than -50 km s-1 and/or blueshifted wings with 84% velocities less than -300 km s-1) is seen in only four BAT AGNs (NGC 7479 is the most convincing case). Evidence for molecular inflows (i.e., OH absorption profiles with median velocities more redshifted than 50 km s-1) is seen in seven objects, although an inverted P-Cygni profile is detected unambiguously in only one object (Circinus). Our data show that both the starburst and AGN contribute to driving OH outflows, but the fastest OH winds require AGNs with quasar-like luminosities. We also confirm that the total absorption strength of OH 119 μm is a good proxy for dust optical depth as it correlates strongly with the 9.7 μm silicate absorption feature, a measure of obscuration originating in both the nuclear torus and host galaxy disk. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  7. The Search for Molecular Outflows in Local Volume AGNs with Herschel-PACS

    NASA Astrophysics Data System (ADS)

    Stone, M.; Veilleux, S.; Meléndez, M.; Sturm, E.; Graciá-Carpio, J.; González-Alfonso, E.

    2016-08-01

    We present the results from a systematic search for galactic-scale, molecular (OH 119 μm) outflows in a sample of 52 Local Volume (d\\lt 50 Mpc) Burst Alert Telescope detected active galactic nuclei (BAT AGNs) with Herschel-PACS. We combine the results from our analysis of the BAT AGNs with the published Herschel/PACS data of 43 nearby (z\\lt 0.3) galaxy mergers, mostly ultra-luminous infrared galaxies (ULIRGs) and QSOs. The objects in our sample of BAT AGNs have, on average, ˜ 10{--}100 times lower AGN luminosities, star formation rates, and stellar masses than those of the ULIRG and QSO samples. OH 119 μm is detected in 42 of our BAT AGN targets. Evidence for molecular outflows (i.e., OH absorption profiles with median velocities more blueshifted than ‑50 km s‑1 and/or blueshifted wings with 84% velocities less than ‑300 km s‑1) is seen in only four BAT AGNs (NGC 7479 is the most convincing case). Evidence for molecular inflows (i.e., OH absorption profiles with median velocities more redshifted than 50 km s‑1) is seen in seven objects, although an inverted P-Cygni profile is detected unambiguously in only one object (Circinus). Our data show that both the starburst and AGN contribute to driving OH outflows, but the fastest OH winds require AGNs with quasar-like luminosities. We also confirm that the total absorption strength of OH 119 μm is a good proxy for dust optical depth as it correlates strongly with the 9.7 μm silicate absorption feature, a measure of obscuration originating in both the nuclear torus and host galaxy disk. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  8. Absolute neutrino mass measurements

    SciTech Connect

    Wolf, Joachim

    2011-10-06

    The neutrino mass plays an important role in particle physics, astrophysics and cosmology. In recent years the detection of neutrino flavour oscillations proved that neutrinos carry mass. However, oscillation experiments are only sensitive to the mass-squared difference of the mass eigenvalues. In contrast to cosmological observations and neutrino-less double beta decay (0v2{beta}) searches, single {beta}-decay experiments provide a direct, model-independent way to determine the absolute neutrino mass by measuring the energy spectrum of decay electrons at the endpoint region with high accuracy.Currently the best kinematic upper limits on the neutrino mass of 2.2eV have been set by two experiments in Mainz and Troitsk, using tritium as beta emitter. The next generation tritium {beta}-experiment KATRIN is currently under construction in Karlsruhe/Germany by an international collaboration. KATRIN intends to improve the sensitivity by one order of magnitude to 0.2eV. The investigation of a second isotope ({sup 137}Rh) is being pursued by the international MARE collaboration using micro-calorimeters to measure the beta spectrum. The technology needed to reach 0.2eV sensitivity is still in the R and D phase. This paper reviews the present status of neutrino-mass measurements with cosmological data, 0v2{beta} decay and single {beta}-decay.

  9. A rational reduction of CI expansions: combining localized molecular orbitals and selected charge excitations.

    PubMed

    Krah, Tim; Ben Amor, Nadia; Maynau, Daniel; Berger, J A; Robert, Vincent

    2014-07-01

    Based on localized molecular orbitals, the proposed method reduces large configuration interaction (CI) spaces while maintaining agreement with reference values. Our strategy concentrates the numerical effort on physically pertinent CI-contributions and is to be considered as a tool to tackle large systems including numerous open-shells. To show the efficiency of our method we consider two 4-electron parent systems. First, we illustrate our approach by describing the van der Waals interactions in the (H2)2 system. By systematically including local correlation, dispersion and charge transfer mechanisms, we show that 90% of the reference full CI dissociation energy of the H2 dimer is reproduced using only 3% of the full CI space. Second, the conformational cis/trans rotation barrier of the butadiene molecule is remarkably reproduced (97% of the reference value) with less than 1% of the reference space. This work paves the way to numerical strategies which afford the electronic structure determination of large open-shell systems avoiding the exponential limitation. At the same time, a physical analysis of the contents of the wave function is offered.

  10. Local geometry of electromagnetic fields and its role in molecular multipole transitions.

    PubMed

    Yang, Nan; Cohen, Adam E

    2011-05-12

    Electromagnetic fields with complex spatial variation routinely arise in Nature. We study the response of a small molecule to monochromatic fields of arbitrary three-dimensional geometry. First, we consider the allowed configurations of the fields and field gradients at a single point in space. Many configurations cannot be generated from a single plane wave, regardless of polarization, but any allowed configuration can be generated by superposition of multiple plane waves. There is no local configuration of the fields and gradients that requires near-field effects. Second, we derive a set of local electromagnetic quantities, each of which couples to a particular multipole transition. These quantities are small or zero in plane waves, but can be large in regions of certain superpositions of plane waves. Our findings provide a systematic framework for designing far-field and near-field experiments to drive multipole transitions. The proposed experiments provide information on molecular structure that is inaccessible to other spectroscopic techniques and open the possibility for new types of optical control of molecules.

  11. Spectral energy analysis of locally resonant nanophononic metamaterials by molecular simulations

    NASA Astrophysics Data System (ADS)

    Honarvar, Hossein; Hussein, Mahmoud I.

    2016-02-01

    A nanophononic metamaterial is a new type of nanostructured material that features an array, or a forest, of intrinsically distributed resonating substructures. Each substructure exhibits numerous local resonances, each of which may hybridize with the phonon dispersion of the underlying host material, causing significant reductions in the group velocities and consequently a reduction in the lattice thermal conductivity. In this Rapid Communication, molecular dynamics simulations are utilized to investigate both the dynamics and the thermal transport properties of a nanophononic metamaterial configuration consisting of a freely suspended silicon membrane with an array of silicon nanopillars standing on the surface. The simulations yield results consistent with earlier lattice-dynamics-based predictions which showed a reduction in the thermal conductivity due to the presence of the local resonators. Using a spectral energy density approach, in which only simulation data are utilized and no a priori information on the nanostructure resonant phonon modes is provided, we show direct evidence of the existence of resonance hybridizations as an inherent mechanism contributing to the slowing down of thermal transport in the host medium.

  12. Cage effect in supercooled molecular liquids: Local anisotropies and collective solid-like response

    NASA Astrophysics Data System (ADS)

    Bernini, S.; Leporini, D.

    2016-04-01

    Both local geometry and collective extended excitations drive the moves of a particle in the cage of its neighbours in dense liquids. The strength of their influence is investigated by the molecular dynamics simulations of a supercooled liquid of fully flexible trimers with semirigid or rigid bonds. The rattling in the cage is investigated on different length scales. First, the rattling anisotropy due to local order is characterized by two order parameters sensing the monomers succeeding or failing to escape from the cage. Then the collective response of the surroundings excited by the monomer-monomer collisions is considered. The collective response is initially restricted to the nearest neighbours of the colliding particle by a Voronoi analysis revealing elastic contributions. Then the long-range excitation of the farthest neighbours is scrutinised by searching spatially extended correlations between the simultaneously fast displacements of the caged particle and the surroundings. It is found that the longitudinal component has stronger spatial modulation than the transverse one with a wavelength of about one particle diameter, in close resemblance with experimental findings on colloids. It is concluded that the cage rattling is largely affected by solid-like extended modes.

  13. Cage effect in supercooled molecular liquids: Local anisotropies and collective solid-like response.

    PubMed

    Bernini, S; Leporini, D

    2016-04-14

    Both local geometry and collective extended excitations drive the moves of a particle in the cage of its neighbours in dense liquids. The strength of their influence is investigated by the molecular dynamics simulations of a supercooled liquid of fully flexible trimers with semirigid or rigid bonds. The rattling in the cage is investigated on different length scales. First, the rattling anisotropy due to local order is characterized by two order parameters sensing the monomers succeeding or failing to escape from the cage. Then the collective response of the surroundings excited by the monomer-monomer collisions is considered. The collective response is initially restricted to the nearest neighbours of the colliding particle by a Voronoi analysis revealing elastic contributions. Then the long-range excitation of the farthest neighbours is scrutinised by searching spatially extended correlations between the simultaneously fast displacements of the caged particle and the surroundings. It is found that the longitudinal component has stronger spatial modulation than the transverse one with a wavelength of about one particle diameter, in close resemblance with experimental findings on colloids. It is concluded that the cage rattling is largely affected by solid-like extended modes. PMID:27083736

  14. Cage effect in supercooled molecular liquids: Local anisotropies and collective solid-like response.

    PubMed

    Bernini, S; Leporini, D

    2016-04-14

    Both local geometry and collective extended excitations drive the moves of a particle in the cage of its neighbours in dense liquids. The strength of their influence is investigated by the molecular dynamics simulations of a supercooled liquid of fully flexible trimers with semirigid or rigid bonds. The rattling in the cage is investigated on different length scales. First, the rattling anisotropy due to local order is characterized by two order parameters sensing the monomers succeeding or failing to escape from the cage. Then the collective response of the surroundings excited by the monomer-monomer collisions is considered. The collective response is initially restricted to the nearest neighbours of the colliding particle by a Voronoi analysis revealing elastic contributions. Then the long-range excitation of the farthest neighbours is scrutinised by searching spatially extended correlations between the simultaneously fast displacements of the caged particle and the surroundings. It is found that the longitudinal component has stronger spatial modulation than the transverse one with a wavelength of about one particle diameter, in close resemblance with experimental findings on colloids. It is concluded that the cage rattling is largely affected by solid-like extended modes.

  15. Absolute configuration of isovouacapenol C

    PubMed Central

    Fun, Hoong-Kun; Yodsaoue, Orapun; Karalai, Chatchanok; Chantrapromma, Suchada

    2010-01-01

    The title compound, C27H34O5 {systematic name: (4aR,5R,6R,6aS,7R,11aS,11bR)-4a,6-dihy­droxy-4,4,7,11b-tetra­methyl-1,2,3,4,4a,5,6,6a,7,11,11a,11b-dodeca­hydro­phenanthro[3,2-b]furan-5-yl benzoate}, is a cassane furan­oditerpene, which was isolated from the roots of Caesalpinia pulcherrima. The three cyclo­hexane rings are trans fused: two of these are in chair conformations with the third in a twisted half-chair conformation, whereas the furan ring is almost planar (r.m.s. deviation = 0.003 Å). An intra­molecular C—H⋯O inter­action generates an S(6) ring. The absolute configurations of the stereogenic centres at positions 4a, 5, 6, 6a, 7, 11a and 11b are R, R, R, S, R, S and R, respectively. In the crystal, mol­ecules are linked into infinite chains along [010] by O—H⋯O hydrogen bonds. C⋯O [3.306 (2)–3.347 (2) Å] short contacts and C—H⋯π inter­actions also occur. PMID:21588364

  16. Leishmania donovani eukaryotic initiation factor 5A: molecular characterization, localization and homology modelling studies.

    PubMed

    Singh, Sushma; Raju, K; Jatekar, Deepika; Dinesh, Neeradi; Paul, M Stanley; Sobhia, M E

    2014-08-01

    Eukaryotic translation initiation factor 5A (eIF5A) is a small acidic protein highly conserved from archaea to mammals. eIF5A is the only protein which undergoes a unique lysine residue modification to hypusine. Hypusinylation is important for the function of eIF5A which is reported to be essential for cell viability. eIF5A promotes formation of the first peptide bond at the onset of protein synthesis. However, its function in Leishmania donovani is unclear. The present study focuses on the characterization and localization of L. donovani eIF5A protein. The eIF5A gene contains an ORF of 501×bp encoding 166 amino acid residues with a predicted molecular mass and isoelectric point of 17.8 kDa and 4.83 respectively. A phylogenetic tree analysis revealed its close proximity to trypanosomes however it is distantly located from Trichomonas vaginalis and Plasmodium falciparum. The L. donovani eIF5A was expressed as a 6× His tagged protein whose identity was confirmed by western blot and MALDI. Biophysical investigation by CD revealed the predominant presence of 49% β sheet structure which correlated well with secondary structure prediction. To gain insight into the role of eIF5A in L. donovani, we investigated the subcellular distribution of eIF5A. A GFP-fusion of L. donovani eIF5A was found to be localized in cytoplasm as confirmed by subcellular fractionation. Our studies indicated that eIF5A is primarily localized to cytoplasm and is undetectable in nuclear fraction. The homology model of eIF5A of L. donovani was built and the resulting model showed acceptable Ramachandran statistics. The model is reliable and can be used to study eIF5A binding with its effector molecules.

  17. Development of Prediction Models for the Reactivity of Organic Compounds with Ozone in Aqueous Solution by Quantum Chemical Calculations: The Role of Delocalized and Localized Molecular Orbitals.

    PubMed

    Lee, Minju; Zimmermann-Steffens, Saskia G; Arey, J Samuel; Fenner, Kathrin; von Gunten, Urs

    2015-08-18

    Second-order rate constants (kO3) for the reaction of ozone with micropollutants are essential parameters for the assessment of micropollutant elimination efficiency during ozonation in water and wastewater treatment. Prediction models for kO3 were developed for aromatic compounds, olefins, and amines by quantum chemical molecular orbital calculations employing ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods. The kO3 values for aromatic compounds correlated well with the energy of a delocalized molecular orbital first appearing on an aromatic ring (i.e., the highest occupied molecular orbital (HOMO) or HOMO-n (n ≥ 0) when the HOMO is not located on the aromatic ring); the number of compounds tested (N) was 112, and the correlation coefficient (R(2)) values were 0.82-1.00. The kO3 values for olefins and amines correlated well with the energy of a localized molecular orbital (i.e., the natural bond orbital (NBO)) energy of the carbon-carbon π bond of olefins (N = 45, R(2) values of 0.82-0.85) and the NBO energy of the nitrogen lone-pair electrons of amines (N = 59, R(2) values of 0.81-0.83), respectively. Considering the performance of the kO3 prediction model and the computational costs, the HF/6-31G method is recommended for all aromatic groups and olefins investigated herein, whereas the HF/MIDI!, HF/6-31G*, or HF/6-311++G** methods are recommended for amines. Based on their mean absolute errors, the above models could predict kO3 within a factor of 4, on average, relative to the experimentally determined values. Overall, good correlations were also observed (R(2) values of 0.77-0.96) between kO3 predictions by quantum molecular orbital descriptors in this study and by the Hammett (σ) and Taft (σ*) constants from previously developed quantitative structure-activity relationship (QSAR) models. Hence, the quantum molecular orbital descriptors are an alternative to σ and σ*-values in QSAR applications and can also be utilized to

  18. Development of Prediction Models for the Reactivity of Organic Compounds with Ozone in Aqueous Solution by Quantum Chemical Calculations: The Role of Delocalized and Localized Molecular Orbitals.

    PubMed

    Lee, Minju; Zimmermann-Steffens, Saskia G; Arey, J Samuel; Fenner, Kathrin; von Gunten, Urs

    2015-08-18

    Second-order rate constants (kO3) for the reaction of ozone with micropollutants are essential parameters for the assessment of micropollutant elimination efficiency during ozonation in water and wastewater treatment. Prediction models for kO3 were developed for aromatic compounds, olefins, and amines by quantum chemical molecular orbital calculations employing ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods. The kO3 values for aromatic compounds correlated well with the energy of a delocalized molecular orbital first appearing on an aromatic ring (i.e., the highest occupied molecular orbital (HOMO) or HOMO-n (n ≥ 0) when the HOMO is not located on the aromatic ring); the number of compounds tested (N) was 112, and the correlation coefficient (R(2)) values were 0.82-1.00. The kO3 values for olefins and amines correlated well with the energy of a localized molecular orbital (i.e., the natural bond orbital (NBO)) energy of the carbon-carbon π bond of olefins (N = 45, R(2) values of 0.82-0.85) and the NBO energy of the nitrogen lone-pair electrons of amines (N = 59, R(2) values of 0.81-0.83), respectively. Considering the performance of the kO3 prediction model and the computational costs, the HF/6-31G method is recommended for all aromatic groups and olefins investigated herein, whereas the HF/MIDI!, HF/6-31G*, or HF/6-311++G** methods are recommended for amines. Based on their mean absolute errors, the above models could predict kO3 within a factor of 4, on average, relative to the experimentally determined values. Overall, good correlations were also observed (R(2) values of 0.77-0.96) between kO3 predictions by quantum molecular orbital descriptors in this study and by the Hammett (σ) and Taft (σ*) constants from previously developed quantitative structure-activity relationship (QSAR) models. Hence, the quantum molecular orbital descriptors are an alternative to σ and σ*-values in QSAR applications and can also be utilized to

  19. Absolute Identification by Relative Judgment

    ERIC Educational Resources Information Center

    Stewart, Neil; Brown, Gordon D. A.; Chater, Nick

    2005-01-01

    In unidimensional absolute identification tasks, participants identify stimuli that vary along a single dimension. Performance is surprisingly poor compared with discrimination of the same stimuli. Existing models assume that identification is achieved using long-term representations of absolute magnitudes. The authors propose an alternative…

  20. Be Resolute about Absolute Value

    ERIC Educational Resources Information Center

    Kidd, Margaret L.

    2007-01-01

    This article explores how conceptualization of absolute value can start long before it is introduced. The manner in which absolute value is introduced to students in middle school has far-reaching consequences for their future mathematical understanding. It begins to lay the foundation for students' understanding of algebra, which can change…

  1. Correlation of intercentromeric distance, mosaicism, and sexual phenotype: molecular localization of breakpoints in isodicentric Y chromosomes.

    PubMed

    Beaulieu Bergeron, Mélanie; Brochu, Pierre; Lemyre, Emmanuelle; Lemieux, Nicole

    2011-11-01

    Isodicentric chromosomes are among the structural abnormalities of the Y chromosome that are commonly identified in patients. The simultaneous 45,X cell line that is generated in cell division due to instability of the isodicentric Y chromosome [idic(Y)] has long been hypothesized to explain the variable sexual development of these patients, although gonads have been studied in only a subset of cases. We report here on the molecular localization of breakpoints in ten patients with an idic(Y). Breakpoints were mapped by FISH using BACs; gonads and fibroblasts were also analyzed when possible to evaluate the level of mosaicism. First, we demonstrate great tissue variability in the distribution of idic(Y). Second, palindromes and direct repeats were near the breakpoint of several idic(Y), suggesting that these sequences play a role in the formation of idic(Y). Finally, our data suggest that intercentromeric distance has a negative influence on the stability of idic(Y), as a greater proportion of cells with breakage or loss of the idic(Y) were found in idic(Y) with a greater intercentromeric distance. Females had a significantly greater intercentromeric distance on their idic(Y) than did males. In conclusion, our study indicates that the Y chromosome contains sequences that are more prone to formation of isodicentric chromosomes. We also demonstrate that patients with an intercentromeric distance greater than 20 Mb on their idic(Y) are at increased risk of having a female sexual phenotype.

  2. Mechanistic Insights into Molecular Targeting and Combined Modality Therapy for Aggressive, Localized Prostate Cancer

    PubMed Central

    Dal Pra, Alan; Locke, Jennifer A.; Borst, Gerben; Supiot, Stephane; Bristow, Robert G.

    2016-01-01

    Radiation therapy (RT) is one of the mainstay treatments for prostate cancer (PCa). The potentially curative approaches can provide satisfactory results for many patients with non-metastatic PCa; however, a considerable number of individuals may present disease recurrence and die from the disease. Exploiting the rich molecular biology of PCa will provide insights into how the most resistant tumor cells can be eradicated to improve treatment outcomes. Important for this biology-driven individualized treatment is a robust selection procedure. The development of predictive biomarkers for RT efficacy is therefore of utmost importance for a clinically exploitable strategy to achieve tumor-specific radiosensitization. This review highlights the current status and possible opportunities in the modulation of four key processes to enhance radiation response in PCa by targeting the: (1) androgen signaling pathway; (2) hypoxic tumor cells and regions; (3) DNA damage response (DDR) pathway; and (4) abnormal extra-/intracell signaling pathways. In addition, we discuss how and which patients should be selected for biomarker-based clinical trials exploiting and validating these targeted treatment strategies with precision RT to improve cure rates in non-indolent, localized PCa. PMID:26909338

  3. Molecular imaging of brain localization of liposomes in mice using MALDI mass spectrometry

    PubMed Central

    Fülöp, Annabelle; Sammour, Denis A.; Erich, Katrin; von Gerichten, Johanna; van Hoogevest, Peter; Sandhoff, Roger; Hopf, Carsten

    2016-01-01

    Phospholipids have excellent biocompatibility and are therefore often used as main components of liposomal drug carriers. In traditional bioanalytics, the in-vivo distribution of liposomal drug carriers is assessed using radiolabeled liposomal constituents. This study presents matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) as an alternative, label-free method for ex-vivo molecular imaging of liposomal drug carriers in mouse tissue. To this end, indocyanine green as cargo and two liposomal markers, 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine conjugated with monodisperse polyethylene glycol (PEG36-DSPE) were incorporated into liposomal carriers and administered to mice. We used MALDI MSI of the two lipid markers in both positive and negative ion mode for visualization of liposome integrity and distribution in mouse organs. Additional MSI of hemoglobin in the same tissue slice and pixel-by-pixel computational analysis of co-occurrence of lipid markers and hemoglobin served as indicator of liposome localization either in parenchyma or in blood vessels. Our proof-of-concept study suggests that liposomal components and indocyanine green distributed into all investigated organs. PMID:27650487

  4. Mechanistic Insights into Molecular Targeting and Combined Modality Therapy for Aggressive, Localized Prostate Cancer.

    PubMed

    Dal Pra, Alan; Locke, Jennifer A; Borst, Gerben; Supiot, Stephane; Bristow, Robert G

    2016-01-01

    Radiation therapy (RT) is one of the mainstay treatments for prostate cancer (PCa). The potentially curative approaches can provide satisfactory results for many patients with non-metastatic PCa; however, a considerable number of individuals may present disease recurrence and die from the disease. Exploiting the rich molecular biology of PCa will provide insights into how the most resistant tumor cells can be eradicated to improve treatment outcomes. Important for this biology-driven individualized treatment is a robust selection procedure. The development of predictive biomarkers for RT efficacy is therefore of utmost importance for a clinically exploitable strategy to achieve tumor-specific radiosensitization. This review highlights the current status and possible opportunities in the modulation of four key processes to enhance radiation response in PCa by targeting the: (1) androgen signaling pathway; (2) hypoxic tumor cells and regions; (3) DNA damage response (DDR) pathway; and (4) abnormal extra-/intracell signaling pathways. In addition, we discuss how and which patients should be selected for biomarker-based clinical trials exploiting and validating these targeted treatment strategies with precision RT to improve cure rates in non-indolent, localized PCa. PMID:26909338

  5. Molecular imaging of brain localization of liposomes in mice using MALDI mass spectrometry.

    PubMed

    Fülöp, Annabelle; Sammour, Denis A; Erich, Katrin; von Gerichten, Johanna; van Hoogevest, Peter; Sandhoff, Roger; Hopf, Carsten

    2016-01-01

    Phospholipids have excellent biocompatibility and are therefore often used as main components of liposomal drug carriers. In traditional bioanalytics, the in-vivo distribution of liposomal drug carriers is assessed using radiolabeled liposomal constituents. This study presents matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) as an alternative, label-free method for ex-vivo molecular imaging of liposomal drug carriers in mouse tissue. To this end, indocyanine green as cargo and two liposomal markers, 1,2-dipalmitoyl-sn-glycero-3-phosphoglycerol (DPPG) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine conjugated with monodisperse polyethylene glycol (PEG36-DSPE) were incorporated into liposomal carriers and administered to mice. We used MALDI MSI of the two lipid markers in both positive and negative ion mode for visualization of liposome integrity and distribution in mouse organs. Additional MSI of hemoglobin in the same tissue slice and pixel-by-pixel computational analysis of co-occurrence of lipid markers and hemoglobin served as indicator of liposome localization either in parenchyma or in blood vessels. Our proof-of-concept study suggests that liposomal components and indocyanine green distributed into all investigated organs. PMID:27650487

  6. Localization and orientation of heavy-atom cluster compounds in protein crystals using molecular replacement

    PubMed Central

    Dahms, Sven O.; Kuester, Miriam; Streb, Carsten; Roth, Christian; Sträter, Norbert; Than, Manuel E.

    2013-01-01

    Heavy-atom clusters (HA clusters) containing a large number of specifically arranged electron-dense scatterers are especially useful for experimental phase determination of large complex structures, weakly diffracting crystals or structures with large unit cells. Often, the determination of the exact orientation of the HA cluster and hence of the individual heavy-atom positions proves to be the critical step in successful phasing and subsequent structure solution. Here, it is demonstrated that molecular replacement (MR) with either anomalous or isomorphous differences is a useful strategy for the correct placement of HA cluster compounds. The polyoxometallate cluster hexasodium α-metatungstate (HMT) was applied in phasing the structure of death receptor 6. Even though the HA cluster is bound in alternate partially occupied orientations and is located at a special position, its correct localization and orientation could be determined at resolutions as low as 4.9 Å. The broad applicability of this approach was demonstrated for five different derivative crystals that included the compounds tantalum tetradeca­bromide and trisodium phosphotungstate in addition to HMT. The correct placement of the HA cluster depends on the length of the intramolecular vectors chosen for MR, such that both a larger cluster size and the optimal choice of the wavelength used for anomalous data collection strongly affect the outcome. PMID:23385464

  7. Probing absolute spin polarization at the nanoscale.

    PubMed

    Eltschka, Matthias; Jäck, Berthold; Assig, Maximilian; Kondrashov, Oleg V; Skvortsov, Mikhail A; Etzkorn, Markus; Ast, Christian R; Kern, Klaus

    2014-12-10

    Probing absolute values of spin polarization at the nanoscale offers insight into the fundamental mechanisms of spin-dependent transport. Employing the Zeeman splitting in superconducting tips (Meservey-Tedrow-Fulde effect), we introduce a novel spin-polarized scanning tunneling microscopy that combines the probing capability of the absolute values of spin polarization with precise control at the atomic scale. We utilize our novel approach to measure the locally resolved spin polarization of magnetic Co nanoislands on Cu(111). We find that the spin polarization is enhanced by 65% when increasing the width of the tunnel barrier by only 2.3 Å due to the different decay of the electron orbitals into vacuum. PMID:25423049

  8. Singular perturbation of absolute stability.

    NASA Technical Reports Server (NTRS)

    Siljak, D. D.

    1972-01-01

    It was previously shown (author, 1969) that the regions of absolute stability in the parameter space can be determined when the parameters appear on the right-hand side of the system equations, i.e., the regular case. Here, the effect on absolute stability of a small parameter attached to higher derivatives in the equations (the singular case) is studied. The Lur'e-Postnikov class of nonlinear systems is considered.

  9. Localization of high-molecular-weight adhesion proteins of nontypeable Haemophilus influenzae by immunoelectron microscopy.

    PubMed Central

    Bakaletz, L O; Barenkamp, S J

    1994-01-01

    A family of high-molecular-weight (HMW) surface-exposed proteins important in the attachment of nontypeable Haemophilus influenzae (NTHi) to human epithelial cells was previously identified (J. W. St. Geme III, S. Falkow, and S. J. Barenkamp, Proc. Natl. Acad. Sci. USA 90:2875-2879, 1993). In the present investigation, indirect immunogold labeling and electron microscopy were used to localize these proteins on three clinical isolates of NTHi, mutants deficient in expression of one or both HMW proteins, and embedded sections of human oropharyngeal cells after incubation with NTHi strain 12. The filamentous material comprising the proteins was labeled with monoclonal antibodies directed against two prototype HMW proteins (HMW1 and HMW2) of prototype NTHi strain 12. Gold labeling was observed as a cap or discrete aggregate off one pole or centrally along one long axis of the bacterial cell. Heavily labeled, non-bacterial-cell-associated, disk-like aggregates of the HMW proteins were frequently noted in both bacterial preparations as well as in association with the oropharyngeal cell surface and intracellularly. Mutants demonstrated diminished labeling or an absence thereof, respectively, which correlated well with their previously demonstrated reduced ability or inability to adhere to Chang conjunctival epithelial cells in vitro. The Haemophilus HMW proteins share antigenic determinants with and demonstrate amino acid sequence similarity to the filamentous hemagglutinin protein of Bordetella pertussis, a critical adhesin of that organism. The studies presented here demonstrate that the Haemophilus proteins and B. pertussis filamentous hemagglutinin show impressive morphologic and perhaps additional functional similarity. Images PMID:7927710

  10. Molecular Characterization and Subcellular Localization of Arabidopsis Class VIII Myosin, ATM1*

    PubMed Central

    Haraguchi, Takeshi; Tominaga, Motoki; Matsumoto, Rie; Sato, Kei; Nakano, Akihiko; Yamamoto, Keiichi; Ito, Kohji

    2014-01-01

    Land plants possess myosin classes VIII and XI. Although some information is available on the molecular properties of class XI myosins, class VIII myosins are not characterized. Here, we report the first analysis of the enzymatic properties of class VIII myosin. The motor domain of Arabidopsis class VIII myosin, ATM1 (ATM1-MD), and the motor domain plus one IQ motif (ATM1-1IQ) were expressed in a baculovirus system and characterized. ATM1-MD and ATM1-1IQ had low actin-activated Mg2+-ATPase activity (Vmax = 4 s−1), although their affinities for actin were high (Kactin = 4 μm). The actin-sliding velocities of ATM1-MD and ATM1-1IQ were 0.02 and 0.089 μm/s, respectively, from which the value for full-length ATM1 is calculated to be ∼0.2 μm/s. The results of actin co-sedimentation assay showed that the duty ratio of ATM1 was ∼90%. ADP dissociation from the actin·ATM1 complex (acto-ATM1) was extremely slow, which accounts for the low actin-sliding velocity, low actin-activated ATPase activity, and high duty ratio. The rate of ADP dissociation from acto-ATM1 was markedly biphasic with fast and slow phase rates (5.1 and 0.41 s−1, respectively). Physiological concentrations of free Mg2+ modulated actin-sliding velocity and actin-activated ATPase activity by changing the rate of ADP dissociation from acto-ATM1. GFP-fused full-length ATM1 expressed in Arabidopsis was localized to plasmodesmata, plastids, newly formed cell walls, and actin filaments at the cell cortex. Our results suggest that ATM1 functions as a tension sensor/generator at the cell cortex and other structures in Arabidopsis. PMID:24637024

  11. Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.

    PubMed

    Douzery, Emmanuel J P; Delsuc, Frédéric; Stanhope, Michael J; Huchon, Dorothée

    2003-01-01

    Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.

  12. Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations.

    PubMed

    Li, Hongzhi; Fajer, Mikolai; Yang, Wei

    2007-01-14

    A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of biophysical problems, in which localized sampling is required. Besides its superior capability and robustness in localized conformational sampling, this simulated scaling method can also naturally lead to efficient "alchemical" free energy predictions when dual-topology alchemical hybrid potential is applied; thereby simultaneously, both of the chemically and conformationally distinct portions of two end point chemical states can be efficiently sampled. As demonstrated in this work, the present method is also feasible for the quantum mechanical and quantum mechanical/molecular mechanical simulations.

  13. Measurement of absolute gravity acceleration in Firenze

    NASA Astrophysics Data System (ADS)

    de Angelis, M.; Greco, F.; Pistorio, A.; Poli, N.; Prevedelli, M.; Saccorotti, G.; Sorrentino, F.; Tino, G. M.

    2011-01-01

    This paper reports the results from the accurate measurement of the acceleration of gravity g taken at two separate premises in the Polo Scientifico of the University of Firenze (Italy). In these laboratories, two separate experiments aiming at measuring the Newtonian constant and testing the Newtonian law at short distances are in progress. Both experiments require an independent knowledge on the local value of g. The only available datum, pertaining to the italian zero-order gravity network, was taken more than 20 years ago at a distance of more than 60 km from the study site. Gravity measurements were conducted using an FG5 absolute gravimeter, and accompanied by seismic recordings for evaluating the noise condition at the site. The absolute accelerations of gravity at the two laboratories are (980 492 160.6 ± 4.0) μGal and (980 492 048.3 ± 3.0) μGal for the European Laboratory for Non-Linear Spectroscopy (LENS) and Dipartimento di Fisica e Astronomia, respectively. Other than for the two referenced experiments, the data here presented will serve as a benchmark for any future study requiring an accurate knowledge of the absolute value of the acceleration of gravity in the study region.

  14. Why to compare absolute numbers of mitochondria.

    PubMed

    Schmitt, Sabine; Schulz, Sabine; Schropp, Eva-Maria; Eberhagen, Carola; Simmons, Alisha; Beisker, Wolfgang; Aichler, Michaela; Zischka, Hans

    2014-11-01

    Prompted by pronounced structural differences between rat liver and rat hepatocellular carcinoma mitochondria, we suspected these mitochondrial populations to differ massively in their molecular composition. Aiming to reveal these mitochondrial differences, we came across the issue on how to normalize such comparisons and decided to focus on the absolute number of mitochondria. To this end, fluorescently stained mitochondria were quantified by flow cytometry. For rat liver mitochondria, this approach resulted in mitochondrial protein contents comparable to earlier reports using alternative methods. We determined similar protein contents for rat liver, heart and kidney mitochondria. In contrast, however, lower protein contents were determined for rat brain mitochondria and for mitochondria from the rat hepatocellular carcinoma cell line McA 7777. This result challenges mitochondrial comparisons that rely on equal protein amounts as a typical normalization method. Exemplarily, we therefore compared the activity and susceptibility toward inhibition of complex II of rat liver and hepatocellular carcinoma mitochondria and obtained significant discrepancies by either normalizing to protein amount or to absolute mitochondrial number. Importantly, the latter normalization, in contrast to the former, demonstrated a lower complex II activity and higher susceptibility toward inhibition in hepatocellular carcinoma mitochondria compared to liver mitochondria. These findings demonstrate that solely normalizing to protein amount may obscure essential molecular differences between mitochondrial populations.

  15. Absolute flux scale for radioastronomy

    SciTech Connect

    Ivanov, V.P.; Stankevich, K.S.

    1986-07-01

    The authors propose and provide support for a new absolute flux scale for radio astronomy, which is not encumbered with the inadequacies of the previous scales. In constructing it the method of relative spectra was used (a powerful tool for choosing reference spectra). A review is given of previous flux scales. The authors compare the AIS scale with the scale they propose. Both scales are based on absolute measurements by the ''artificial moon'' method, and they are practically coincident in the range from 0.96 to 6 GHz. At frequencies above 6 GHz, 0.96 GHz, the AIS scale is overestimated because of incorrect extrapolation of the spectra of the primary and secondary standards. The major results which have emerged from this review of absolute scales in radio astronomy are summarized.

  16. Frequency-dependent local field factors in dielectric liquids by a polarizable force field and molecular dynamics simulations

    SciTech Connect

    Davari, Nazanin; Haghdani, Shokouh; Åstrand, Per-Olof

    2015-12-31

    A force field model for calculating local field factors, i.e. the linear response of the local electric field for example at a nucleus in a molecule with respect to an applied electric field, is discussed. It is based on a combined charge-transfer and point-dipole interaction model for the polarizability, and thereby it includes two physically distinct terms for describing electronic polarization: changes in atomic charges arising from transfer of charge between the atoms and atomic induced dipole moments. A time dependence is included both for the atomic charges and the atomic dipole moments and if they are assumed to oscillate with the same frequency as the applied electric field, a model for frequency-dependent properties are obtained. Furthermore, if a life-time of excited states are included, a model for the complex frequency-dependent polariability is obtained including also information about excited states and the absorption spectrum. We thus present a model for the frequency-dependent local field factors through the first molecular excitation energy. It is combined with molecular dynamics simulations of liquids where a large set of configurations are sampled and for which local field factors are calculated. We are normally not interested in the average of the local field factor but rather in configurations where it is as high as possible. In electrical insulation, we would like to avoid high local field factors to reduce the risk for electrical breakdown, whereas for example in surface-enhanced Raman spectroscopy, high local field factors are desired to give dramatically increased intensities.

  17. Measurement of molecular length of self-assembled monolayer probed by localized surface plasmon resonance

    NASA Astrophysics Data System (ADS)

    Ito, Juri; Kajikawa, Kotaro

    2016-02-01

    We propose a method to measure the variation of the molecular length of self-assembled monolayers (SAMs) when it is exposed to solutions at different pH conditions. The surface immobilized gold nanospheres (SIGNs) shows strong absorption peak at the wavelengths of 600-800 nm when p-polarized light is illuminated. The peak wavelength depends on the length of the gap distance between the SIGNs and the substrate. The gap is supported by the SAM molecules. According to the analytical calculation based on multiple expansion, the relation between the peak wavelength of the SIGN structures and the gap distance is calculated, to evaluate the molecular length of the SAM through the optical absorption spectroscopy for the SIGN structures. The molecular length of the SIGN structure was measured in air, water, acidic, and basic solutions. It was found that the molecular lengths are longer in acidic solutions.

  18. Relativistic Absolutism in Moral Education.

    ERIC Educational Resources Information Center

    Vogt, W. Paul

    1982-01-01

    Discusses Emile Durkheim's "Moral Education: A Study in the Theory and Application of the Sociology of Education," which holds that morally healthy societies may vary in culture and organization but must possess absolute rules of moral behavior. Compares this moral theory with current theory and practice of American educators. (MJL)

  19. Absolute transition probabilities of phosphorus.

    NASA Technical Reports Server (NTRS)

    Miller, M. H.; Roig, R. A.; Bengtson, R. D.

    1971-01-01

    Use of a gas-driven shock tube to measure the absolute strengths of 21 P I lines and 126 P II lines (from 3300 to 6900 A). Accuracy for prominent, isolated neutral and ionic lines is estimated to be 28 to 40% and 18 to 30%, respectively. The data and the corresponding theoretical predictions are examined for conformity with the sum rules.-

  20. Computational prediction of antibody binding sites on tetracycline antibiotics: electrostatic potentials and average local ionization energies on molecular surfaces.

    PubMed

    Kulshrestha, Pankaj; Sukumar, N; Murray, Jane S; Giese, Rossman F; Wood, Troy D

    2009-01-29

    Enzyme linked immunosorbent assay (ELISA) was used for the analysis of tetracycline, chlortetracycline, oxytetracycline, and their transformed compounds in environmental water samples. The antibodies employed in ELISA showed high relative affinity for tetracycline, epitetracycline, chlortetracycline, and epichlortetracycline as compared to anhydrotetracycline, epianhydrotetracycline, and anhydrochlortetracycline. The specificity and crossreactivity of these antibodies are discussed in relation to the electrostatic potentials and average local ionization energies computed on the molecular surfaces of tetracycline antibiotics and their transformed compounds with an objective of identifying common features as well as differences that may be related to the experimentally observed variation in cross-reactivity values. The computations were performed at both the HF/STO-3G and HF/6-31+G* levels using the Gaussian 98 program. The results in this study are based upon molecular electrostatic potentials and local ionization energies computed on isodensity molecular surfaces. The surface electrostatic potentials are characterized in terms of a group of statistically defined quantities, which include the average deviation, the positive, negative, and total variances, positive and negative surface extrema, and a parameter indicating the degree of electrostatic balance.

  1. Localized spatially nonlinear matter waves in atomic-molecular Bose-Einstein condensates with space-modulated nonlinearity.

    PubMed

    Yao, Yu-Qin; Li, Ji; Han, Wei; Wang, Deng-Shan; Liu, Wu-Ming

    2016-01-01

    The intrinsic nonlinearity is the most remarkable characteristic of the Bose-Einstein condensates (BECs) systems. Many studies have been done on atomic BECs with time- and space- modulated nonlinearities, while there is few work considering the atomic-molecular BECs with space-modulated nonlinearities. Here, we obtain two kinds of Jacobi elliptic solutions and a family of rational solutions of the atomic-molecular BECs with trapping potential and space-modulated nonlinearity and consider the effect of three-body interaction on the localized matter wave solutions. The topological properties of the localized nonlinear matter wave for no coupling are analysed: the parity of nonlinear matter wave functions depends only on the principal quantum number n, and the numbers of the density packets for each quantum state depend on both the principal quantum number n and the secondary quantum number l. When the coupling is not zero, the localized nonlinear matter waves given by the rational function, their topological properties are independent of the principal quantum number n, only depend on the secondary quantum number l. The Raman detuning and the chemical potential can change the number and the shape of the density packets. The stability of the Jacobi elliptic solutions depends on the principal quantum number n, while the stability of the rational solutions depends on the chemical potential and Raman detuning.

  2. Localized spatially nonlinear matter waves in atomic-molecular Bose-Einstein condensates with space-modulated nonlinearity

    PubMed Central

    Yao, Yu-Qin; Li, Ji; Han, Wei; Wang, Deng-Shan; Liu, Wu-Ming

    2016-01-01

    The intrinsic nonlinearity is the most remarkable characteristic of the Bose-Einstein condensates (BECs) systems. Many studies have been done on atomic BECs with time- and space- modulated nonlinearities, while there is few work considering the atomic-molecular BECs with space-modulated nonlinearities. Here, we obtain two kinds of Jacobi elliptic solutions and a family of rational solutions of the atomic-molecular BECs with trapping potential and space-modulated nonlinearity and consider the effect of three-body interaction on the localized matter wave solutions. The topological properties of the localized nonlinear matter wave for no coupling are analysed: the parity of nonlinear matter wave functions depends only on the principal quantum number n, and the numbers of the density packets for each quantum state depend on both the principal quantum number n and the secondary quantum number l. When the coupling is not zero, the localized nonlinear matter waves given by the rational function, their topological properties are independent of the principal quantum number n, only depend on the secondary quantum number l. The Raman detuning and the chemical potential can change the number and the shape of the density packets. The stability of the Jacobi elliptic solutions depends on the principal quantum number n, while the stability of the rational solutions depends on the chemical potential and Raman detuning. PMID:27403634

  3. Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

    DOE PAGES

    Giera, Brian; Lawrence Livermore National Lab.; Henson, Neil; Kober, Edward M.; Shell, M. Scott; Squires, Todd M.

    2015-02-27

    We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drivemore » strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.« less

  4. Electric Double-Layer Structure in Primitive Model Electrolytes. Comparing Molecular Dynamics with Local-Density Approximations

    SciTech Connect

    Giera, Brian; Henson, Neil; Kober, Edward M.; Shell, M. Scott; Squires, Todd M.

    2015-02-27

    We evaluate the accuracy of local-density approximations (LDAs) using explicit molecular dynamics simulations of binary electrolytes comprised of equisized ions in an implicit solvent. The Bikerman LDA, which considers ions to occupy a lattice, poorly captures excluded volume interactions between primitive model ions. Instead, LDAs based on the Carnahan–Starling (CS) hard-sphere equation of state capture simulated values of ideal and excess chemical potential profiles extremely well, as is the relationship between surface charge density and electrostatic potential. Excellent agreement between the EDL capacitances predicted by CS-LDAs and computed in molecular simulations is found even in systems where ion correlations drive strong density and free charge oscillations within the EDL, despite the inability of LDAs to capture the oscillations in the detailed EDL profiles.

  5. Optomechanics for absolute rotation detection

    NASA Astrophysics Data System (ADS)

    Davuluri, Sankar

    2016-07-01

    In this article, we present an application of optomechanical cavity for the absolute rotation detection. The optomechanical cavity is arranged in a Michelson interferometer in such a way that the classical centrifugal force due to rotation changes the length of the optomechanical cavity. The change in the cavity length induces a shift in the frequency of the cavity mode. The phase shift corresponding to the frequency shift in the cavity mode is measured at the interferometer output to estimate the angular velocity of absolute rotation. We derived an analytic expression to estimate the minimum detectable rotation rate in our scheme for a given optomechanical cavity. Temperature dependence of the rotation detection sensitivity is studied.

  6. Moral absolutism and ectopic pregnancy.

    PubMed

    Kaczor, C

    2001-02-01

    If one accepts a version of absolutism that excludes the intentional killing of any innocent human person from conception to natural death, ectopic pregnancy poses vexing difficulties. Given that the embryonic life almost certainly will die anyway, how can one retain one's moral principle and yet adequately respond to a situation that gravely threatens the life of the mother and her future fertility? The four options of treatment most often discussed in the literature are non-intervention, salpingectomy (removal of tube with embryo), salpingostomy (removal of embryo alone), and use of methotrexate (MXT). In this essay, I review these four options and introduce a fifth (the milking technique). In order to assess these options in terms of the absolutism mentioned, it will also be necessary to discuss various accounts of the intention/foresight distinction. I conclude that salpingectomy, salpingostomy, and the milking technique are compatible with absolutist presuppositions, but not the use of methotrexate.

  7. Moral absolutism and ectopic pregnancy.

    PubMed

    Kaczor, C

    2001-02-01

    If one accepts a version of absolutism that excludes the intentional killing of any innocent human person from conception to natural death, ectopic pregnancy poses vexing difficulties. Given that the embryonic life almost certainly will die anyway, how can one retain one's moral principle and yet adequately respond to a situation that gravely threatens the life of the mother and her future fertility? The four options of treatment most often discussed in the literature are non-intervention, salpingectomy (removal of tube with embryo), salpingostomy (removal of embryo alone), and use of methotrexate (MXT). In this essay, I review these four options and introduce a fifth (the milking technique). In order to assess these options in terms of the absolutism mentioned, it will also be necessary to discuss various accounts of the intention/foresight distinction. I conclude that salpingectomy, salpingostomy, and the milking technique are compatible with absolutist presuppositions, but not the use of methotrexate. PMID:11262641

  8. The Absolute Spectrum Polarimeter (ASP)

    NASA Technical Reports Server (NTRS)

    Kogut, A. J.

    2010-01-01

    The Absolute Spectrum Polarimeter (ASP) is an Explorer-class mission to map the absolute intensity and linear polarization of the cosmic microwave background and diffuse astrophysical foregrounds over the full sky from 30 GHz to 5 THz. The principal science goal is the detection and characterization of linear polarization from an inflationary epoch in the early universe, with tensor-to-scalar ratio r much greater than 1O(raised to the power of { -3}) and Compton distortion y < 10 (raised to the power of{-6}). We describe the ASP instrument and mission architecture needed to detect the signature of an inflationary epoch in the early universe using only 4 semiconductor bolometers.

  9. Classification images predict absolute efficiency.

    PubMed

    Murray, Richard F; Bennett, Patrick J; Sekuler, Allison B

    2005-02-24

    How well do classification images characterize human observers' strategies in perceptual tasks? We show mathematically that from the classification image of a noisy linear observer, it is possible to recover the observer's absolute efficiency. If we could similarly predict human observers' performance from their classification images, this would suggest that the linear model that underlies use of the classification image method is adequate over the small range of stimuli typically encountered in a classification image experiment, and that a classification image captures most important aspects of human observers' performance over this range. In a contrast discrimination task and in a shape discrimination task, we found that observers' absolute efficiencies were generally well predicted by their classification images, although consistently slightly (approximately 13%) higher than predicted. We consider whether a number of plausible nonlinearities can account for the slight under prediction, and of these we find that only a form of phase uncertainty can account for the discrepancy.

  10. Absolute calibration of optical flats

    DOEpatents

    Sommargren, Gary E.

    2005-04-05

    The invention uses the phase shifting diffraction interferometer (PSDI) to provide a true point-by-point measurement of absolute flatness over the surface of optical flats. Beams exiting the fiber optics in a PSDI have perfect spherical wavefronts. The measurement beam is reflected from the optical flat and passed through an auxiliary optic to then be combined with the reference beam on a CCD. The combined beams include phase errors due to both the optic under test and the auxiliary optic. Standard phase extraction algorithms are used to calculate this combined phase error. The optical flat is then removed from the system and the measurement fiber is moved to recombine the two beams. The newly combined beams include only the phase errors due to the auxiliary optic. When the second phase measurement is subtracted from the first phase measurement, the absolute phase error of the optical flat is obtained.

  11. [On the influence of local molecular environment on the redox potential of electron transfer cofactors in bacterial photosynthetic reaction centers].

    PubMed

    Krasil'nikov, P M; Noks, P P; Rubin, A B

    2011-01-01

    The addition of cryosolvents (glycerol, dimethylsulfoxide) to a water solution containing bacterial photosynthetic reaction centers changes the redox potential of the bacteriochlorophyll dimer, but does not affect the redox potential of the quinone primary acceptor. It has been shown that the change in redox potential can be produced by changes of the electrostatic interactions between cofactors and the local molecular environment modified by additives entered into the solution. The degree of influence of a solvent on the redox potential of various cofactors is determined by degree of availability of these cofactors for molecules of solvent, which depends on the arrangement of cofactors in the structure of reaction centers.

  12. Molecular and morphological diversity in locally grown non-commercial (heirloom) mango varieties of North India.

    PubMed

    Bajpai, Anju; Muthukumar, M; Ahmad, Israr; Ravishankar, K V; Parthasarthy, V A; Sthapit, Bhuwon; Rao, Ramanatha; Verma, J P; Rajan, S

    2016-03-01

    Mango (Mangifera indica L.) has been cultivated and conserved in different agro-ecologies including Malihabad region in northern part of India, that is well known for housing diverse types (heirloom and commercial varieties). In the present study, 37 mango types comprising of 27 heirloom varieties from Malihabad region and 10 commercial varieties grown in North and Eastern India were assessed for morphological attributes and molecular diversity. The employed SSR markers amplified 2-13 alleles individually, cumulatively amplifying 124 alleles. These were studied for allelic diversity and genetic dissimilarity ranged from 0.035 to 0.892 arranging the varieties in three major clusters. The results revealed that majority of unique heirloom mangoes from Malihabad were different from the eastern part of the country. It is interesting to note Dashehari, a commercial variety from Malihabad was not aligned with heirloom varieties. Commercial varieties like Gulabkhas and Langra were placed in a separate group including Bombay Green, Himsagar, Dashehari, etc., indicating their dissimilarity with heirloom varieties at molecular level and thus, indicating importance for later from conservation point of view. Furthermore, the hierarchical clustering of varieties based on fruit morphology, assembled these into four groups largely influenced by fruit size. The maximum agreement subtree indicated seemingly good fit as thirteen varieties were arrayed in common grouping pattern. Appreciable dissimilarity among the heirloom varieties demonstrated by molecular analysis, underlines the importance for their on-farm conservation. PMID:27097441

  13. EVIDENCE FOR 1000 km s{sup -1} MOLECULAR OUTFLOWS IN THE LOCAL ULIRG POPULATION

    SciTech Connect

    Chung, Aeree; Yun, Min S.; Naraynan, Gopal; Heyer, Mark; Erickson, Neal R.

    2011-05-01

    The feedback from galactic outflows is thought to play an important role in shaping the gas content, star formation history, and ultimately the stellar mass function of galaxies. Here we present evidence for massive molecular outflows associated with ultra-luminous infrared galaxies (ULIRGs) in the co-added Redshift Search Receiver {sup 12}CO (1-0) spectrum. Our stacked spectrum of 27 ULIRGs at z = 0.043-0.11 ({nu}{sub rest} = 110-120 GHz) shows broad wings around the CO line with {Delta}V(FWZI) {approx} 2000 km s{sup -1}. Its integrated line flux accounts for up to 25% {+-} 5% of the total CO line luminosity. When interpreted as a massive molecular outflow wind, the associated mechanical energy can be explained by a concentrated starburst with star formation rate (SFR) {>=}100 M{sub sun} yr{sup -1}, which agrees well with their SFR derived from the FIR luminosity. Using the high signal-to-noise stacked composite spectrum, we also probe {sup 13}CO and {sup 12}CN emission in the sample and discuss how the chemical abundance of molecular gas may vary depending on the physical conditions of the nuclear region.

  14. Molecular and morphological diversity in locally grown non-commercial (heirloom) mango varieties of North India.

    PubMed

    Bajpai, Anju; Muthukumar, M; Ahmad, Israr; Ravishankar, K V; Parthasarthy, V A; Sthapit, Bhuwon; Rao, Ramanatha; Verma, J P; Rajan, S

    2016-03-01

    Mango (Mangifera indica L.) has been cultivated and conserved in different agro-ecologies including Malihabad region in northern part of India, that is well known for housing diverse types (heirloom and commercial varieties). In the present study, 37 mango types comprising of 27 heirloom varieties from Malihabad region and 10 commercial varieties grown in North and Eastern India were assessed for morphological attributes and molecular diversity. The employed SSR markers amplified 2-13 alleles individually, cumulatively amplifying 124 alleles. These were studied for allelic diversity and genetic dissimilarity ranged from 0.035 to 0.892 arranging the varieties in three major clusters. The results revealed that majority of unique heirloom mangoes from Malihabad were different from the eastern part of the country. It is interesting to note Dashehari, a commercial variety from Malihabad was not aligned with heirloom varieties. Commercial varieties like Gulabkhas and Langra were placed in a separate group including Bombay Green, Himsagar, Dashehari, etc., indicating their dissimilarity with heirloom varieties at molecular level and thus, indicating importance for later from conservation point of view. Furthermore, the hierarchical clustering of varieties based on fruit morphology, assembled these into four groups largely influenced by fruit size. The maximum agreement subtree indicated seemingly good fit as thirteen varieties were arrayed in common grouping pattern. Appreciable dissimilarity among the heirloom varieties demonstrated by molecular analysis, underlines the importance for their on-farm conservation.

  15. Chromosomal localization and molecular characterization of three different 5S ribosomal DNA clusters in the sea urchin Paracentrotus lividus.

    PubMed

    Caradonna, Fabio; Bellavia, Daniele; Clemente, Ann Maria; Sisino, Giorgia; Barbieri, Rainer

    2007-09-01

    In this paper the chromosomal localization and molecular cloning and characterization of three 5S rDNA clusters of 700 bp (base pairs), 900 bp, and 950 bp in the sea urchin Paracentrotus lividus are reported. Southern blot hybridization demonstrated the existence of three 5S rDNA repeats of differing length in the P. lividus genome. Fluorescence in situ hybridization analysis, performed in parallel on both haploid and diploid metaphases and interphase nuclei using different 5S rDNA units as probes, localized these 5S rDNA clusters in 3 different pairs of P. lividus chromosomes. This is the first complete gene mapping not only in a sea urchin but also in the phylum of echinoderms as a whole. PMID:17893727

  16. Localized electroporation and molecular delivery into single living cells by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Nawarathna, D.; Unal, K.; Wickramasinghe, H. Kumar

    2008-10-01

    We present an efficient and fast method for selective and localized electroporation of a single living cell from a population of millions to tens of cells using the modified tip of an atomic force microscope. Electroporation was observed in real time using an inverted microscope. This technique is proposed as a tool for efficient and controlled delivery of biomolecules, proteins, drugs, and genes.

  17. DNA as a molecular local thermal probe for the analysis of magnetic hyperthermia.

    PubMed

    Dias, Jorge T; Moros, María; Del Pino, Pablo; Rivera, Sara; Grazú, Valeria; de la Fuente, Jesus M

    2013-10-25

    Too hot to handle: The surroundings of magnetic nanoparticles can be heated by applying a magnetic field. Polymer-coated magnetic nanoparticles were functionalized with single-stranded DNA molecules and further hybridized with DNA modified with different fluorophores. By correlating the denaturation profiles of the DNA with the local temperature, temperature gradients for the vicinity of the excited nanoparticles were determined.

  18. Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

    PubMed Central

    2008-01-01

    Background Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources. Results We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus. Conclusion Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution. PMID:18302790

  19. ATOMIC AND MOLECULAR PHYSICS: Four-parameter analytical local model potential for atoms

    NASA Astrophysics Data System (ADS)

    Yu, Fei; Sun, Jiu-Xun; Tian, Rong-Gang; Yang, Wei

    2009-10-01

    Analytical local model potential for modeling the interaction in an atom reduces the computational effort in electronic structure calculations significantly. A new four-parameter analytical local model potential is proposed for atoms Li through Lr, and the values of four parameters are shell-independent and obtained by fitting the results of Xa method. At the same time, the energy eigenvalues, the radial wave functions and the total energies of electrons are obtained by solving the radial Schrödinger equation with a new form of potential function by Numerov's numerical method. The results show that our new form of potential function is suitable for high, medium and low Z atoms. A comparison among the new potential function and other analytical potential functions shows the greater flexibility and greater accuracy of the present new potential function.

  20. An improved generalized Newton method for absolute value equations.

    PubMed

    Feng, Jingmei; Liu, Sanyang

    2016-01-01

    In this paper, we suggest and analyze an improved generalized Newton method for solving the NP-hard absolute value equations [Formula: see text] when the singular values of A exceed 1. We show that the global and local quadratic convergence of the proposed method. Numerical experiments show the efficiency of the method and the high accuracy of calculation. PMID:27462490

  1. Molecular kinetic theory of strongly nonequilibrium processes of mass, momentum, and energy transfer: Local equilibrium criteria

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.

    2015-09-01

    Consequences of the complete system of transfer equations of the properties (momentum, energy, and mass) of particles and their pairs are considered under local equilibrium conditions with regard to the Bogoliubov hierarchy of relaxation times between the first and second distribution functions (DFs) and distinctions in the characteristic relaxation times of particle momentum, energy, and mass. It is found that even under the local equilibrium condition in the Bogoliubov hierarchy of relaxation times between the first and second DFs, pair correlations are maintained between all dynamic variables (velocity, temperature, and density) whose values are proportional to the gradients of transferable properties. A criterion is introduced requiring there be no local equilibrium condition upon reaching the critical value at which the description of the transfer process becomes incorrect in classical nonequilibrium thermodynamics. External forces are considered in the equations for strongly nonequilibrium processes. Along with allowing for intermolecular potentials, it becomes possible to discuss the concept of passive forces (introduced in thermodynamics by Gibbs) from the standpoint of the kinetic theory. It is shown that use of this concept does not reflect modern representations of real processes.

  2. Localized and propagating surface plasmon resonance based fiber optic sensor for the detection of tetracycline using molecular imprinting

    NASA Astrophysics Data System (ADS)

    Shrivastav, Anand M.; Mishra, Satyendra K.; Gupta, Banshi D.

    2015-03-01

    In the present study we report a novel approach for the fabrication of localized and propagating surface plasmon resonance based fiber optic sensor for the detection of tetracycline using molecular imprinting (MIP) technique. The sensor is fabricated by coating layers of silver film, silver nanoparticles and MIP film prepared using tetracycline molecule as template over an unclad core of the multimode optical fiber. Nanoparticles of sizes in the range 10-30 nm are synthesized by hydrothermal process. A polychromatic light source is used to launch the light from one end of the fiber and the absorption spectrum for a given concentration of the tetracycline solution around the probe is measured at the other end of the fiber using a spectrometer interfaced with a computer. The absorption spectra are recorded for the concentration range of tetracycline from 10-8 M to 10-5 M. A shift of 102 nm in peak absorbance wavelength is obtained for this concentration range. The sensor works in the promising concentration range of tetracycline found in foods etc. The sensor has various advantages such as high sensitivity, low cost, fast response and capability of online monitoring and remote sensing. Further, the sensitivity of the sensor is about double the sensor based on localized surface plasmon resonance and molecular imprinting.

  3. Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

    NASA Astrophysics Data System (ADS)

    Rino, José Pedro; Borges, Denilson; Mota, Rita C.; Silva, Maurício A. P.

    2008-05-01

    Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has successfully described the structural, dynamical, and structural phase transformation induced by pressure in ZnTe [D. S. Borges and J. P. Rino, Phys. Rev. B 72, 014107 (2005)]. The two-body term of the interaction potential consists of Coulomb interaction resulting from charge transfer, steric repulsion due to atomic sizes, charge-dipole interaction to include the effect of electronic polarizability of anions, and dipole-dipole (van der Waals) interactions. The three-body covalent term is a modification of the Stillinger-Weber potential. Molecular dynamics simulations in isobaric-isenthalpic ensemble have been performed for systems amounting to 4096 and 64 000 particles. Starting from a crystalline zinc-blende (ZB) structure, the system is initially heated until a very homogeneous liquid is obtained. The vitreous zinc telluride phase is attained by cooling the liquid at sufficiently fast cooling rates, while slower cooling rates lead to a disordered ZB crystalline structure. Two- and three-body correlations for the liquid and vitreous phases are analyzed through pair distribution functions, static structure factors, and bond angle distributions. In particular, the neutron static structure factor for the liquid phase is in very good agreement with both the reported experimental data and first-principles simulations.

  4. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin.

    PubMed Central

    Caves, L. S.; Evanseck, J. D.; Karplus, M.

    1998-01-01

    Multiple molecular dynamics (MD) simulations of crambin with different initial atomic velocities are used to sample conformations in the vicinity of the native structure. Individual trajectories of length up to 5 ns sample only a fraction of the conformational distribution generated by ten independent 120 ps trajectories at 300 K. The backbone atom conformational space distribution is analyzed using principal components analysis (PCA). Four different major conformational regions are found. In general, a trajectory samples only one region and few transitions between the regions are observed. Consequently, the averages of structural and dynamic properties over the ten trajectories differ significantly from those obtained from individual trajectories. The nature of the conformational sampling has important consequences for the utilization of MD simulations for a wide range of problems, such as comparisons with X-ray or NMR data. The overall average structure is significantly closer to the X-ray structure than any of the individual trajectory average structures. The high frequency (less than 10 ps) atomic fluctuations from the ten trajectories tend to be similar, but the lower frequency (100 ps) motions are different. To improve conformational sampling in molecular dynamics simulations of proteins, as in nucleic acids, multiple trajectories with different initial conditions should be used rather than a single long trajectory. PMID:9541397

  5. Molecular cloning, chromosomal localization, and functional characterization of a human liver Na+/bile acid cotransporter.

    PubMed Central

    Hagenbuch, B; Meier, P J

    1994-01-01

    We have used a cDNA probe from a cloned rat liver Na+/taurocholate cotransporting polypeptide (Ntcp) to screen a human liver cDNA library. A 1,599-bp cDNA clone that encodes a human Na+/taurocholate cotransporting polypeptide (NTCP) was isolated. The human NTCP consists of 349 amino acids (calculated molecular mass of 38 kD) and exhibits 77% amino acid homology with the rat Ntcp. In vitro translation experiments indicate that the protein is glycosylated and has a molecular weight similar to the rat Ntcp. Injection of in vitro transcribed cRNA into Xenopus laevis oocytes resulted in the expression of Na(+)-dependent taurocholate uptake. Saturation kinetics indicated that the human NTCP has a higher affinity for taurocholate (apparent Km = 6 microM) than the previously cloned rat protein (apparent Km = 25 microM). NTCP-mediated taurocholate uptake into oocytes was inhibited by all major bile acid derivatives (100 microM), bumetanide (500 microM), and bromosulphophthalein (100 microM). Southern blot analysis of genomic DNA from a panel of human/hamster somatic cell hybrids mapped the human NTCP gene to chromosome 14. PMID:8132774

  6. Morphology and Molecular Gas Fractions of Local Luminous Infrared Galaxies as a Function of Infrared Luminosity and Merger Stage

    NASA Astrophysics Data System (ADS)

    Larson, K. L.; Sanders, D. B.; Barnes, J. E.; Ishida, C. M.; Evans, A. S.; U, V.; Mazzarella, J. M.; Kim, D.-C.; Privon, G. C.; Mirabel, I. F.; Flewelling, H. A.

    2016-07-01

    We present a new, detailed analysis of the morphologies and molecular gas fractions (MGFs) for a complete sample of 65 local luminous infrared galaxies from Great Observatories All-Sky Luminous Infrared Galaxies (LIRG) Survey using high resolution I-band images from The Hubble Space Telescope, the University of Hawaii 2.2 m Telescope and the Pan-STARRS1 Survey. Our classification scheme includes single undisturbed galaxies, minor mergers, and major mergers, with the latter divided into five distinct stages from pre-first pericenter passage to final nuclear coalescence. We find that major mergers of molecular gas-rich spirals clearly play a major role for all sources with {L}{IR}\\gt {10}11.5{L}ȯ ; however, below this luminosity threshold, minor mergers and secular processes dominate. Additionally, galaxies do not reach {L}{IR}\\gt {10}12.0{L}ȯ until late in the merger process when both disks are near final coalescence. The mean MGF ({MGF} = {M}{{{H}}2}/({M}* +{M}{{{H}}2})) for non-interacting and early-stage major merger LIRGs is 18 ± 2%, which increases to 33 ± 3%, for intermediate stage major merger LIRGs, consistent with the hypothesis that, during the early-mid stages of major mergers, most of the initial large reservoir of atomic gas (HI) at large galactocentric radii is swept inward where it is converted into molecular gas (H2).

  7. Morphological and sequence-related amplified polymorphism-based molecular diversity of local and exotic wheat genotypes.

    PubMed

    Abdelkhalik, S M; Salem, A K M; Abdelaziz, A R; Ammar, M H

    2016-04-28

    Assessing genetic diversity is a prerequisite for the genetic improvement of wheat. Molecular markers offer accurate and reproducible means for assessing genetic diversity. Field performance and sequence-related amplified polymorphism (SRAP)-based assessment of molecular diversity was carried out on a set of 10 local and introduced bread wheat (Triticum sativum L.) genotypes grown in the middle arid region of Saudi Arabia. The results revealed highly significant differences among the studied phenological traits and revealed a significant amount of genetic diversity across the tested genotypes. The overall performance revealed the superiority of KSU 102 in terms of yield and its components, with a yield potential of 8.7 tons/ha. Highly significant and positive correlations were observed among grain yield and biological yield, and also, spike length and spike weight. Thirteen SRAP primer combinations successfully amplified 954 fragments. The total number of genetic loci analyzed was 312. The overall polymorphism ratio was 99.67%, ranging from 98 to 100%. The polymorphic information content values ranged from 0.67 for ME11 x EM5 to 0.97 for ME9 x EM4 and ME11 x EM6, respectively. The wheat genotypes were clustered based on their genetic constitution and origin. The results demonstrate the power of SRAP primers for detecting molecular diversity and for varietal discrimination. The results show that high levels of genetic diversity exist, and suggest the potential of the tested materials for wheat crop improvement in the arid central region of Saudi Arabia.

  8. The AFGL absolute gravity program

    NASA Technical Reports Server (NTRS)

    Hammond, J. A.; Iliff, R. L.

    1978-01-01

    A brief discussion of the AFGL's (Air Force Geophysics Laboratory) program in absolute gravity is presented. Support of outside work and in-house studies relating to gravity instrumentation are discussed. A description of the current transportable system is included and the latest results are presented. These results show good agreement with measurements at the AFGL site by an Italian system. The accuracy obtained by the transportable apparatus is better than 0.1 microns sq sec 10 microgal and agreement with previous measurements is within the combined uncertainties of the measurements.

  9. Familial Aggregation of Absolute Pitch

    PubMed Central

    Baharloo, Siamak; Service, Susan K.; Risch, Neil; Gitschier, Jane; Freimer, Nelson B.

    2000-01-01

    Absolute pitch (AP) is a behavioral trait that is defined as the ability to identify the pitch of tones in the absence of a reference pitch. AP is an ideal phenotype for investigation of gene and environment interactions in the development of complex human behaviors. Individuals who score exceptionally well on formalized auditory tests of pitch perception are designated as “AP-1.” As described in this report, auditory testing of siblings of AP-1 probands and of a control sample indicates that AP-1 aggregates in families. The implications of this finding for the mapping of loci for AP-1 predisposition are discussed. PMID:10924408

  10. Local electric fields and molecular properties in heterogeneous environments through polarizable embedding.

    PubMed

    List, Nanna Holmgaard; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob

    2016-04-21

    In spectroscopies, the local field experienced by a molecule embedded in an environment will be different from the externally applied electromagnetic field, and this difference may significantly alter the response and transition properties of the molecule. The polarizable embedding (PE) model has previously been developed to model the local field contribution stemming from the direct molecule-environment coupling of the electromagnetic response properties of molecules in solution as well as in heterogeneous environments, such as proteins. Here we present an extension of this approach to address the additional effective external field effect, i.e., the manifestations of the environment polarization induced by the external field, which allows for the calculation of properties defined in terms of the external field. Within a response framework, we report calculations of the one- and two-photon absorption (1PA and 2PA, respectively) properties of PRODAN-methanol clusters as well as the fluorescent protein DsRed. Our results demonstrate the necessity of accounting for both the dynamical reaction field and effective external field contributions to the local field in order to reproduce full quantum chemical reference calculations. For the lowest π→π* transition in DsRed, inclusion of effective external field effects gives rise to a 1.9- and 3.5-fold reduction in the 1PA and 2PA cross-sections, respectively. The effective external field is, however, strongly influenced by the heterogeneity of the protein matrix, and the resulting effect can lead to either screening or enhancement depending on the nature of the transition under consideration. PMID:27007060

  11. Local isotropic diffusion approximation for coupled internal and overall molecular motions in NMR spin relaxation.

    PubMed

    Gill, Michelle L; Palmer, Arthur G

    2014-09-25

    The present work demonstrates that NMR spin relaxation rate constants for molecules interconverting between states with different diffusion tensors can be modeled theoretically by combining orientational correlation functions for exchanging spherical molecules with locally isotropic approximations for the diffusion anisotropic tensors. The resulting expressions are validated by comparison with correlation functions obtained by Monte Carlo simulations and are accurate for moderate degrees of diffusion anisotropy typically encountered in investigations of globular proteins. The results are complementary to an elegant, but more complex, formalism that is accurate for all degrees of diffusion anisotropy [Ryabov, Y.; Clore, G. M.; Schwieters, C. D. J. Chem. Phys. 2012, 136, 034108].

  12. A new type of localized fast moving electronic excitations in molecular chains

    NASA Astrophysics Data System (ADS)

    Korshunova, A. N.; Lakhno, V. D.

    2014-06-01

    It is shown that in a Holstein molecular chain placed in a strong longitudinal electric field some new types of excitations can arise. These excitations can transfer a charge over large distance (more than 1000 nucleotide pairs) along the chain retaining approximately their shapes. Excitations are formed only when a strong electric field either exists or quickly arises under especially preassigned conditions. These excitations transfer a charge even in the case when Holstein polarons are practically immobile. The results obtained are applied to synthetic homogeneous PolyG/PolyC DNA duplexes. They can also be provide the basis for explanation of famous H.W. Fink and C. Schönenberger experiment on long-range charge transfer in DNA.

  13. Reaction-diffusion-advection approach to spatially localized treadmilling aggregates of molecular motors

    NASA Astrophysics Data System (ADS)

    Yochelis, Arik; Bar-On, Tomer; Gov, Nir S.

    2016-04-01

    Unconventional myosins belong to a class of molecular motors that walk processively inside cellular protrusions towards the tips, on top of actin filament. Surprisingly, in addition, they also form retrograde moving self-organized aggregates. The qualitative properties of these aggregates are recapitulated by a mass conserving reaction-diffusion-advection model and admit two distinct families of modes: traveling waves and pulse trains. Unlike the traveling waves that are generated by a linear instability, pulses are nonlinear structures that propagate on top of linearly stable uniform backgrounds. Asymptotic analysis of isolated pulses via a simplified reaction-diffusion-advection variant on large periodic domains, allows to draw qualitative trends for pulse properties, such as the amplitude, width, and propagation speed. The results agree well with numerical integrations and are related to available empirical observations.

  14. Molecular Topology and Local Dynamics Govern the Viscosity of Imidazolium-Based Ionic Liquids.

    PubMed

    Zhang, Yong; Xue, Lianjie; Khabaz, Fardin; Doerfler, Rose; Quitevis, Edward L; Khare, Rajesh; Maginn, Edward J

    2015-11-25

    A series of branched ionic liquids (ILs) based on the 1-(iso-alkyl)-3-methylimidazolium cation from 1-(1-methylethyl)-3-methylimidazolium bistriflimide to 1-(5-methylhexyl)-3-methylimidazolium bistriflimide and linear ILs based on the 1-(n-alkyl)-3-methylimidazolium cation from 1-propyl-3-methylimidazolium bistriflimide to 1-heptyl-3-methylimidazolum bistriflimide were recently synthesized and their physicochemical properties characterized. For the ILs with the same number of carbons in the alkyl chain, the branched IL was found to have the same density but higher viscosity than the linear one. In addition, the branched IL 1-(2-methylpropyl)-3-methylimidazolium bistriflimide ([2mC3C1Im][NTf2]) was found to have an abnormally high viscosity. Motivated by these experimental observations, the same ILs were studied using molecular dynamics (MD) simulations in the current work. The viscosities of each IL were calculated using the equilibrium MD method at 400 K and the nonequilibrium MD method at 298 K. The results agree with the experimental trend. The ion pair (IP) lifetime, spatial distribution function, and associated potential of mean force, cation size and shape, and interaction energy components were calculated from MD simulations. A quantitative correlation between the liquid structure and the viscosity was observed. Analysis shows that the higher viscosities in the branched ILs are due to the relatively more stable packing between the cations and anions indicated by the lower minima in the potential of mean force (PMF) surface. The abnormal viscosity of [2mC3C1Im][NTf2] was found to be the result of the specific side chain length and molecular structure.

  15. Molecular cloning and chromosomal localization of human holocarboxylase synthetase, a gene responsible for biotin dependency

    SciTech Connect

    Suzuki, Y.; Aoki, Y.; Ishida, Y.

    1994-09-01

    Holocarboxylase synthetase (HCS) catalyzes biotin incorporation into various carboxylases that require biotin as a prosthetic group. They are acetyl-CoA carboxylase, a rate-limiting enzyme of fatty acid synthesis; pyruvate carboxylase, a key enzyme of gluconeogenesis; propionyl-CoA carboxylase and 3-methylcrotonyl-CoA carboxylase, enzymes involved in amino acid catabolism. HCS is therefore involved in various metabolic processes and is a key enzyme for biotin utilization by mammalian cells. Deficiency of HCS in man is known to cause biotin-responsive multiple carboxylase deficiency. Isolation of cDNA clones for the enzyme is essential to understand HCS and its deficiency at the molecular level. We purified bovine liver HCS and sequenced its proteolytic peptides. Degenerative oligonucleotide primers were synthesized from the two peptide sequences and used to amplify a putative HCS cDNA fragment from human liver by PCR. Using the amplified DNA fragment as a probe, we screened {lambda}gt10 human liver cDNA library and isolated 12 positive clones. The isolated cDNAs encoded a protein of 726 amino acids with molecular mass of 80,759. The protein contained several sequences identical or similar to those of peptides derived from the bovine liver HCS. The predicted protein had a homologous region with BirA which acts as both a biotin-[acetyl-CoA-carboxylase] ligase and a biotin repressor in E. coli, suggesting a functional relationship between the two proteins. We expressed the protein using pET3 a vector in E. coli (BL21 strain) and raised antiserum against the expressed protein. The antiserum immunoprecipitated HCS activities of human lymphoblasts and bovine liver. A one-base deletion and a missense mutation were found in cells from siblings with HCS deficiency. The human HCS gene was assigned to chromosome 21, region 21q22.1 by fluorescence in situ hybridization analysis.

  16. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    PubMed

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  17. Local Sharing as a Predominant Determinant of Synaptic Matrix Molecular Dynamics

    PubMed Central

    Zamorano, Pedro; Dresbach, Thomas; Boeckers, Tobias; Gundelfinger, Eckart D; Garner, Craig C; Ziv, Noam E

    2006-01-01

    Recent studies suggest that central nervous system synapses can persist for weeks, months, perhaps lifetimes, yet little is known as to how synapses maintain their structural and functional characteristics for so long. As a step toward a better understanding of synaptic maintenance we examined the loss, redistribution, reincorporation, and replenishment dynamics of Synapsin I and ProSAP2/Shank3, prominent presynaptic and postsynaptic matrix molecules, respectively. Fluorescence recovery after photobleaching and photoactivation experiments revealed that both molecules are continuously lost from, redistributed among, and reincorporated into synaptic structures at time-scales of minutes to hours. Exchange rates were not affected by inhibiting protein synthesis or proteasome-mediated protein degradation, were accelerated by stimulation, and greatly exceeded rates of replenishment from somatic sources. These findings indicate that the dynamics of key synaptic matrix molecules may be dominated by local protein exchange and redistribution, whereas protein synthesis and degradation serve to maintain and regulate the sizes of local, shared pools of these proteins. PMID:16903782

  18. Molecular cloning and subcellular localization of Tektin2-binding protein 1 (Ccdc 172) in rat spermatozoa.

    PubMed

    Yamaguchi, Airi; Kaneko, Takane; Inai, Tetsuichiro; Iida, Hiroshi

    2014-04-01

    Tektins (TEKTs) are composed of a family of filament-forming proteins localized in cilia and flagella. Five types of mammalian TEKTs have been reported, all of which have been verified to be present in sperm flagella. TEKT2, which is indispensable for sperm structure, mobility, and fertilization, was present at the periphery of the outer dense fiber (ODF) in the sperm flagella. By yeast two-hybrid screening, we intended to isolate flagellar proteins that could interact with TEKT2, which resulted in the isolation of novel two genes from the mouse testis library, referred as a TEKT2-binding protein 1 (TEKT2BP1) and -protein 2 (TEKT2BP2). In this study, we characterized TEKT2BP1, which is registered as a coiled-coil domain-containing protein 172 (Ccdc172) in the latest database. RT-PCR analysis indicated that TEKT2BP1 was predominantly expressed in rat testis and that its expression was increased after 3 weeks of postnatal development. Immunocytochemical studies discovered that TEKT2BP1 localized in the middle piece of rat spermatozoa, predominantly concentrated at the mitochondria sheath of the flagella. We hypothesize that the TEKT2-TEKT2BP1 complex might be involved in the structural linkage between the ODF and mitochondria in the middle piece of the sperm flagella.

  19. Molecular cloning, expression analysis and subcellular localization of four DELLA genes from hybrid poplar.

    PubMed

    Liu, Sian; Xuan, Lei; Xu, Li-An; Huang, Minren; Xu, Meng

    2016-01-01

    Gibberellic acid (GA) signaling regulates diverse aspects of plant growth and developmental processes. The DELLA repressors of GA signaling are named for an N-terminal conserved DELLA domain. In this study, four genes encoding DELLA proteins, PeRGA1, PeRGA2, PeGAI1 and PeGAI2, were isolated and characterized in poplar. A gene structural analysis revealed that the DELLA genes were all intron-free. Multiple protein sequence alignments revealed that these proteins contained seven highly conserved domains: the DELLA domain, the TVHYNP domain, leucine heptad repeat I (LHR I), the VHIID domain, leucine heptad repeat II (LHR II), the PFYRE domain, and the SAM domain. Temporal expression patterns of these genes were profiled during the adventitious root development of poplar. The four DELLA genes were expressed in root, stem and leaf in a dynamic manner. The subcellular localization demonstrated that these DELLA genes were mainly localized to the nucleus. These results suggest that the four DELLA genes may play diverse regulatory roles in the adventitious root, stem and leaf development of poplar, and contribute to improving our understanding of conserved and divergent aspects of DELLA proteins that restrain GA signaling in various species. PMID:27478746

  20. Molecular cloning and subcellular localization of Tektin2-binding protein 1 (Ccdc 172) in rat spermatozoa.

    PubMed

    Yamaguchi, Airi; Kaneko, Takane; Inai, Tetsuichiro; Iida, Hiroshi

    2014-04-01

    Tektins (TEKTs) are composed of a family of filament-forming proteins localized in cilia and flagella. Five types of mammalian TEKTs have been reported, all of which have been verified to be present in sperm flagella. TEKT2, which is indispensable for sperm structure, mobility, and fertilization, was present at the periphery of the outer dense fiber (ODF) in the sperm flagella. By yeast two-hybrid screening, we intended to isolate flagellar proteins that could interact with TEKT2, which resulted in the isolation of novel two genes from the mouse testis library, referred as a TEKT2-binding protein 1 (TEKT2BP1) and -protein 2 (TEKT2BP2). In this study, we characterized TEKT2BP1, which is registered as a coiled-coil domain-containing protein 172 (Ccdc172) in the latest database. RT-PCR analysis indicated that TEKT2BP1 was predominantly expressed in rat testis and that its expression was increased after 3 weeks of postnatal development. Immunocytochemical studies discovered that TEKT2BP1 localized in the middle piece of rat spermatozoa, predominantly concentrated at the mitochondria sheath of the flagella. We hypothesize that the TEKT2-TEKT2BP1 complex might be involved in the structural linkage between the ODF and mitochondria in the middle piece of the sperm flagella. PMID:24394471

  1. Molecular Analysis and Localization of CaARA7 a Conventional RAB5 GTPase from Characean Algae.

    PubMed

    Hoepflinger, Marion C; Geretschlaeger, Anja; Sommer, Aniela; Hoeftberger, Margit; Hametner, Christina; Ueda, Takashi; Foissner, Ilse

    2015-05-01

    RAB5 GTPases are important regulators of endosomal membrane traffic. Among them Arabidopsis thaliana ARA7/RABF2b is highly conserved and homologues are present in fungal, animal and plant kingdoms. In land plants ARA7 and its homologues are involved in endocytosis and transport towards the vacuole. Here we report on the isolation of an ARA7 homologue (CaARA7/CaRABF2) in the highly evolved characean green alga Chara australis. It encodes a polypeptide of 202 amino acids with a calculated molecular mass of 22.2 kDa and intrinsic GTPase activity. Immunolabelling of internodal cells with a specific antibody reveals CaARA7 epitopes at multivesicular endosomes (MVEs) and at MVE-containing wortmannin (WM) compartments. When transiently expressed in epidermal cells of Nicotiana benthamiana leaves, fluorescently tagged CaARA7 localizes to small organelles (putative MVEs) and WM compartments, and partially colocalizes with AtARA7 and CaARA6, a plant specific RABF1 GTPase. Mutations in membrane anchoring and GTP binding sites alter localization of CaARA7 and affect GTPase activity, respectively. This first detailed study of a conventional RAB5 GTPase in green algae demonstrates that CaARA7 is similar to RAB5 GTPases from land plants and other organisms and shows conserved structure and localization. PMID:25639563

  2. Molecular Analysis and Localization of CaARA7 a Conventional RAB5 GTPase from Characean Algae.

    PubMed

    Hoepflinger, Marion C; Geretschlaeger, Anja; Sommer, Aniela; Hoeftberger, Margit; Hametner, Christina; Ueda, Takashi; Foissner, Ilse

    2015-05-01

    RAB5 GTPases are important regulators of endosomal membrane traffic. Among them Arabidopsis thaliana ARA7/RABF2b is highly conserved and homologues are present in fungal, animal and plant kingdoms. In land plants ARA7 and its homologues are involved in endocytosis and transport towards the vacuole. Here we report on the isolation of an ARA7 homologue (CaARA7/CaRABF2) in the highly evolved characean green alga Chara australis. It encodes a polypeptide of 202 amino acids with a calculated molecular mass of 22.2 kDa and intrinsic GTPase activity. Immunolabelling of internodal cells with a specific antibody reveals CaARA7 epitopes at multivesicular endosomes (MVEs) and at MVE-containing wortmannin (WM) compartments. When transiently expressed in epidermal cells of Nicotiana benthamiana leaves, fluorescently tagged CaARA7 localizes to small organelles (putative MVEs) and WM compartments, and partially colocalizes with AtARA7 and CaARA6, a plant specific RABF1 GTPase. Mutations in membrane anchoring and GTP binding sites alter localization of CaARA7 and affect GTPase activity, respectively. This first detailed study of a conventional RAB5 GTPase in green algae demonstrates that CaARA7 is similar to RAB5 GTPases from land plants and other organisms and shows conserved structure and localization.

  3. Molecular Analysis and Localization of CaARA7 a Conventional RAB5 GTPase from Characean Algae

    PubMed Central

    Hoepflinger, Marion C.; Geretschlaeger, Anja; Sommer, Aniela; Hoeftberger, Margit; Hametner, Christina; Ueda, Takashi; Foissner, Ilse

    2015-01-01

    RAB5 GTPases are important regulators of endosomal membrane traffic. Among them Arabidopsis thaliana ARA7/RABF2b is highly conserved and homologues are present in fungal, animal and plant kingdoms. In land plants ARA7 and its homologues are involved in endocytosis and transport towards the vacuole. Here we report on the isolation of an ARA7 homologue (CaARA7/CaRABF2) in the highly evolved characean green alga Chara australis. It encodes a polypeptide of 202 amino acids with a calculated molecular mass of 22.2 kDa and intrinsic GTPase activity. Immunolabelling of internodal cells with a specific antibody reveals CaARA7 epitopes at multivesicular endosomes (MVEs) and at MVE-containing wortmannin (WM) compartments. When transiently expressed in epidermal cells of Nicotiana benthamiana leaves, fluorescently tagged CaARA7 localizes to small organelles (putative MVEs) and WM compartments, and partially colocalizes with AtARA7 and CaARA6, a plant specific RABF1 GTPase. Mutations in membrane anchoring and GTP binding sites alter localization of CaARA7 and affect GTPase activity, respectively. This first detailed study of a conventional RAB5 GTPase in green algae demonstrates that CaARA7 is similar to RAB5 GTPases from land plants and other organisms and shows conserved structure and localization. PMID:25639563

  4. A general relativistic model for free-fall absolute gravimeters

    NASA Astrophysics Data System (ADS)

    Tan, Yu-Jie; Shao, Cheng-Gang; Li, Jia; Hu, Zhong-Kun

    2016-04-01

    Although the relativistic manifestations of gravitational fields in gravimetry were first studied 40 years ago, the relativistic effects combined with free-fall absolute gravimeters have rarely been considered. In light of this, we present a general relativistic model for free-fall absolute gravimeters in a local-Fermi coordinates system, where we focus on effects related to the measuring devices: relativistic transverse Doppler effects, gravitational redshift effects and Earth’s rotation effects. Based on this model, a general relativistic expression of the measured gravity acceleration is obtained.

  5. Molecular cloning, genomic organization, and chromosomal localization of the human pancreatitis-associated protein (PAP) gene

    SciTech Connect

    Dusetti, N.J.; Frigerio, J.M.; Dagorn, J.C.; Iovanna, J.L. ); Fox, M.F.; Swallow, D.M. )

    1994-01-01

    Pancreatitis-associated protein (PAP) is a secretory pancreatic protein present in small amounts in normal pancreas and overexpressed during the acute phase of pancreatitis. In this paper, the authors describe the cloning, characterization, and chromosomal mapping of the human PAP gene. The gene spans 2748 bp and contains six exons interrupted by five introns. The gene has a typical promoter containing the sequences TATAAA and CCAAT 28 and 52 bp upstream of the cap site, respectively. They found striking similarities in genomic organization as well as in the promoter sequences between the human and rat PAP genes. The human PAP gene was mapped to chromosome 2p12 using rodent-human hybrid cells and in situ chromosomal hybridization. This localization coincides with that of the reg/lithostathine gene, which encodes a pancreatic secretory protein structurally related to PAP, suggesting that both genes derived from the same ancestral gene by duplication. 35 refs., 4 figs., 1 tab.

  6. Metallic Glass Wire Based Localization of Kinesin/Microtubule Bio-molecular Motility System

    NASA Astrophysics Data System (ADS)

    Kim, K.; Sikora, A.; Yaginuma, S.; Nakayama, K. S.; Nakazawa, H.; Umetsu, M.; Hwang, W.; Teizer, W.

    2014-03-01

    We report electrophoretic accumulation of microtubules along metallic glass (Pd42.5Cu30Ni7.5P20) wires free-standing in solution. Microtubules are dynamic cytoskeletal filaments. Kinesin is a cytoskeletal motor protein. Functions of these bio-molecules are central to various dynamic cellular processes. Functional artificial organization of bio-molecules is a prerequisite for transferring their native functions into device applications. Fluorescence microscopy at the individual-microtubule level reveals microtubules aligning along the wire axis during the electrophoretic migration. Casein-treated electrodes are effective for releasing trapped microtubules upon removal of the external field. Furthermore, we demonstrate gliding motion of microtubules on kinesin-treated metallic glass wires. The reversible manner in the local adsorption of microtubules, the flexibility of wire electrodes, and the compatibility between the wire electrode and the bio-molecules are beneficial for spatio-temporal manipulation of the motility machinery in 3 dimensions.

  7. Molecular epidemiology of dengue 2 viruses in the Philippines: genotype shift and local evolution.

    PubMed

    Salda, Leonora T D; Parquet, Maria D C; Matias, Ronald R; Natividad, Filipinas F; Kobayashi, Noboyuki; Morita, Kouichi

    2005-10-01

    The pre-membrane (prM) and envelope (E) genes of 41 viruses isolated from dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS) patients from 1995 to 2002 were sequenced to determine the genetic variability of dengue 2 (DENV 2) viruses in the Philippines. The envelope sequence data were compared with a global sample of DENV 2 obtained from GenBank. Phylogenetic analysis revealed that two distinct genotypes, Asian 2 and Cosmopolitan, are currently circulating locally, each with the potential to cause severe hemorrhagic disease. After the initial isolation in 1998, the Cosmopolitan genotype has gradually and effectively replaced Asian genotype 2 in the Philippines. Members of this genotype were closely related to viruses from Australia, Singapore, and Thailand.

  8. Type 3 iodothyronine deiodinase in neonatal goats: molecular cloning, expression, localization, and methylation signature.

    PubMed

    Zhong, Tao; Jin, Peng-Fei; Zhao, Wei; Wang, Lin-Jie; Li, Li; Zhang, Hong-Ping

    2016-07-01

    Type 3 iodothyronine deiodinase (DIO3) is an important enzyme in the metabolism of thyroid hormones. It plays critical roles in fetal development and neonatal growth and is especially important for brain development in mammals. In the present study, we profiled the expression pattern and methylation signature of the DIO3 gene in goats. The complete coding sequence of caprine DIO3 encoded a protein of 301 amino acids and harbored an internal selenocysteine-encoding TGA codon. The DIO3 messenger RNA (mRNA) was predominantly expressed in the neonatal goat liver (P < 0.01), while expression in other tissues was quite low, with the lowest levels in the lung. In in situ hybridization, the DIO3 mRNA was predominantly localized in the liver and the lowest content was detected in the lung. The DIO3 transcript was widely localized in neurons and the neuropil. Methylation profiling of the DIO3 CpG island showed a significant difference between the 5' region (CpGs_1∼24) and the 3' region (CpG_25∼51) of the coding region. Furthermore, no significant difference in methylation status was observed among the six tested tissues with levels in the range of 29.11-33.12 %. The CpG islands in the intergenic-differentially methylated region (IG-DMR) showed significantly different methylated levels among tissues, and the highest methylated level was observed in lung (CpG island 1, 69.34 %) and longissimus dorsi (LD) (CpG island 2, 52.62 %) tissues. Our study lays a foundation for understanding DIO3 function and the diseases caused by altered methylation profiles of the DIO3 gene. PMID:27108114

  9. Elucidating redox-level dispersion and local dielectric effects within electroactive molecular films.

    PubMed

    Bueno, Paulo R; Davis, Jason J

    2014-02-18

    The electron exchange between a redox-active molecular film and its underlying electrode can be cleanly tracked, in a frequency-resolved manner, through associated capacitive charging. If acquired data is treated with a classical (non quantum) model, mathematically equivalent to a Nernst distribution for one redox energy level, redox site coverage is both underestimated and environmentally variable. This physically unrealistic model fails to account for the energetic dispersion intrinsically related to the quantized characteristics of coupled redox and electrode states. If one maps this redox capacitive charging as a function of electrode potential one not only reproduces observations made by standard electroanalytical methods but additionally and directly resolves the spread of redox state energies the electrode is communicating with. In treating a population of surface-confined redox states as constituting a density of states, these analyses further resolve the effects of electrolyte dielectric on energetic spread in accordance with the electron-transfer models proposed by Marcus and others. These observations additionally underpin a directly (spectrally) resolved dispersion in electron-transfer kinetics. PMID:24392706

  10. Molecular detection and genetic characterization of kobuviruses and astroviruses in asymptomatic local pigs in East Africa

    PubMed Central

    Okoth, Edward; Junga, Joseph O.; Ogara, William O.; Njahira, Moses N.; Wang, Qiuhong; Vlasova, Anastasia N.; Djikeng, Appolinaire

    2014-01-01

    In this study, swine fecal specimens (n = 251) collected from nursing and weaned piglets raised under smallholder production systems were screened for the presence of kobuviruses by RT-PCR. Porcine kobuviruses were detected in 13.1 % (33/251) of the samples. We demonstrated that porcine kobuvirus infections exist in indigenous pigs in Kenya and Uganda and that the prevalence was higher in young piglets than older pigs: nursing piglets (15 %), post-weaning (3-month-old) pigs (17 %), 4-month-old pigs (10 %). Genetic analysis of the partial RNA-dependent RNA polymerase (RdRp) region (690 nt) revealed that kobuviruses circulating in East Africa are diverse, sharing nucleotide sequence identities ranging from 89.7 to 99.1 % and 88 to 92.3 % among them and with known porcine kobuviruses, respectively. The nucleotide sequence identities between our kobuvirus strains and those of human, bovine and canine kobuviruses were 69.4-70.7 %, 73.1-74.4 % and 67-70.7 %, respectively. Additionally, upon sequencing selected samples that showed consistent 720-bp RT-PCR bands while using the same primer set, we detected porcine astroviruses in our samples belonging to type 2 and type 3 mamastroviruses. To our knowledge, this study reports the first detection and molecular analysis of both porcine kobuviruses and astroviruses in an African region. Further studies are required to determine the role of these viruses in gastrointestinal infections of pigs in this region and to determine the genetic diversity of the circulating strains to develop accurate diagnostic tools and implement appropriate control strategies. PMID:24327095

  11. Vacancy defects and the formation of local haeckelite structures in graphene from tight-binding molecular dynamics

    SciTech Connect

    Lee, Gun-Do; Yoon, Euijoon; Wang, C. Z.; Ho, K. M.; Hwang, Nong-Moon

    2006-12-15

    The dynamics of multivacancy defects in a graphene layer is investigated by tight-binding molecular dynamics simulations and by first principles calculation. The simulations show that four single vacancies in the graphene layer first coalesce into two double vacancies, each consisting of a pentagon-heptagon-pentagon (5-8-5) defective structure. While one of the 5-8-5 defects further reconstructs into a 555-777 defect, which is composed of three pentagonal rings and three heptagonal rings, another 5-8-5 defect diffuses toward the reconstructed 555-777 defect. During the 5-8-5 defect diffusion process, three interesting mechanisms, i.e., 'dimer diffusion', 'chain diffusion', and 'single atom diffusion', are observed. Finally, the four single vacancies reconstruct into two adjacent 555-777 defects, which is a local haeckelite structure.

  12. Local structure and molecular motions in imidazolium hydrogen malonate crystal as studied by 2H and 13C NMR

    NASA Astrophysics Data System (ADS)

    Mizuno, M.; Chizuwa, M.; Umiyama, T.; Kumagai, Y.; Miyatou, T.; Ohashi, R.; Ida, T.; Tansho, M.; Shimizu, T.

    2015-04-01

    The local structure and molecular motion of the imidazolium hydrogen malonate crystal were investigated using solid-state 2H and 13C NMR. The imidazolium ion undergoes isotropic rotation, which is correlated with a defect in the crystal, as observed by 2H NMR broadline spectra above 263 K. A 180∘ flip of the imidazolium ion in the regular site was observed from 2H NMR quadrupole Carr-Purcell-Meiboom-Gill (QCPMG) spectra. The Grotthuss mechanism was accompanied by a 180∘ flip of the imidazolium ion in regular sites. Moreover, the proton transfer associated with the imidazolium ion of the defective crystal is important for proton conductivity of the imidazolium hydrogen malonate crystal.

  13. Cosmology with negative absolute temperatures

    NASA Astrophysics Data System (ADS)

    Vieira, J. P. P.; Byrnes, Christian T.; Lewis, Antony

    2016-08-01

    Negative absolute temperatures (NAT) are an exotic thermodynamical consequence of quantum physics which has been known since the 1950's (having been achieved in the lab on a number of occasions). Recently, the work of Braun et al. [1] has rekindled interest in negative temperatures and hinted at a possibility of using NAT systems in the lab as dark energy analogues. This paper goes one step further, looking into the cosmological consequences of the existence of a NAT component in the Universe. NAT-dominated expanding Universes experience a borderline phantom expansion (w < ‑1) with no Big Rip, and their contracting counterparts are forced to bounce after the energy density becomes sufficiently large. Both scenarios might be used to solve horizon and flatness problems analogously to standard inflation and bouncing cosmologies. We discuss the difficulties in obtaining and ending a NAT-dominated epoch, and possible ways of obtaining density perturbations with an acceptable spectrum.

  14. Apparatus for absolute pressure measurement

    NASA Technical Reports Server (NTRS)

    Hecht, R. (Inventor)

    1969-01-01

    An absolute pressure sensor (e.g., the diaphragm of a capacitance manometer) was subjected to a superimposed potential to effectively reduce the mechanical stiffness of the sensor. This substantially increases the sensitivity of the sensor and is particularly useful in vacuum gauges. An oscillating component of the superimposed potential induced vibrations of the sensor. The phase of these vibrations with respect to that of the oscillating component was monitored, and served to initiate an automatic adjustment of the static component of the superimposed potential, so as to bring the sensor into resonance at the frequency of the oscillating component. This establishes a selected sensitivity for the sensor, since a definite relationship exists between resonant frequency and sensitivity.

  15. Cosmology with negative absolute temperatures

    NASA Astrophysics Data System (ADS)

    Vieira, J. P. P.; Byrnes, Christian T.; Lewis, Antony

    2016-08-01

    Negative absolute temperatures (NAT) are an exotic thermodynamical consequence of quantum physics which has been known since the 1950's (having been achieved in the lab on a number of occasions). Recently, the work of Braun et al. [1] has rekindled interest in negative temperatures and hinted at a possibility of using NAT systems in the lab as dark energy analogues. This paper goes one step further, looking into the cosmological consequences of the existence of a NAT component in the Universe. NAT-dominated expanding Universes experience a borderline phantom expansion (w < -1) with no Big Rip, and their contracting counterparts are forced to bounce after the energy density becomes sufficiently large. Both scenarios might be used to solve horizon and flatness problems analogously to standard inflation and bouncing cosmologies. We discuss the difficulties in obtaining and ending a NAT-dominated epoch, and possible ways of obtaining density perturbations with an acceptable spectrum.

  16. Molecular characterization of Wolbachia infection in bed bugs (Cimex lectularius) collected from several localities in France.

    PubMed

    Akhoundi, Mohammad; Cannet, Arnaud; Loubatier, Céline; Berenger, Jean-Michel; Izri, Arezki; Marty, Pierre; Delaunay, Pascal

    2016-01-01

    Wolbachia symbionts are maternally inherited intracellular bacteria that have been detected in numerous insects including bed bugs. The objective of this study, the first epidemiological study in Europe, was to screen Wolbachia infection among Cimex lectularius collected in the field, using PCR targeting the surface protein gene (wsp), and to compare obtained Wolbachia strains with those reported from laboratory colonies of C. lectularius as well as other Wolbachia groups. For this purpose, 284 bed bug specimens were caught and studied from eight different regions of France including the suburbs of Paris, Bouches-du-Rhône, Lot-et-Garonne, and five localities in Alpes-Maritimes. Among the samples, 166 were adults and the remaining 118 were considered nymphs. In all, 47 out of 118 nymphs (40%) and 61 out of 166 adults (37%) were found positive on wsp screening. Among the positive cases, 10 samples were selected randomly for sequencing. The sequences had 100% homology with wsp sequences belonging to the F-supergroup strains of Wolbachia. Therefore, we confirm the similarity of Wolbachia strains detected in this epidemiological study to Wolbachia spp. reported from laboratory colonies of C. lectularius. PMID:27492563

  17. Atom-scale depth localization of biologically important chemical elements in molecular layers.

    PubMed

    Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

    2016-08-23

    In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers' global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces. PMID:27503887

  18. Molecular cloning, characterization, subcellular localization and dynamics of p23, the mammalian KDEL receptor

    PubMed Central

    1993-01-01

    We have isolated a cDNA clone (mERD2) for the mammalian (bovine) homologue of the yeast ERD2 gene, which codes for the yeast HDEL receptor. The deduced amino acid sequence bears extensive homology to its yeast counterpart and is almost identical to a previously described human sequence. The sequence predicts a very hydrophobic protein with multiple membrane spanning domains, as confirmed by analysis of the in vitro translation product. The protein encoded by mERD2 (p23) has widespread occurrence, being present in all the cell types examined. p23 was localized to the cis-side of the Golgi apparatus and to a spotty intermediate compartment which mediates ER to Golgi transport. A majority of the intracellular staining could be accumulated in the intermediate compartment by a low temperature (15 degrees C) or brefeldin A. During recovery from these treatments, the spotty intermediate compartment staining of p23 was shifted to the perinuclear staining of the Golgi apparatus and tubular structures marked by p23 were observed. These tubular structures may serve to mediate transport between the intermediate compartment and the Golgi apparatus. PMID:8380600

  19. Molecular characterization of Wolbachia infection in bed bugs (Cimex lectularius) collected from several localities in France

    PubMed Central

    Akhoundi, Mohammad; Cannet, Arnaud; Loubatier, Céline; Berenger, Jean-Michel; Izri, Arezki; Marty, Pierre; Delaunay, Pascal

    2016-01-01

    Wolbachia symbionts are maternally inherited intracellular bacteria that have been detected in numerous insects including bed bugs. The objective of this study, the first epidemiological study in Europe, was to screen Wolbachia infection among Cimex lectularius collected in the field, using PCR targeting the surface protein gene (wsp), and to compare obtained Wolbachia strains with those reported from laboratory colonies of C. lectularius as well as other Wolbachia groups. For this purpose, 284 bed bug specimens were caught and studied from eight different regions of France including the suburbs of Paris, Bouches-du-Rhône, Lot-et-Garonne, and five localities in Alpes-Maritimes. Among the samples, 166 were adults and the remaining 118 were considered nymphs. In all, 47 out of 118 nymphs (40%) and 61 out of 166 adults (37%) were found positive on wsp screening. Among the positive cases, 10 samples were selected randomly for sequencing. The sequences had 100% homology with wsp sequences belonging to the F-supergroup strains of Wolbachia. Therefore, we confirm the similarity of Wolbachia strains detected in this epidemiological study to Wolbachia spp. reported from laboratory colonies of C. lectularius. PMID:27492563

  20. Atom-scale depth localization of biologically important chemical elements in molecular layers

    PubMed Central

    Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

    2016-01-01

    In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers’ global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces. PMID:27503887

  1. Atom-scale depth localization of biologically important chemical elements in molecular layers.

    PubMed

    Schneck, Emanuel; Scoppola, Ernesto; Drnec, Jakub; Mocuta, Cristian; Felici, Roberto; Novikov, Dmitri; Fragneto, Giovanna; Daillant, Jean

    2016-08-23

    In nature, biomolecules are often organized as functional thin layers in interfacial architectures, the most prominent examples being biological membranes. Biomolecular layers play also important roles in context with biotechnological surfaces, for instance, when they are the result of adsorption processes. For the understanding of many biological or biotechnologically relevant phenomena, detailed structural insight into the involved biomolecular layers is required. Here, we use standing-wave X-ray fluorescence (SWXF) to localize chemical elements in solid-supported lipid and protein layers with near-Ångstrom precision. The technique complements traditional specular reflectometry experiments that merely yield the layers' global density profiles. While earlier work mostly focused on relatively heavy elements, typically metal ions, we show that it is also possible to determine the position of the comparatively light elements S and P, which are found in the most abundant classes of biomolecules and are therefore particularly important. With that, we overcome the need of artificial heavy atom labels, the main obstacle to a broader application of high-resolution SWXF in the fields of biology and soft matter. This work may thus constitute the basis for the label-free, element-specific structural investigation of complex biomolecular layers and biological surfaces.

  2. The murine ufo receptor: molecular cloning, chromosomal localization and in situ expression analysis.

    PubMed

    Faust, M; Ebensperger, C; Schulz, A S; Schleithoff, L; Hameister, H; Bartram, C R; Janssen, J W

    1992-07-01

    We have cloned the mouse homologue of the ufo oncogene. It encodes a novel tyrosine kinase receptor characterized by a unique extracellular domain containing two immunoglobulin-like and two fibronectin type III repeats. Comparison of the predicted ufo amino acid sequences of mouse and man revealed an overall identity of 87.6%. The ufo locus maps to mouse chromosome 7A3-B1 and thereby extends the known conserved linkage group between mouse chromosome 7 and human chromosome 19. RNA in situ hybridization analysis established the onset of specific ufo expression in the late embryogenesis at day 12.5 post coitum (p.c.) and localized ufo transcription to distinct substructures of a broad spectrum of developing tissues (e.g. subepidermal cells of the skin, mesenchymal cells of the periosteum). In adult animals ufo is expressed in cells forming organ capsules as well as in connective tissue structures. ufo may function as a signal transducer between specific cell types of mesodermal origin.

  3. Molecular Characterization of Selected Local and Exotic Cattle Using RAPD Marker

    PubMed Central

    Khatun, M. Mahfuza; Hossain, Khondoker Moazzem; Mahbubur Rahman, S. M.

    2012-01-01

    In order to develop specific genetic markers and determine the genetic diversity of Bangladeshi native cattle (Pabna, Red Chittagong) and exotic breeds (Sahiwal), randomly amplified polymorphic DNA (RAPD) analysis was performed using 12 primers. Genomic DNA was extracted from 20 cattle (local and exotic) blood samples and extracted DNA was observed by gel electrophoresis. Among the random primers three were matched and found to be polymorphic. Genetic relations between cattle’s were determined by RAPD polymorphisms from a total of 66.67%. Statistical analysis of the data, estimating the genetic distances between cattle and sketching the cluster trees were estimated by using MEGA 5.05 software. Comparatively highest genetic distance (0.834) was found between RCC-82 and SL-623. The lowest genetic distance (0.031) was observed between M-1222 and M-5730. The genetic diversity of Red Chittagong and Sahiwal cattle was relatively higher for a prescribed breed. Adequate diversity in performance and adaptability can be exploited from the study results for actual improvement accruing to conservation and development of indigenous cattle resources. PMID:25049622

  4. Molecular determinants of prokaryotic voltage-gated sodium channels for recognition of local anesthetics.

    PubMed

    Shimomura, Takushi; Irie, Katsumasa; Fujiyoshi, Yoshinori

    2016-08-01

    Local anesthetics (LAs) inhibit mammalian voltage-gated Na(+) channels (Navs) and are thus clinically important. LAs also inhibit prokaryotic Navs (BacNavs), which have a simpler structure than mammalian Navs. To elucidate the detailed mechanisms of LA inhibition to BacNavs, we used NavBh, a BacNav from Bacillus halodurans, to analyze the interactions of several LAs and quaternary ammoniums (QAs). Based on the chemical similarity of QA with the tertiary-alkylamine (TAA) group of LAs, QAs were used to determine the residues required for the recognition of TAA by NavBh. We confirmed that two residues, Thr220 and Phe227, are important for LA binding; a methyl group of Thr220 is important for recognizing both QAs and LAs, whereas Phe227 is involved in holding blockers at the binding site. In addition, we found that NavBh holds blockers in a closed state, consistent with the large inner cavity observed in the crystal structures of BacNavs. These findings reveal the inhibition mechanism of LAs in NavBh, where the methyl group of Thr220 provides the main receptor site for the TAA group and the bulky phenyl group of Phe227 holds the blockers inside the large inner cavity. These two residues correspond to the two LA recognition residues in mammalian Navs, which suggests the relevance of the LA recognition between BacNavs and mammalian Navs. PMID:27273848

  5. Cytogenetic and molecular localization of tipE: A gene affecting sodium channels in Drosophila melanogaster

    SciTech Connect

    Feng, G.; Deak, P.; Hall, L.M.

    1995-04-01

    Voltage-sensitive sodium channels play a key role in nerve cells where they are responsible for the increase in sodium permeability during the rising phase of action potentials. In Drosophila melanogaster a subset of temperature-sensitive paralytic mutations affect sodium channel function. One such mutation is temperature-induced paralysis locus E (tipE), which has been shown by electrophysiology and ligand binding studies to reduce sodium channel numbers. Three new {gamma}-ray-induced tipE alleles associated with either visible deletions in 64AB or a translocation breakpoint within 64B2 provide landmarks for positional cloning of tipE. Beginning with the flanking cloned gene Ras2, a 140-kb walk across the translocation breakpoint was completed. Germline transformation using a 42-kb cosmid clone and successively smaller subclones localized the tipE gene within a 7.4-kb genomic DNA segment. Although this chromosome region is rich in transcripts, only three overlapping mRNAs (5.4, 4.4, and 1.7 kb) lie completely within the smallest rescuing construct. The small sizes of the rescuing construct and transcripts suggests that tipE does not encode a standard sodium channel {alpha}-subunit with four homologous repeats. Sequencing these transcripts will elucidate the role of the tipE gene product in sodium channel functional regulation. 55 refs., 4 figs., 2 tabs.

  6. In vivo seeding and cross-seeding of localized amyloidosis: a molecular link between type 2 diabetes and Alzheimer disease.

    PubMed

    Oskarsson, Marie E; Paulsson, Johan F; Schultz, Sebastian W; Ingelsson, Martin; Westermark, Per; Westermark, Gunilla T

    2015-03-01

    Several proteins have been identified as amyloid forming in humans, and independent of protein origin, the fibrils are morphologically similar. Therefore, there is a potential for structures with amyloid seeding ability to induce both homologous and heterologous fibril growth; thus, molecular interaction can constitute a link between different amyloid forms. Intravenous injection with preformed fibrils from islet amyloid polypeptide (IAPP), proIAPP, or amyloid-beta (Aβ) into human IAPP transgenic mice triggered IAPP amyloid formation in pancreas in 5 of 7 mice in each group, demonstrating that IAPP amyloid could be enhanced through homologous and heterologous seeding with higher efficiency for the former mechanism. Proximity ligation assay was used for colocalization studies of IAPP and Aβ in islet amyloid in type 2 diabetic patients and Aβ deposits in brains of patients with Alzheimer disease. Aβ reactivity was not detected in islet amyloid although islet β cells express AβPP and convertases necessary for Aβ production. By contrast, IAPP and proIAPP were detected in cerebral and vascular Aβ deposits, and presence of proximity ligation signal at both locations showed that the peptides were <40 nm apart. It is not clear whether IAPP present in brain originates from pancreas or is locally produced. Heterologous seeding between IAPP and Aβ shown here may represent a molecular link between type 2 diabetes and Alzheimer disease.

  7. Molecular characterization and expression of a novel kinesin which localizes with the kinetoplast in the human pathogen, Leishmania donovani.

    PubMed

    Gerald, Noel J; Coppens, Isabelle; Dwyer, Dennis M

    2008-04-01

    Using a variety of molecular and cell biological approaches, we identified, characterized and expressed a novel kinesin, LdK39B in the protozoan pathogen Leishmania donovani. Results of RT-PCR revealed two distinct LdK39B products with different splice leader mini-exon sites, indicative of two potentially mature mRNA transcripts. Analyses indicated that LdK39B had a calculated molecular mass of >261, 327 Da and contained multiple amino acid repeat units. Several GFP-LdK39B fusion constructs were generated and used for episomal-expression in these parasites. Results of confocal and immunoelectron microscopy indicated that the GFP-LdK39B-fusion proteins localized to a region adjacent to the flagellar pocket and the kinetoplast i.e. the mitochondrial-DNA containing organelle that is physically tethered to the flagellar basal bodies. Sub-cellular fractionation results showed that GFP-LdK39B proteins were insoluble in nature and remained tightly associated with purified flagella/kinetoplasts following their extraction with detergent and high salts. Our cumulative results suggest that the LdK39B may play a scaffold-like role in facilitating and maintaining the unique spatial/structural association between the flagellum-basal body-kinetoplast complex in these parasites. PMID:18240272

  8. An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation.

    PubMed

    Steiner, Denise; van Gunsteren, Wilfred F

    2012-07-01

    Deriving structural information about a protein from NMR experimental data is still a non-trivial challenge to computational biochemistry. This is because of the low ratio of the number of independent observables to the number of molecular degrees of freedom, the approximations involved in the different relationships between particular observable quantities and molecular conformation, and the averaged character of the experimental data. For example, protein (3)J-coupling data are seldom used for structure refinement because of the multiple-valuedness and limited accuracy of the Karplus relationship linking a (3)J-coupling to a torsional angle. Moreover, sampling of the large conformational space is still problematic. Using the 99-residue protein plastocyanin as an example we investigated whether use of a thermodynamically calibrated force field, inclusion of solvent degrees of freedom, and application of adaptive local-elevation sampling that accounts for conformational averaging produces a more realistic representation of the ensemble of protein conformations than standard single-structure refinement in a non-explicit solvent using restraints that do not account for averaging and are partly based on non-observed data. Yielding better agreement with observed experimental data, the protein conformational ensemble is less restricted than when using standard single-structure refinement techniques, which are likely to yield a picture of the protein which is too rigid.

  9. Rat kidney thromboxane receptor: molecular cloning, signal transduction, and intrarenal expression localization.

    PubMed Central

    Abe, T; Takeuchi, K; Takahashi, N; Tsutsumi, E; Taniyama, Y; Abe, K

    1995-01-01

    Thromboxane (TX) plays important roles in control of renal hemodynamics and water and electrolyte metabolism, and is involved in the pathophysiology of many renal diseases. The aim of the present study is to isolate a rat kidney cDNA encoding functional TX receptor, and to reveal its intrarenal expression localization. A clone (rTXR2) was isolated from a rat kidney cDNA library by a homology screening approach. rTXR2 was shown to encode the amino acid sequence containing seven transmembrane spanning domains representing rat (r) TX receptor. The membrane from COS-7 cells transiently transfected with rTXR2 cDNA was shown to be specifically bound by a thromboxane receptor antagonist, SQ29548. Either in Xenopus oocyte expression or in transfected COS-7 cells, rTX receptor was shown to be linked with Ca2+ messenger system. TX receptor-mediated increase in cytosolic Ca2+ was also observed in cultured glomerular mesangial cells. In situ hybridization showed that rTX receptor mRNA was detected in renal glomeruli, smooth muscle cells in renal arterioles, and transitional cell epithelium of renal pelvis. Reverse transcription linked to PCR applied to microdissected nephron segments indicated the presence of rTX receptor mRNA exclusively in the glomerulus. In conclusion, we have cloned a functional rat kidney TX receptor, which is expressed specifically in renal glomerulus, arterial smooth muscle cells, and transitional cell epithelium of renal pelvis. The present study will provide important insights into the etiology and pathophysiology of renal diseases with relation to TX metabolism. Images PMID:7635958

  10. A Spitzer Survey of Mid-infrared Molecular Emission from Protoplanetary Disks. II. Correlations and Local Thermal Equilibrium Models

    NASA Astrophysics Data System (ADS)

    Salyk, C.; Pontoppidan, K. M.; Blake, G. A.; Najita, J. R.; Carr, J. S.

    2011-04-01

    We present an analysis of Spitzer Infrared Spectrograph observations of H2O, OH, HCN, C2H2, and CO2 emission, and Keck-NIRSPEC observations of CO emission, from a diverse sample of T Tauri and Herbig Ae/Be circumstellar disks. We find that detections and strengths of most mid-IR molecular emission features are correlated with each other, suggesting a common origin and similar excitation conditions for this mid-infrared line forest. Aside from the remarkable differences in molecular line strengths between T Tauri, Herbig Ae/Be, and transitional disks discussed in Pontoppidan et al., we note that the line detection efficiency is anti-correlated with the 13/30 μm spectral slope, which is a measure of the degree of grain settling in the disk atmosphere. We also note a correlation between detection efficiency and Hα equivalent width, and tentatively with accretion rate, suggesting that accretional heating contributes to line excitation. If detected, H2O line fluxes are correlated with the mid-IR continuum flux, and other co-varying system parameters, such as L sstarf. However, significant sample variation, especially in molecular line ratios, remains, and its origin has yet to be explained. Local thermal equilibrium (LTE) models of the H2O emission show that line strength is primarily related to the best-fit emitting area, and this accounts for most source-to-source variation in H2O emitted flux. Best-fit temperatures and column densities cover only a small range of parameter space, near ~1018 cm-2 and 450 K for all sources, suggesting a high abundance of H2O in many planet-forming regions. Other molecules have a range of excitation temperatures from ~500to1500 K, also consistent with an origin in planet-forming regions. We find molecular ratios relative to water of ~10-3 for all molecules, with the exception of CO, for which n(CO)/n(H2O) ~ 1. However, LTE fitting caveats and differences in the way thermo-chemical modeling results are reported make comparisons with

  11. A SPITZER SURVEY OF MID-INFRARED MOLECULAR EMISSION FROM PROTOPLANETARY DISKS. II. CORRELATIONS AND LOCAL THERMAL EQUILIBRIUM MODELS

    SciTech Connect

    Salyk, C.; Pontoppidan, K. M.; Blake, G. A.; Najita, J. R.; Carr, J. S.

    2011-04-20

    We present an analysis of Spitzer Infrared Spectrograph observations of H{sub 2}O, OH, HCN, C{sub 2}H{sub 2}, and CO{sub 2} emission, and Keck-NIRSPEC observations of CO emission, from a diverse sample of T Tauri and Herbig Ae/Be circumstellar disks. We find that detections and strengths of most mid-IR molecular emission features are correlated with each other, suggesting a common origin and similar excitation conditions for this mid-infrared line forest. Aside from the remarkable differences in molecular line strengths between T Tauri, Herbig Ae/Be, and transitional disks discussed in Pontoppidan et al., we note that the line detection efficiency is anti-correlated with the 13/30 {mu}m spectral slope, which is a measure of the degree of grain settling in the disk atmosphere. We also note a correlation between detection efficiency and H{alpha} equivalent width, and tentatively with accretion rate, suggesting that accretional heating contributes to line excitation. If detected, H{sub 2}O line fluxes are correlated with the mid-IR continuum flux, and other co-varying system parameters, such as L{sub *}. However, significant sample variation, especially in molecular line ratios, remains, and its origin has yet to be explained. Local thermal equilibrium (LTE) models of the H{sub 2}O emission show that line strength is primarily related to the best-fit emitting area, and this accounts for most source-to-source variation in H{sub 2}O emitted flux. Best-fit temperatures and column densities cover only a small range of parameter space, near {approx}10{sup 18} cm{sup -2} and 450 K for all sources, suggesting a high abundance of H{sub 2}O in many planet-forming regions. Other molecules have a range of excitation temperatures from {approx}500to1500 K, also consistent with an origin in planet-forming regions. We find molecular ratios relative to water of {approx}10{sup -3} for all molecules, with the exception of CO, for which n(CO)/n(H{sub 2}O) {approx} 1. However, LTE

  12. Frequency-domain analysis of absolute gravimeters

    NASA Astrophysics Data System (ADS)

    Svitlov, S.

    2012-12-01

    An absolute gravimeter is analysed as a linear time-invariant system in the frequency domain. Frequency responses of absolute gravimeters are derived analytically based on the propagation of the complex exponential signal through their linear measurement functions. Depending on the model of motion and the number of time-distance coordinates, an absolute gravimeter is considered as a second-order (three-level scheme) or third-order (multiple-level scheme) low-pass filter. It is shown that the behaviour of an atom absolute gravimeter in the frequency domain corresponds to that of the three-level corner-cube absolute gravimeter. Theoretical results are applied for evaluation of random and systematic measurement errors and optimization of an experiment. The developed theory agrees with known results of an absolute gravimeter analysis in the time and frequency domains and can be used for measurement uncertainty analyses, building of vibration-isolation systems and synthesis of digital filtering algorithms.

  13. On the separability of the extended molecule: Constructing the best localized molecular orbitals for an organic molecule bridging two model electrodes

    SciTech Connect

    Moreira, Rodrigo A.; Melo, Celso P. de

    2014-09-28

    Based on a quantum chemical valence formalism that allows the rigorous construction of best-localized molecular orbitals on specific parts of an extended system, we examined the separability of individual components of model systems relevant to the description of electron transport in molecular devices. We started by examining how to construct the maximally localized electronic density at the tip of a realistic model of a gold electrode. By varying the number of gold atoms included in the local region where to project the total electronic density, we quantitatively assess how many molecular orbitals are entirely localized in that region. We then considered a 1,4-benzene-di-thiol molecule connected to two model gold electrodes and examined how to localize the electronic density of the total system in the extended molecule, a fractional entity comprising the organic molecule plus an increasing number of the closest metal atoms. We were able to identify in a rigorous manner the existence of three physically different electronic populations, each one corresponding to a distinct set of molecular orbitals. First, there are those entirely localized in the extended molecule, then there is a second group of those completely distributed in the gold atoms external to that region, and, finally, there are those delocalized over the entire system. This latter group can be associated to the shared electronic population between the extended molecule and the rest of the system. We suggest that the treatment here presented could be useful in the theoretical analysis of the electronic transport in nanodevices whenever the use of localized molecular states are required by the physics of the specific problem, such as in cases of weak coupling and super-exchange limits.

  14. Molecular Insights into the Local Anesthetic Receptor within Voltage-Gated Sodium Channels Using Hydroxylated Analogs of Mexiletine.

    PubMed

    Desaphy, Jean-François; Dipalma, Antonella; Costanza, Teresa; Carbonara, Roberta; Dinardo, Maria Maddalena; Catalano, Alessia; Carocci, Alessia; Lentini, Giovanni; Franchini, Carlo; Camerino, Diana Conte

    2012-01-01

    results confirm our former hypothesis by showing that the presence of hydroxyl groups to the aryloxy moiety of mexiletine greatly reduced sodium channel block, and provide molecular insights into the intimate interaction of local anesthetics with their receptor. PMID:22403541

  15. Absolute calibration in the 1750 - 3350 A region

    NASA Technical Reports Server (NTRS)

    Strongylis, G. J.; Bohlin, R. C.

    1977-01-01

    The absolute flux measurements in the rocket ultraviolet made by Bohlin, Frimout, and Lillie (BFL) are revised using a more correct treatment of the air extinction that enters the air calibration of their instrument. The absorption by molecular oxygen and ozone, Rayleigh scattering, and extinction by aerosols is tabulated for general use in ultraviolet calibrations performed in air. The revised absolute flux of eta UMa and final fluxes for alpha Lyr and zeta Oph are presented in the 1750-3350 A region. The absolute flux of the star eta UMa is compared to four other independent determinations in the 1200-3400 A region and a maximum difference of 35% is found near 1500 A between the OAO-2 and Apollo 17 fluxes. The rocket measurements of BFL, the ANS and TD-1 satellite data, and the Apollo 17 data are compared to the ultraviolet fluxes from the OAO-2, demonstrating a photometric reproducibility of about + or - 3 percent. Therefore, all four sets of spectrophotometry can be reduced to a common absolute scale.

  16. Prognostic and Predictive Value of Baseline and Posttreatment Molecular Marker Expression in Locally Advanced Rectal Cancer Treated With Neoadjuvant Chemoradiotherapy

    SciTech Connect

    Bertolini, Federica . E-mail: bertolini.federica@policlinico.mo.it; Bengala, Carmelo; Losi, Luisa; Pagano, Maria; Iachetta, Francesco; Dealis, Cristina; Jovic, Gordana; Depenni, Roberta; Zironi, Sandra; Falchi, Anna Maria; Luppi, Gabriele; Conte, Pier Franco

    2007-08-01

    Purpose: To evaluate expression of a panel of molecular markers, including p53, p21, MLH1, MSH2, MIB-1, thymidylate synthase, epidermal growth factor receptor (EGFR), and tissue vascular endothelial growth factor (VEGF), before and after treatment in patients treated with neoadjuvant chemoradiotherapy for locally advanced rectal cancer, to correlate the constitutive profile and dynamics of expression with pathologic response and outcome. Methods and Materials: Expression of biomarkers was evaluated by immunohistochemistry in tumor samples from 91 patients with clinical Stage II and III rectal cancer treated with preoperative pelvic radiotherapy (50 Gy) plus concurrent 5-fluorouracil by continuous intravenous infusion. Results: A pathologic complete remission was observed in 14 patients (15.4%). Patients with MLH1-positive tumors had a higher pathologic complete response rate (24.3% vs. 9.4%; p = 0.055). Low expression of constitutive p21, absence of EGFR expression after chemoradiotherapy, and high Dworak's tumor regression grade (TRG) were significantly associated with improved disease-free survival and overall survival. A high MIB-1 value after chemoradiotherapy was significantly associated with worse overall survival. Multivariate analysis confirmed the prognostic value of constitutive p21 expression as well as EGFR expression and MIB-1 value after chemoradiotherapy among patients not achieving TRG 3-4. Conclusions: In our study, we observed the independent prognostic value of EGFR expression after chemoradiotherapy on disease-free survival. Moreover, our study suggests that a constitutive high p21 expression and a high MIB-1 value after neoadjuvant chemoradiotherapy treatment could predict worse outcome in locally advanced rectal cancer.

  17. Localized Si enrichment in coherent self-assembled Ge islands grown by molecular beam epitaxy on (001)Si single crystal

    NASA Astrophysics Data System (ADS)

    Valvo, M.; Bongiorno, C.; Giannazzo, F.; Terrasi, A.

    2013-01-01

    Transmission electron microscopy (TEM), atomic force microscopy, and Rutherford backscattering spectrometry (RBS) have been used to investigate the morphology, structure, and composition of self-assembled Ge islands grown on Si (001) substrates by molecular beam epitaxy (MBE) at different temperatures. Increasing the temperature from 550 °C to 700 °C causes progressive size and shape uniformity, accompanied by enhanced Si-Ge intermixing within the islands and their wetting layer. Elemental maps obtained by energy filtered-TEM (EF-TEM) clearly show pronounced Si concentration not only in correspondence of island base perimeters, but also along their curved surface boundaries. This phenomenon is strengthened by an increase of the growth temperature, being practically negligible at 550 °C, while very remarkable already at 650 °C. The resulting island shape is affected, since this localized Si enrichment not only provides strain relief near their highly stressed base perimeters but it also influences the cluster surface energy by effective alloying, so as to form Si-enriched SiGe interfaces. Further increase to 700 °C causes a shape transition where more homogenous Si-Ge concentration profiles are observed. The crucial role played by local "flattened" alloyed clusters, similar to truncated pyramids with larger bases and enhanced Si enrichment at coherently stressed interfaces, has been further clarified by EF-TEM analysis of a multi-layered Ge/Si structure containing stacked Ge islands grown at 650 °C. Sharp accumulation of Si has been here observed not only in proximity of the uncapped island surface in the topmost layer but also at the buried Ge/Si interfaces and even in the core of such capped Ge islands.

  18. Molecular cloning, expression analysis and subcellular localization of a Transparent Testa 12 ortholog in brown cotton (Gossypium hirsutum L.).

    PubMed

    Gao, Jun-Shan; Wu, Nan; Shen, Zhi-Lin; Lv, Kai; Qian, Sen-He; Guo, Ning; Sun, Xu; Cai, Yong-Ping; Lin, Yi

    2016-02-01

    Transparent Testa 12 (TT12) is a kind of transmembrane transporter of proanthocyanidins (PAs), which belongs to a membrane-localized multidrug and toxin efflux (MATE) family, but the molecular basis of PAs transport is still poorly understood. Here, we cloned a full-length TT12 cDNA from the fiber of brown cotton (Gossypium hirsutum), named GhTT12 (GenBank accession No. KF240564), which comprised 1733 bp with an open reading frame (ORF) of 1503 bp and encoded a putative protein containing 500 amino acid residues with a typical MATE conserved domain. The GhTT12 gene had 96.8% similarity to AA genome in Gossypium arboretum. Quantitative RT-PCR analysis denoted that the relative expression of GhTT12 in brown cotton was 1-5 folds higher than that in white cotton. The mRNA level was the highest at 5 days post anthesis (DPA) and reduced gradually during the fiber development. Expressing GhTT12-fused green fluorescent protein (GFP) in Nicotiana tabacum showed that GhTT12-GFP was localized in the vacuole membrane. The content of PAs increased firstly and decreased afterwards, and reached the maximum at 15 DPA in brown cotton. But for white cotton, the content of PAs remained at a low level during the fiber development. We speculate that GhTT12 may participate in the transportation of PAs from the cytoplasmic matrix to the vacuole. Taken together, our data revealed that GhTT12 was functional as a PAs transmembrane transporter.

  19. A molecular dynamics study of local pressures and interfacial tensions of SDS micelles and dodecane droplets in water

    NASA Astrophysics Data System (ADS)

    Kitabata, Masahiro; Fujimoto, Kazushi; Yoshii, Noriyuki; Okazaki, Susumu

    2016-06-01

    To obtain the radial (normal) and lateral (transverse) components of the local pressure tensor, PN(R) and PT(R), respectively, and the interfacial tension of micelles, molecular dynamics (MD) calculations were performed for spherical sodium dodecyl sulfate (SDS) micelles. The local pressure tensor was calculated as a function of radial distance R using the Irving-Kirkwood formula. Similar MD calculations were also carried out for an n-dodecane droplet in water to compare the differences in the local pressure and interfacial tension values with those of the micelles. The calculated interfacial tensions were 20 ± 5 and 44 ± 10 mN/m for the SDS micelles and dodecane droplets, respectively. The excess free energies due to the interfacial tension were 340 and 1331 kJ/mol for the SDS micelle and dodecane droplet, respectively. The micelles are stabilized by 991 kJ/mol by covering their hydrophobic cores with hydrophilic groups. The dodecane droplet has a large interfacial tension caused by the zero or positive values of PN(R) - PT(R) at all values of R. In contrast, the small interfacial tension in the SDS micelles comes from the negative PN(R) - PT(R) values over a wide range of R. The pressure difference between the inside and outside of the oil droplet and its interfacial tension well satisfies the Laplace equation. However, the hydrophobic core of the SDS micelle is quite different from the liquid alkane, and the SDS micelles do not follow Laplace's picture. Decomposing the interfacial tension into contributions from various interactions, it is found that those between charged and polar groups dominate the interfacial tension of the SDS micelles. The positive electrostatic potential (1.3 V) on the micelle surface and the negative potential (-0.15 V) on the oil droplet contribute to the interfacial tensions by 19 and 0.5 mN/m, respectively. Thus, the interfacial tension of the SDS micelles is produced by electrostatic interactions, in contrast to the dodecane

  20. Influence of arsenic stress on synthesis and localization of low-molecular-weight thiols in Pteris vittata.

    PubMed

    Sakai, Yuki; Watanabe, Toshihiro; Wasaki, Jun; Senoura, Takeshi; Shinano, Takuro; Osaki, Mitsuru

    2010-12-01

    The roles of low-molecular-weight thiols (LMWTs), such as glutathione and phytochelatins, in arsenic (As) tolerance and hyperaccumulation in Pteris vittata an As-hyperaccumulator fern remain to be better understood. This study aimed to thoroughly characterize LMWT synthesis in P. vittata to understand the roles played by LMWTs in As tolerance and hyperaccumulation. LMWT synthesis in P. vittata was induced directly by As, and not by As-mediated oxidative stress. Expression of PvECS2, one of the putative genes of γ-glutamylcysteine synthetase (γECS), increases in P. vittata shoots at 48h after the onset of As exposure, almost corresponding to the increase in the concentrations of γ-glutamylcysteine and glutathione. Furthermore, localization of As showed similar trends to those of LMWTs in fronds at both whole-frond and cellular levels. This study thus indicates the specific contribution of LMWTs to As tolerance in P. vittata. γECS may be responsible for the As-induced enhancement of LMWT synthesis.

  1. Finite-temperature elastic constants of paramagnetic materials within the disordered local moment picture from ab initio molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Mozafari, E.; Shulumba, N.; Steneteg, P.; Alling, B.; Abrikosov, Igor A.

    2016-08-01

    We present a theoretical scheme to calculate the elastic constants of magnetic materials in the high-temperature paramagnetic state. Our approach is based on a combination of disordered local moments picture and ab initio molecular dynamics (DLM-MD). Moreover, we investigate a possibility to enhance the efficiency of the simulations of elastic properties using the recently introduced method: symmetry imposed force constant temperature-dependent effective potential (SIFC-TDEP). We have chosen cubic paramagnetic CrN as a model system. This is done due to its technological importance and its demonstrated strong coupling between magnetic and lattice degrees of freedom. We have studied the temperature-dependent single-crystal and polycrystalline elastic constants of paramagentic CrN up to 1200 K. The obtained results at T = 300 K agree well with the experimental values of polycrystalline elastic constants as well as the Poisson ratio at room temperature. We observe that the Young's modulus is strongly dependent on temperature, decreasing by ˜14 % from T = 300 K to 1200 K. In addition we have studied the elastic anisotropy of CrN as a function of temperature and we observe that CrN becomes substantially more isotropic as the temperature increases. We demonstrate that the use of Birch law may lead to substantial errors for calculations of temperature induced changes of elastic moduli. The proposed methodology can be used for accurate predictions of mechanical properties of magnetic materials at temperatures above their magnetic order-disorder phase transition.

  2. Absolute Income, Relative Income, and Happiness

    ERIC Educational Resources Information Center

    Ball, Richard; Chernova, Kateryna

    2008-01-01

    This paper uses data from the World Values Survey to investigate how an individual's self-reported happiness is related to (i) the level of her income in absolute terms, and (ii) the level of her income relative to other people in her country. The main findings are that (i) both absolute and relative income are positively and significantly…

  3. Investigating Absolute Value: A Real World Application

    ERIC Educational Resources Information Center

    Kidd, Margaret; Pagni, David

    2009-01-01

    Making connections between various representations is important in mathematics. In this article, the authors discuss the numeric, algebraic, and graphical representations of sums of absolute values of linear functions. The initial explanations are accessible to all students who have experience graphing and who understand that absolute value simply…

  4. Preschoolers' Success at Coding Absolute Size Values.

    ERIC Educational Resources Information Center

    Russell, James

    1980-01-01

    Forty-five 2-year-old and forty-five 3-year-old children coded relative and absolute sizes using 1.5-inch, 6-inch, and 18-inch cardboard squares. Results indicate that absolute coding is possible for children of this age. (Author/RH)

  5. Introducing the Mean Absolute Deviation "Effect" Size

    ERIC Educational Resources Information Center

    Gorard, Stephen

    2015-01-01

    This paper revisits the use of effect sizes in the analysis of experimental and similar results, and reminds readers of the relative advantages of the mean absolute deviation as a measure of variation, as opposed to the more complex standard deviation. The mean absolute deviation is easier to use and understand, and more tolerant of extreme…

  6. Monolithically integrated absolute frequency comb laser system

    DOEpatents

    Wanke, Michael C.

    2016-07-12

    Rather than down-convert optical frequencies, a QCL laser system directly generates a THz frequency comb in a compact monolithically integrated chip that can be locked to an absolute frequency without the need of a frequency-comb synthesizer. The monolithic, absolute frequency comb can provide a THz frequency reference and tool for high-resolution broad band spectroscopy.

  7. Estimating the absolute wealth of households

    PubMed Central

    Gerkey, Drew; Hadley, Craig

    2015-01-01

    Abstract Objective To estimate the absolute wealth of households using data from demographic and health surveys. Methods We developed a new metric, the absolute wealth estimate, based on the rank of each surveyed household according to its material assets and the assumed shape of the distribution of wealth among surveyed households. Using data from 156 demographic and health surveys in 66 countries, we calculated absolute wealth estimates for households. We validated the method by comparing the proportion of households defined as poor using our estimates with published World Bank poverty headcounts. We also compared the accuracy of absolute versus relative wealth estimates for the prediction of anthropometric measures. Findings The median absolute wealth estimates of 1 403 186 households were 2056 international dollars per capita (interquartile range: 723–6103). The proportion of poor households based on absolute wealth estimates were strongly correlated with World Bank estimates of populations living on less than 2.00 United States dollars per capita per day (R2 = 0.84). Absolute wealth estimates were better predictors of anthropometric measures than relative wealth indexes. Conclusion Absolute wealth estimates provide new opportunities for comparative research to assess the effects of economic resources on health and human capital, as well as the long-term health consequences of economic change and inequality. PMID:26170506

  8. Absolute optical metrology : nanometers to kilometers

    NASA Technical Reports Server (NTRS)

    Dubovitsky, Serge; Lay, O. P.; Peters, R. D.; Liebe, C. C.

    2005-01-01

    We provide and overview of the developments in the field of high-accuracy absolute optical metrology with emphasis on space-based applications. Specific work on the Modulation Sideband Technology for Absolute Ranging (MSTAR) sensor is described along with novel applications of the sensor.

  9. Absolute Quantification of Rifampicin by MALDI Imaging Mass Spectrometry Using Multiple TOF/TOF Events in a Single Laser Shot

    NASA Astrophysics Data System (ADS)

    Prentice, Boone M.; Chumbley, Chad W.; Caprioli, Richard M.

    2016-09-01

    Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for the visualization of molecular distributions within tissue sections. While providing excellent molecular specificity and spatial information, absolute quantification by MALDI IMS remains challenging. Especially in the low molecular weight region of the spectrum, analysis is complicated by matrix interferences and ionization suppression. Though tandem mass spectrometry (MS/MS) can be used to ensure chemical specificity and improve sensitivity by eliminating chemical noise, typical MALDI MS/MS modalities only scan for a single MS/MS event per laser shot. Herein, we describe TOF/TOF instrumentation that enables multiple fragmentation events to be performed in a single laser shot, allowing the intensity of the analyte to be referenced to the intensity of the internal standard in each laser shot while maintaining the benefits of MS/MS. This approach is illustrated by the quantitative analyses of rifampicin (RIF), an antibiotic used to treat tuberculosis, in pooled human plasma using rifapentine (RPT) as an internal standard. The results show greater than 4-fold improvements in relative standard deviation as well as improved coefficients of determination (R2) and accuracy (>93% quality controls, <9% relative errors). This technology is used as an imaging modality to measure absolute RIF concentrations in liver tissue from an animal dosed in vivo. Each microspot in the quantitative image measures the local RIF concentration in the tissue section, providing absolute pixel-to-pixel quantification from different tissue microenvironments. The average concentration determined by IMS is in agreement with the concentration determined by HPLC-MS/MS, showing a percent difference of 10.6%.

  10. Effect of Localized Spin Concentration on Giant Magnetoresistance in Molecular Conductor TPP[FexCo1-x(Pc)(CN)2]2

    NASA Astrophysics Data System (ADS)

    Ikeda, Mitsuo; Kanda, Akinori; Murakawa, Hiroshi; Matsuda, Masaki; Inabe, Tamotsu; Tajima, Hiroyuki; Hanasaki, Noriaki

    2016-02-01

    We studied the effect of the localized spin concentration on the giant magnetoresistance (GMR) and the charge order (CO) in the phthalocyanine (Pc) molecular conductors TPP[FexCo1-x(Pc)(CN)2]2 (TPP = tetraphenylphosphonium), in which the localized spin concentration can be controlled by adjusting the Fe concentration x. Resistivity studies indicated that the CO state was stabilized by localized spins. The negative magnetoresistance was observed even in the region of a localized spin concentration of as low as about 5%. In the high-concentration region, the negative magnetoresistance changed into a positive one at low temperatures. This result shows that a magnetic field stabilizes the CO state, unless the magnetic field is sufficiently strong to break the antiferromagnetic order of the localized spins.

  11. Molecular detection of antimicrobial resistance in local isolates of Staphylococcus epidermidis from urinary tract infections in Faisalabad region of Pakistan

    PubMed Central

    Farid, Anam; Naz, Iram; Ashraf, Asma; Ali, Aamir; Rehman, Asad-ur; Sarwar, Yasra; Haque, Abdul

    2015-01-01

    Staphylococci are one of the foremost causes of urinary tract infections (UTIs) in humans. The emergence of multiple drug resistance (MDR) among Staphylococci poses serious challenges in antimicrobial therapy for UTIs. Most work has been done on S. aureus while coagulase negative Staphylococci (mainly S. epidermidis) are often neglected. This study was conducted to establish a baseline profile of drug resistance in local S. epidermidis isolates from UTIs. Eighty urine samples were collected from suspected UTIs cases and screened for S. epidermidis. Twenty isolates were suspected as S. epidermidis based on colony morphology and Gram staining. Molecular detection by polymerase chain reaction (PCR) confirmed 13 isolates as S. epidermidis. Using disc diffusion method, phenotypic drug resistance of the isolates was observed towards erythromycin (100 %), gentamycin, azithromycin and tetracycline (92.3 %), ampicillin and oxytetracyclin (84.6 %), amikacin and srteptomycin (76.9 %), methicillin (69.2 %), cephradine, cefaclor and cefazolin (53.8 %) and vancomycin (15.3 %). Eighteen most commonly reported genes responsible for conferring resistance towards these drugs were targeted by PCR: among these tetM gene was found most prevalent (46.1 %) followed by tetK (30.7 %), aac(6')/aph(2”) (30.7 %), aacA-aphD (23 %), ermA (23 %), blaZ (23 %), mecA (23 %) blaTEM-1 (23 %), MeccA (23 %) and mecA (15.3 %). No gene fragment for vancomycin resistance was detected. The salient finding was that all S. epidermidis isolates were multiple drugs resistant as they showed resistance against at least three structurally different antimicrobial agents. It is concluded that in addition to the mostly used antimicrobial agent vancomycin, the cephalosporins including cephradine, cefaclor and cefazolin are also the drugs of choice against UTIs caused by S. epidermidis. PMID:26648821

  12. Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

    PubMed

    Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

    2016-07-01

    Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease.

  13. Molecular detection of antimicrobial resistance in local isolates of Staphylococcus epidermidis from urinary tract infections in Faisalabad region of Pakistan.

    PubMed

    Farid, Anam; Naz, Iram; Ashraf, Asma; Ali, Aamir; Rehman, Asad-Ur; Sarwar, Yasra; Haque, Abdul

    2015-01-01

    Staphylococci are one of the foremost causes of urinary tract infections (UTIs) in humans. The emergence of multiple drug resistance (MDR) among Staphylococci poses serious challenges in antimicrobial therapy for UTIs. Most work has been done on S. aureus while coagulase negative Staphylococci (mainly S. epidermidis) are often neglected. This study was conducted to establish a baseline profile of drug resistance in local S. epidermidis isolates from UTIs. Eighty urine samples were collected from suspected UTIs cases and screened for S. epidermidis. Twenty isolates were suspected as S. epidermidis based on colony morphology and Gram staining. Molecular detection by polymerase chain reaction (PCR) confirmed 13 isolates as S. epidermidis. Using disc diffusion method, phenotypic drug resistance of the isolates was observed towards erythromycin (100 %), gentamycin, azithromycin and tetracycline (92.3 %), ampicillin and oxytetracyclin (84.6 %), amikacin and srteptomycin (76.9 %), methicillin (69.2 %), cephradine, cefaclor and cefazolin (53.8 %) and vancomycin (15.3 %). Eighteen most commonly reported genes responsible for conferring resistance towards these drugs were targeted by PCR: among these tetM gene was found most prevalent (46.1 %) followed by tetK (30.7 %), aac(6')/aph(2") (30.7 %), aacA-aphD (23 %), ermA (23 %), blaZ (23 %), mecA (23 %) blaTEM-1 (23 %), MeccA (23 %) and mecA (15.3 %). No gene fragment for vancomycin resistance was detected. The salient finding was that all S. epidermidis isolates were multiple drugs resistant as they showed resistance against at least three structurally different antimicrobial agents. It is concluded that in addition to the mostly used antimicrobial agent vancomycin, the cephalosporins including cephradine, cefaclor and cefazolin are also the drugs of choice against UTIs caused by S. epidermidis.

  14. Molecular characterization of two small heat shock protein genes in rice: their expression patterns, localizations, networks, and heterogeneous overexpressions.

    PubMed

    Ham, Deok-Jae; Moon, Jun-Chul; Hwang, Sun-Goo; Jang, Cheol Seong

    2013-09-28

    Heat stress is an example of a severe abiotic stress that plants can suffer in the field, causing a significant detrimental effect on their growth and productivity. Understanding the mechanism of plant response to heat stress is important for improving the productivity of crop plants under global warming. We used a microarray dataset that is deposited in the public database to evaluate plant responses to heat stress, and we selected the top 10 genes that are highly expressed under heat stress in rice. Two genes, OsSHSP1 (Os03g16030) and OsSHSP2 (Os01g04380), were selected for further study. These genes were highly induced in response to salt and drought but not in response to cold. In addition, OsSHSP1 and OsSHSP2 gene transcripts were induced under abscisic acid and salicylic acid but not under jasmonic acid and ethylene. Subcellular localization of proteins of 35S::OsSHSP1 were associated with the cytosol, whereas those of and 35S::OsSHSP2 were associated with the cytosol and nucleus. Heterogeneous overexpression of both genes exhibited higher germination rates than those of wild-type plants under the salt treatment, but not under heat or drought stress, supporting a hypothesis regarding functional specialization of members of small heat-shock protein family over evolutionary time. The network of both genes harboring nine sHSPs as well as at least 13 other chaperone genes might support the idea of a role for sHSPs in the chaperone network. Our findings might provide clues to shed light on the molecular functions of OsSHSP1 and OsSHSP2 in response to abiotic stresses, especially heat stress.

  15. THE HERSCHEL EXPLOITATION OF LOCAL GALAXY ANDROMEDA (HELGA). VI. THE DISTRIBUTION AND PROPERTIES OF MOLECULAR CLOUD ASSOCIATIONS IN M31

    SciTech Connect

    Kirk, J. M.; Gear, W. K.; Smith, M. W. L.; Ford, G.; Eales, S. A.; Gomez, H. L.; Fritz, J.; Baes, M.; De Looze, I.; Gentile, G.; Gordon, K.; Verstappen, J.; Viaene, S.; Bendo, G. J.; O'Halloran, B.; Madden, S. C.; Lebouteiller, V.; Boselli, A.; Cooray, A.; and others

    2015-01-01

    In this paper we present a catalog of giant molecular clouds (GMCs) in the Andromeda (M31) galaxy extracted from the Herschel Exploitation of Local Galaxy Andromeda (HELGA) data set. GMCs are identified from the Herschel maps using a hierarchical source extraction algorithm. We present the results of this new catalog and characterize the spatial distribution and spectral energy properties of its clouds based on the radial dust/gas properties found by Smith et al. A total of 326 GMCs in the mass range 10{sup 4}-10{sup 7} M {sub ☉} are identified; their cumulative mass distribution is found to be proportional to M {sup –2.34}, in agreement with earlier studies. The GMCs appear to follow the same correlation of cloud mass to L {sub CO} observed in the Milky Way. However, comparison between this catalog and interferometry studies also shows that the GMCs are substructured below the Herschel resolution limit, suggesting that we are observing associations of GMCs. Following Gordon et al., we study the spatial structure of M31 by splitting the observed structure into a set of spiral arms and offset rings. We fit radii of 10.3 and 15.5 kpc to the two most prominent rings. We then fit a logarithmic spiral with a pitch angle of 8.°9 to the GMCs not associated with either ring. Last, we comment on the effects of deprojection on our results and investigate the effect different models for M31's inclination will have on the projection of an unperturbed spiral arm system.

  16. Molecular detection of antimicrobial resistance in local isolates of Staphylococcus epidermidis from urinary tract infections in Faisalabad region of Pakistan.

    PubMed

    Farid, Anam; Naz, Iram; Ashraf, Asma; Ali, Aamir; Rehman, Asad-Ur; Sarwar, Yasra; Haque, Abdul

    2015-01-01

    Staphylococci are one of the foremost causes of urinary tract infections (UTIs) in humans. The emergence of multiple drug resistance (MDR) among Staphylococci poses serious challenges in antimicrobial therapy for UTIs. Most work has been done on S. aureus while coagulase negative Staphylococci (mainly S. epidermidis) are often neglected. This study was conducted to establish a baseline profile of drug resistance in local S. epidermidis isolates from UTIs. Eighty urine samples were collected from suspected UTIs cases and screened for S. epidermidis. Twenty isolates were suspected as S. epidermidis based on colony morphology and Gram staining. Molecular detection by polymerase chain reaction (PCR) confirmed 13 isolates as S. epidermidis. Using disc diffusion method, phenotypic drug resistance of the isolates was observed towards erythromycin (100 %), gentamycin, azithromycin and tetracycline (92.3 %), ampicillin and oxytetracyclin (84.6 %), amikacin and srteptomycin (76.9 %), methicillin (69.2 %), cephradine, cefaclor and cefazolin (53.8 %) and vancomycin (15.3 %). Eighteen most commonly reported genes responsible for conferring resistance towards these drugs were targeted by PCR: among these tetM gene was found most prevalent (46.1 %) followed by tetK (30.7 %), aac(6')/aph(2") (30.7 %), aacA-aphD (23 %), ermA (23 %), blaZ (23 %), mecA (23 %) blaTEM-1 (23 %), MeccA (23 %) and mecA (15.3 %). No gene fragment for vancomycin resistance was detected. The salient finding was that all S. epidermidis isolates were multiple drugs resistant as they showed resistance against at least three structurally different antimicrobial agents. It is concluded that in addition to the mostly used antimicrobial agent vancomycin, the cephalosporins including cephradine, cefaclor and cefazolin are also the drugs of choice against UTIs caused by S. epidermidis. PMID:26648821

  17. Son preference in Indian families: absolute versus relative wealth effects.

    PubMed

    Gaudin, Sylvestre

    2011-02-01

    The desire for male children is prevalent in India, where son preference has been shown to affect fertility behavior and intrahousehold allocation of resources. Economic theory predicts less gender discrimination in wealthier households, but demographers and sociologists have argued that wealth can exacerbate bias in the Indian context. I argue that these apparently conflicting theories can be reconciled and simultaneously tested if one considers that they are based on two different notions of wealth: one related to resource constraints (absolute wealth), and the other to notions of local status (relative wealth). Using cross-sectional data from the 1998-1999 and 2005-2006 National Family and Health Surveys, I construct measures of absolute and relative wealth by using principal components analysis. A series of statistical models of son preference is estimated by using multilevel methods. Results consistently show that higher absolute wealth is strongly associated with lower son preference, and the effect is 20%-40% stronger when the household's community-specific wealth score is included in the regression. Coefficients on relative wealth are positive and significant although lower in magnitude. Results are robust to using different samples, alternative groupings of households in local areas, different estimation methods, and alternative dependent variables.

  18. Absolute Gravity Datum in the Age of Cold Atom Gravimeters

    NASA Astrophysics Data System (ADS)

    Childers, V. A.; Eckl, M. C.

    2014-12-01

    The international gravity datum is defined today by the International Gravity Standardization Net of 1971 (IGSN-71). The data supporting this network was measured in the 1950s and 60s using pendulum and spring-based gravimeter ties (plus some new ballistic absolute meters) to replace the prior protocol of referencing all gravity values to the earlier Potsdam value. Since this time, gravimeter technology has advanced significantly with the development and refinement of the FG-5 (the current standard of the industry) and again with the soon-to-be-available cold atom interferometric absolute gravimeters. This latest development is anticipated to provide improvement in the range of two orders of magnitude as compared to the measurement accuracy of technology utilized to develop ISGN-71. In this presentation, we will explore how the IGSN-71 might best be "modernized" given today's requirements and available instruments and resources. The National Geodetic Survey (NGS), along with other relevant US Government agencies, is concerned about establishing gravity control to establish and maintain high order geodetic networks as part of the nation's essential infrastructure. The need to modernize the nation's geodetic infrastructure was highlighted in "Precise Geodetic Infrastructure, National Requirements for a Shared Resource" National Academy of Science, 2010. The NGS mission, as dictated by Congress, is to establish and maintain the National Spatial Reference System, which includes gravity measurements. Absolute gravimeters measure the total gravity field directly and do not involve ties to other measurements. Periodic "intercomparisons" of multiple absolute gravimeters at reference gravity sites are used to constrain the behavior of the instruments to ensure that each would yield reasonably similar measurements of the same location (i.e. yield a sufficiently consistent datum when measured in disparate locales). New atomic interferometric gravimeters promise a significant

  19. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    NASA Astrophysics Data System (ADS)

    Zarycz, M. Natalia C.; Sauer, Stephan P. A.; Provasi, Patricio F.

    2014-10-01

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the 1J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the 1J(N-H) coupling constant in NH3. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  20. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    SciTech Connect

    Zarycz, M. Natalia C. Provasi, Patricio F.; Sauer, Stephan P. A.

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  1. Absolute concentration measurements inside a jet plume using video digitization

    NASA Astrophysics Data System (ADS)

    Vauquelin, O.

    An experimental system based on digitized video image analysis is used to measure the local value of the concentration inside a plume. Experiments are carried out in a wind-tunnel for a smoke-seeded turbulent jet plume illuminated with a laser beam. Each test is filmed, subsequently video images are digitized and analysed in order to determine the smoke absolute concentration corresponding to each pixel gray level. This non-intrusive measurement technique is first calibrated and different laws connecting gray level to concentration are established. As a first application, concentration measurements are made inside a turbulent jet plume and compared with measurements conducted using a classic gas analysis method. We finally present and discuss the possibilities offered for the measurements of absolute concentration fluctuations.

  2. Absolute magnitudes of trans-neptunian objects

    NASA Astrophysics Data System (ADS)

    Duffard, R.; Alvarez-candal, A.; Pinilla-Alonso, N.; Ortiz, J. L.; Morales, N.; Santos-Sanz, P.; Thirouin, A.

    2015-10-01

    Accurate measurements of diameters of trans- Neptunian objects are extremely complicated to obtain. Radiomatric techniques applied to thermal measurements can provide good results, but precise absolute magnitudes are needed to constrain diameters and albedos. Our objective is to measure accurate absolute magnitudes for a sample of trans- Neptunian objects, many of which have been observed, and modelled, by the "TNOs are cool" team, one of Herschel Space Observatory key projects grantes with ~ 400 hours of observing time. We observed 56 objects in filters V and R, if possible. These data, along with data available in the literature, was used to obtain phase curves and to measure absolute magnitudes by assuming a linear trend of the phase curves and considering magnitude variability due to rotational light-curve. In total we obtained 234 new magnitudes for the 56 objects, 6 of them with no reported previous measurements. Including the data from the literature we report a total of 109 absolute magnitudes.

  3. A New Gimmick for Assigning Absolute Configuration.

    ERIC Educational Resources Information Center

    Ayorinde, F. O.

    1983-01-01

    A five-step procedure is provided to help students in making the assignment absolute configuration less bothersome. Examples for both single (2-butanol) and multi-chiral carbon (3-chloro-2-butanol) molecules are included. (JN)

  4. The Simplicity Argument and Absolute Morality

    ERIC Educational Resources Information Center

    Mijuskovic, Ben

    1975-01-01

    In this paper the author has maintained that there is a similarity of thought to be found in the writings of Cudworth, Emerson, and Husserl in his investigation of an absolute system of morality. (Author/RK)

  5. Measurement of Absolute Carbon Isotope Ratios: Mechanisms and Implications

    NASA Astrophysics Data System (ADS)

    Vogel, J. S.; Giacomo, J. A.; Dueker, S. R.

    2012-12-01

    An accelerator mass spectrometer (AMS) produced absolute isotope ratio measurements for 14C/13C as tested against >500 samples of NIST SRM-4990-C (OxII 14C standard) to an accuracy of 2.2±0.6‰ over a period of one year with measurements made to 1% counting statistics. The spectrometer is not maximized for 13C/12C, but measured ∂13C to 0.4±0.1‰ accuracy, with known methods for improvement. An AMS produces elemental anions from a sputter ion source and includes a charge-changing collision in a gas cell to isolate the rare 14C from the common isotopes and molecular isobars. Both these physical processes have been modeled to determine the parameters providing such absolute measures. Neutral resonant ionization in a cesium plasma produces mass-independent ionization, while velocity dependent charge-state distributions in gas collisions produce relative ion beam intensities that are linear in mass at specific collision energies. The mechanisms are not specific to carbon isotopes, but stand alone absolute IRMS (AIR-MS) instruments have not yet been made. Aside from the obvious applications in metrology, AIR-MS is particularly valuable in coupled separatory MS because no internal or external standards are required. Sample definition processes can be compared, even if no exact standard reference sample exists. Isotope dilution measurements do not require standards matching the dilution end-points and can be made over an extended, even extrapolated, range.

  6. DISCOVERY OF AN ACTIVE GALACTIC NUCLEUS DRIVEN MOLECULAR OUTFLOW IN THE LOCAL EARLY-TYPE GALAXY NGC 1266

    SciTech Connect

    Alatalo, K.; Blitz, L.; Young, L. M.; Davis, T. A.; Bureau, M.; Cappellari, M.; Scott, N.; Davies, R. L.; Lopez, L. A.; Shapiro, K. L.; Crocker, A. F.; MartIn, S.; Bois, M.; Emsellem, E.; Bournaud, F.; Duc, P.-A.; Falcon-Barroso, J.

    2011-07-10

    We report the discovery of a powerful molecular wind from the nucleus of the non-interacting nearby S0 field galaxy NGC 1266. The single-dish CO profile exhibits emission to {+-}400 km s{sup -1} and requires a nested Gaussian fit to be properly described. Interferometric observations reveal a massive, centrally concentrated molecular component with a mass of 1.1 x 10{sup 9} M{sub sun} and a molecular outflow with a molecular mass of {approx}2.4 x 10{sup 7} M{sub sun}. The molecular gas close to the systemic velocity consists of a rotating, compact nucleus with a mass of about 4.1 x 10{sup 8} M{sub sun} within a radius of {approx}60 pc. This compact molecular nucleus has a surface density of {approx}2.7 x 10{sup 4} M{sub sun} pc{sup -2}, more than two orders of magnitude larger than that of giant molecular clouds in the disk of the Milky Way, and it appears to sit on the Kennicutt-Schmidt relation despite its extreme kinematics and energetic activity. We interpret this nucleus as a disk that confines the outflowing wind. A mass outflow rate of {approx}13 M{sub sun} yr{sup -1} leads to a depletion timescale of {approx}<85 Myr. The star formation in NGC 1266 is insufficient to drive the outflow, and thus it is likely driven by the active galactic nucleus. The concentration of the majority of the molecular gas in the central 100 pc requires an extraordinary loss of angular momentum, but no obvious companion or interacting galaxy is present to enable the transfer. NGC 1266 is the first known outflowing molecular system that does not show any evidence of a recent interaction.

  7. Saturation Dynamics Measures Absolute Cross Section and Generates Contrast within a Neuron.

    PubMed

    Kumar, Suraj; Singh, Aditya; Singh, Vijay R; George, Jude B; Balaji, J

    2016-09-20

    The intensity required to optically saturate a chromophore is a molecular property that is determined by its absorption cross section (σ) and the excited state lifetime. We present an analytical description of such a system and show that fluorescence around the onset of saturation is characterized by product of absorption cross section and lifetime. Using this approach we formulate a generalized method for measuring the multiphoton cross section of fluorophores and use it to obtain the absolute three-photon cross-section spectra of tryptophan. We find that the tryptophan three-photon cross section ranges from 0.28 S.I. units (m(6)s(2)photon(-2)) at 870 nm to 20 S.I. units at 740 nm. Further, we show that the product of molecular rate of excitation and de-excitation, denoted as β, serves as a vital contrasting agent for imaging local environment. Our contrast parameter, β, is related to fraction of the population present in the excited state and is independent of the fluorophore concentration. We show that β-imaging can be carried out in a regular two-photon microscope setup through a series of intensity scans. Using enhanced green fluorescent protein (EGFP) fluorescence from the brain slices of Thy-1 EGFP transgenic mice, we show that there is an inherent, concentration independent, variation in contrast across the soma and the dendrite.

  8. Saturation Dynamics Measures Absolute Cross Section and Generates Contrast within a Neuron.

    PubMed

    Kumar, Suraj; Singh, Aditya; Singh, Vijay R; George, Jude B; Balaji, J

    2016-09-20

    The intensity required to optically saturate a chromophore is a molecular property that is determined by its absorption cross section (σ) and the excited state lifetime. We present an analytical description of such a system and show that fluorescence around the onset of saturation is characterized by product of absorption cross section and lifetime. Using this approach we formulate a generalized method for measuring the multiphoton cross section of fluorophores and use it to obtain the absolute three-photon cross-section spectra of tryptophan. We find that the tryptophan three-photon cross section ranges from 0.28 S.I. units (m(6)s(2)photon(-2)) at 870 nm to 20 S.I. units at 740 nm. Further, we show that the product of molecular rate of excitation and de-excitation, denoted as β, serves as a vital contrasting agent for imaging local environment. Our contrast parameter, β, is related to fraction of the population present in the excited state and is independent of the fluorophore concentration. We show that β-imaging can be carried out in a regular two-photon microscope setup through a series of intensity scans. Using enhanced green fluorescent protein (EGFP) fluorescence from the brain slices of Thy-1 EGFP transgenic mice, we show that there is an inherent, concentration independent, variation in contrast across the soma and the dendrite. PMID:27653491

  9. Jasminum flexile flower absolute from India--a detailed comparison with three other jasmine absolutes.

    PubMed

    Braun, Norbert A; Kohlenberg, Birgit; Sim, Sherina; Meier, Manfred; Hammerschmidt, Franz-Josef

    2009-09-01

    Jasminum flexile flower absolute from the south of India and the corresponding vacuum headspace (VHS) sample of the absolute were analyzed using GC and GC-MS. Three other commercially available Indian jasmine absolutes from the species: J. sambac, J. officinale subsp. grandiflorum, and J. auriculatum and the respective VHS samples were used for comparison purposes. One hundred and twenty-one compounds were characterized in J. flexile flower absolute, with methyl linolate, benzyl salicylate, benzyl benzoate, (2E,6E)-farnesol, and benzyl acetate as the main constituents. A detailed olfactory evaluation was also performed.

  10. Absolute surface reconstruction by slope metrology and photogrammetry

    NASA Astrophysics Data System (ADS)

    Dong, Yue

    Developing the manufacture of aspheric and freeform optical elements requires an advanced metrology method which is capable of inspecting these elements with arbitrary freeform surfaces. In this dissertation, a new surface measurement scheme is investigated for such a purpose, which is to measure the absolute surface shape of an object under test through its surface slope information obtained by photogrammetric measurement. A laser beam propagating toward the object reflects on its surface while the vectors of the incident and reflected beams are evaluated from the four spots they leave on the two parallel transparent windows in front of the object. The spots' spatial coordinates are determined by photogrammetry. With the knowledge of the incident and reflected beam vectors, the local slope information of the object surface is obtained through vector calculus and finally yields the absolute object surface profile by a reconstruction algorithm. An experimental setup is designed and the proposed measuring principle is experimentally demonstrated by measuring the absolute surface shape of a spherical mirror. The measurement uncertainty is analyzed, and efforts for improvement are made accordingly. In particular, structured windows are designed and fabricated to generate uniform scattering spots left by the transmitted laser beams. Calibration of the fringe reflection instrument, another typical surface slope measurement method, is also reported in the dissertation. Finally, a method for uncertainty analysis of a photogrammetry measurement system by optical simulation is investigated.

  11. Universal Cosmic Absolute and Modern Science

    NASA Astrophysics Data System (ADS)

    Kostro, Ludwik

    The official Sciences, especially all natural sciences, respect in their researches the principle of methodic naturalism i.e. they consider all phenomena as entirely natural and therefore in their scientific explanations they do never adduce or cite supernatural entities and forces. The purpose of this paper is to show that Modern Science has its own self-existent, self-acting, and self-sufficient Natural All-in Being or Omni-Being i.e. the entire Nature as a Whole that justifies the scientific methodic naturalism. Since this Natural All-in Being is one and only It should be considered as the own scientifically justified Natural Absolute of Science and should be called, in my opinion, the Universal Cosmic Absolute of Modern Science. It will be also shown that the Universal Cosmic Absolute is ontologically enormously stratified and is in its ultimate i.e. in its most fundamental stratum trans-reistic and trans-personal. It means that in its basic stratum. It is neither a Thing or a Person although It contains in Itself all things and persons with all other sentient and conscious individuals as well, On the turn of the 20th century the Science has begun to look for a theory of everything, for a final theory, for a master theory. In my opinion the natural Universal Cosmic Absolute will constitute in such a theory the radical all penetrating Ultimate Basic Reality and will substitute step by step the traditional supernatural personal Absolute.

  12. Local vibrational dynamics of hematite (α-Fe{sub 2}O{sub 3}) studied by extended x-ray absorption fine structure and molecular dynamics

    SciTech Connect

    Sanson, A.; Mathon, O.; Pascarelli, S.

    2014-06-14

    The local vibrational dynamics of hematite (α-Fe{sub 2}O{sub 3}) has been investigated by temperature-dependent extended x-ray absorption fine structure spectroscopy and molecular dynamics simulations. The local dynamics of both the short and long nearest-neighbor Fe–O distances has been singled out, i.e., their local thermal expansion and the parallel and perpendicular mean-square relative atomic displacements have been determined, obtaining a partial agreement with molecular dynamics. No evidence of the Morin transition has been observed. More importantly, the strong anisotropy of relative thermal vibrations found for the short Fe–O distance has been related to its negative thermal expansion. The differences between the local dynamics of short and long Fe–O distances are discussed in terms of projection and correlation of atomic motion. As a result, we can conclude that the short Fe–O bond is stiffer to stretching and softer to bending than the long Fe–O bond.

  13. Excess electron reactivity in amino acid aqueous solution revealed by ab initio molecular dynamics simulation: anion-centered localization and anion-relayed electron transfer dissociation.

    PubMed

    Wu, Xiuxiu; Gao, Liang; Liu, Jinxiang; Yang, Hongfang; Wang, Shoushan; Bu, Yuxiang

    2015-10-28

    Studies on the structure, states, and reactivity of excess electrons (EEs) in biological media are of great significance. Although there is information about EE interaction with desolvated biological molecules, solution effects are hardly explored. In this work, we present an ab initio molecular dynamics simulation study on the interaction and reactivity of an EE with glycine in solution. Our simulations reveal two striking results. Firstly, a pre-solvated EE partially localizes on the negatively charged -COO(-) group of the zwitterionic glycine and the remaining part delocalizes over solvent water molecules, forming an anion-centered quasi-localized structure, due to relative alignment of the lowest unoccupied molecular orbital energy levels of potential sites for EE residence in the aqueous solution. Secondly, after a period of anion-centered localization of an EE, the zwitterionic glycine is induced to spontaneously fragment through the cleavage of the N-Cα bond, losing ammonia (deamination), and leaving a ˙CH2-COO(-) anion radical, in good agreement with experimental observations. Introduction of the same groups (-COO(-) or -NH3(+)) in the side chain (taking lysine and aspartic acid as examples) can affect EE localization, with the fragmentation of the backbone part of these amino acids dependent on the properties of the side chain groups. These findings provide insights into EE interaction mechanisms with the backbone parts of amino acids and low energy EE induced fragmentation of amino acids and even peptides and proteins.

  14. Local vibrational dynamics of hematite (α-Fe2O3) studied by extended x-ray absorption fine structure and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sanson, A.; Mathon, O.; Pascarelli, S.

    2014-06-01

    The local vibrational dynamics of hematite (α-Fe2O3) has been investigated by temperature-dependent extended x-ray absorption fine structure spectroscopy and molecular dynamics simulations. The local dynamics of both the short and long nearest-neighbor Fe-O distances has been singled out, i.e., their local thermal expansion and the parallel and perpendicular mean-square relative atomic displacements have been determined, obtaining a partial agreement with molecular dynamics. No evidence of the Morin transition has been observed. More importantly, the strong anisotropy of relative thermal vibrations found for the short Fe-O distance has been related to its negative thermal expansion. The differences between the local dynamics of short and long Fe-O distances are discussed in terms of projection and correlation of atomic motion. As a result, we can conclude that the short Fe-O bond is stiffer to stretching and softer to bending than the long Fe-O bond.

  15. Quantum theory allows for absolute maximal contextuality

    NASA Astrophysics Data System (ADS)

    Amaral, Barbara; Cunha, Marcelo Terra; Cabello, Adán

    2015-12-01

    Contextuality is a fundamental feature of quantum theory and a necessary resource for quantum computation and communication. It is therefore important to investigate how large contextuality can be in quantum theory. Linear contextuality witnesses can be expressed as a sum S of n probabilities, and the independence number α and the Tsirelson-like number ϑ of the corresponding exclusivity graph are, respectively, the maximum of S for noncontextual theories and for the theory under consideration. A theory allows for absolute maximal contextuality if it has scenarios in which ϑ /α approaches n . Here we show that quantum theory allows for absolute maximal contextuality despite what is suggested by the examination of the quantum violations of Bell and noncontextuality inequalities considered in the past. Our proof is not constructive and does not single out explicit scenarios. Nevertheless, we identify scenarios in which quantum theory allows for almost-absolute-maximal contextuality.

  16. Absolute calibration in vivo measurement systems

    SciTech Connect

    Kruchten, D.A.; Hickman, D.P.

    1991-02-01

    Lawrence Livermore National Laboratory (LLNL) is currently investigating a new method for obtaining absolute calibration factors for radiation measurement systems used to measure internally deposited radionuclides in vivo. Absolute calibration of in vivo measurement systems will eliminate the need to generate a series of human surrogate structures (i.e., phantoms) for calibrating in vivo measurement systems. The absolute calibration of in vivo measurement systems utilizes magnetic resonance imaging (MRI) to define physiological structure, size, and composition. The MRI image provides a digitized representation of the physiological structure, which allows for any mathematical distribution of radionuclides within the body. Using Monte Carlo transport codes, the emission spectrum from the body is predicted. The in vivo measurement equipment is calibrated using the Monte Carlo code and adjusting for the intrinsic properties of the detection system. The calibration factors are verified using measurements of existing phantoms and previously obtained measurements of human volunteers. 8 refs.

  17. Stimulus probability effects in absolute identification.

    PubMed

    Kent, Christopher; Lamberts, Koen

    2016-05-01

    This study investigated the effect of stimulus presentation probability on accuracy and response times in an absolute identification task. Three schedules of presentation were used to investigate the interaction between presentation probability and stimulus position within the set. Data from individual participants indicated strong effects of presentation probability on both proportion correct and response times. The effects were moderated by the ubiquitous stimulus position effect. The accuracy and response time data were predicted by an exemplar-based model of perceptual cognition (Kent & Lamberts, 2005). The bow in discriminability was also attenuated when presentation probability for middle items was relatively high, an effect that will constrain future model development. The study provides evidence for item-specific learning in absolute identification. Implications for other theories of absolute identification are discussed. (PsycINFO Database Record

  18. Quantitative standards for absolute linguistic universals.

    PubMed

    Piantadosi, Steven T; Gibson, Edward

    2014-01-01

    Absolute linguistic universals are often justified by cross-linguistic analysis: If all observed languages exhibit a property, the property is taken to be a likely universal, perhaps specified in the cognitive or linguistic systems of language learners and users. In many cases, these patterns are then taken to motivate linguistic theory. Here, we show that cross-linguistic analysis will very rarely be able to statistically justify absolute, inviolable patterns in language. We formalize two statistical methods--frequentist and Bayesian--and show that in both it is possible to find strict linguistic universals, but that the numbers of independent languages necessary to do so is generally unachievable. This suggests that methods other than typological statistics are necessary to establish absolute properties of human language, and thus that many of the purported universals in linguistics have not received sufficient empirical justification.

  19. Absolute photoacoustic thermometry in deep tissue.

    PubMed

    Yao, Junjie; Ke, Haixin; Tai, Stephen; Zhou, Yong; Wang, Lihong V

    2013-12-15

    Photoacoustic thermography is a promising tool for temperature measurement in deep tissue. Here we propose an absolute temperature measurement method based on the dual temperature dependences of the Grüneisen parameter and the speed of sound in tissue. By taking ratiometric measurements at two adjacent temperatures, we can eliminate the factors that are temperature irrelevant but difficult to correct for in deep tissue. To validate our method, absolute temperatures of blood-filled tubes embedded ~9 mm deep in chicken tissue were measured in a biologically relevant range from 28°C to 46°C. The temperature measurement accuracy was ~0.6°C. The results suggest that our method can be potentially used for absolute temperature monitoring in deep tissue during thermotherapy.

  20. Absolute Stability And Hyperstability In Hilbert Space

    NASA Technical Reports Server (NTRS)

    Wen, John Ting-Yung

    1989-01-01

    Theorems on stabilities of feedback control systems proved. Paper presents recent developments regarding theorems of absolute stability and hyperstability of feedforward-and-feedback control system. Theorems applied in analysis of nonlinear, adaptive, and robust control. Extended to provide sufficient conditions for stability in system including nonlinear feedback subsystem and linear time-invariant (LTI) feedforward subsystem, state space of which is Hilbert space, and input and output spaces having finite numbers of dimensions. (In case of absolute stability, feedback subsystem memoryless and possibly time varying. For hyperstability, feedback system dynamical system.)

  1. Absolute Points for Multiple Assignment Problems

    ERIC Educational Resources Information Center

    Adlakha, V.; Kowalski, K.

    2006-01-01

    An algorithm is presented to solve multiple assignment problems in which a cost is incurred only when an assignment is made at a given cell. The proposed method recursively searches for single/group absolute points to identify cells that must be loaded in any optimal solution. Unlike other methods, the first solution is the optimal solution. The…

  2. Absolute partial photoionization cross sections of ozone.

    SciTech Connect

    Berkowitz, J.; Chemistry

    2008-04-01

    Despite the current concerns about ozone, absolute partial photoionization cross sections for this molecule in the vacuum ultraviolet (valence) region have been unavailable. By eclectic re-evaluation of old/new data and plausible assumptions, such cross sections have been assembled to fill this void.

  3. Stimulus Probability Effects in Absolute Identification

    ERIC Educational Resources Information Center

    Kent, Christopher; Lamberts, Koen

    2016-01-01

    This study investigated the effect of stimulus presentation probability on accuracy and response times in an absolute identification task. Three schedules of presentation were used to investigate the interaction between presentation probability and stimulus position within the set. Data from individual participants indicated strong effects of…

  4. Teaching Absolute Value Inequalities to Mature Students

    ERIC Educational Resources Information Center

    Sierpinska, Anna; Bobos, Georgeana; Pruncut, Andreea

    2011-01-01

    This paper gives an account of a teaching experiment on absolute value inequalities, whose aim was to identify characteristics of an approach that would realize the potential of the topic to develop theoretical thinking in students enrolled in prerequisite mathematics courses at a large, urban North American university. The potential is…

  5. Solving Absolute Value Equations Algebraically and Geometrically

    ERIC Educational Resources Information Center

    Shiyuan, Wei

    2005-01-01

    The way in which students can improve their comprehension by understanding the geometrical meaning of algebraic equations or solving algebraic equation geometrically is described. Students can experiment with the conditions of the absolute value equation presented, for an interesting way to form an overall understanding of the concept.

  6. Increasing Capacity: Practice Effects in Absolute Identification

    ERIC Educational Resources Information Center

    Dodds, Pennie; Donkin, Christopher; Brown, Scott D.; Heathcote, Andrew

    2011-01-01

    In most of the long history of the study of absolute identification--since Miller's (1956) seminal article--a severe limit on performance has been observed, and this limit has resisted improvement even by extensive practice. In a startling result, Rouder, Morey, Cowan, and Pfaltz (2004) found substantially improved performance with practice in the…

  7. Absolute Radiometric Calibration Of The Thematic Mapper

    NASA Astrophysics Data System (ADS)

    Slater, P. N.; Biggar, S. F.; Holm, R. G.; Jackson, R. D.; Mao, Y.; Moran, M. S.; Palmer, J. M.; Yuan, B.

    1986-11-01

    The results are presented of five in-flight absolute radiometric calibrations, made in the period July 1984 to November 1985, at White Sands, New Mexico, of the solar reflective bands of the Landsat-5 Thematic Mapper (TM) . The 23 bandcalibrations made on the five dates show a ± 2.8% RMS variation from the mean as a percentage of the mean.

  8. On Relative and Absolute Conviction in Mathematics

    ERIC Educational Resources Information Center

    Weber, Keith; Mejia-Ramos, Juan Pablo

    2015-01-01

    Conviction is a central construct in mathematics education research on justification and proof. In this paper, we claim that it is important to distinguish between absolute conviction and relative conviction. We argue that researchers in mathematics education frequently have not done so and this has lead to researchers making unwarranted claims…

  9. Molecular localization of the t(11; 22)(q24; q12) translocation of Ewing sarcoma by chromosomal in situ suppression hybridization

    SciTech Connect

    Selleri, L.; Hermanson, G.G.; Eubanks, J.H.; Lewis, K.A.; Evans, G.A. )

    1991-02-01

    Chromosome translocations are associated with a variety of human leukemias, lymphomas, and solid tumors. To localize molecular markers flanking the t(11;22)(q24;q12) breakpoint that occurs in virtually all cases of Ewing sarcoma and peripheral neuroepithelioma, high-resolution chromosomal in situ suppression hybridization was carried out using a panel of cosmid clones localized and ordered on chromosome 11q. The location of the Ewing sarcoma translocation breakpoint was determined relative to the nearest two cosmid markers on 11q, clones 23.2 and 5.8, through the analysis of metaphase chromosome hybridization. By in situ hybridization to interphase nuclei, the approximate physical separation of these two markers was determined. In both Ewing sarcoma and peripheral neuroepithelioma, cosmid clone 5.8 is translocated from chromosome 11q24 to the derivative chromosome 22 and a portion of chromosome 22q12 carrying the leukemia inhibitory factor gene is translocated to the derivative chromosome 11. The physical distance between the flanking cosmid markers on chromosome 11 was determined to be in the range of 1,000 kilobases, and genomic analysis using pulsed-field gel electrophoresis showed no abnormalities over a region of 650 kilobases in the vicinity of the leukemia inhibitory factor gene on chromosome 22. This approach localizes the Ewing sarcoma breakpoint to a small region on chromosome 11q24 and provides a rapid and precise technique for the molecular characterization of chromosomal aberrations.

  10. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

    PubMed

    Ferenczy, György G

    2013-04-01

    The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem.

  11. Sensitive and molecular size-selective detection of proteins using a chip-based and heteroliganded gold nanoisland by localized surface plasmon resonance spectroscopy

    PubMed Central

    2011-01-01

    A highly sensitive and molecular size-selective method for the detection of proteins using heteroliganded gold nanoislands and localized surface plasmon resonance (LSPR) is described. Two different heteroligands with different chain lengths (3-mercaptopionicacid and decanethiol) were used in fabricating nanoholes for the size-dependent separation of a protein in comparison with its aggregate. Their ratios on gold nanoisland were optimized for the sensitive detection of superoxide dismutase (SOD1). This protein has been implicated in the pathology of amyotrophic lateral sclerosis (ALS). Upon exposure of the optimized gold nanoisland to a solution of SOD1 and aggregates thereof, changes in the LSPR spectra were observed which are attributed to the size-selective and covalent chemical binding of SOD1 to the nanoholes. With a lower detection limit of 1.0 ng/ml, the method can be used to selectively detect SOD1 in the presence of aggregates at the molecular level. PMID:21711878

  12. In-cell protease assay systems based on trans-localizing molecular beacon proteins using HCV protease as a model system.

    PubMed

    Kim, Jeong Hee; Lee, Min Jun; Hwang, Inhwan; Hwang, Hyun Jin

    2013-01-01

    This study describes a sensitive in-cell protease detection system that enables direct fluorescence detection of a target protease and its inhibition inside living cells. This live-cell imaging system provides a fluorescent molecular beacon protein comprised of an intracellular translocation signal sequence, a protease-specific cleavage sequence, and a fluorescent tag sequence(s). The molecular beacon protein is designed to change its intracellular localization upon cleavage by a target protease, i.e., from the cytosol to a subcellular organelle or from a subcellular organelle to the cytosol. Protease activity can be monitored at the single cell level, and accordingly the entire cell population expressing the protease can be accurately enumerated. The clear cellular change in fluorescence pattern makes this system an ideal tool for various life science and drug discovery research, including high throughput and high content screening applications.

  13. Sensitive and molecular size-selective detection of proteins using a chip-based and heteroliganded gold nanoisland by localized surface plasmon resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Hong, Surin; Lee, Suseung; Yi, Jongheop

    2011-04-01

    A highly sensitive and molecular size-selective method for the detection of proteins using heteroliganded gold nanoislands and localized surface plasmon resonance (LSPR) is described. Two different heteroligands with different chain lengths (3-mercaptopionicacid and decanethiol) were used in fabricating nanoholes for the size-dependent separation of a protein in comparison with its aggregate. Their ratios on gold nanoisland were optimized for the sensitive detection of superoxide dismutase (SOD1). This protein has been implicated in the pathology of amyotrophic lateral sclerosis (ALS). Upon exposure of the optimized gold nanoisland to a solution of SOD1 and aggregates thereof, changes in the LSPR spectra were observed which are attributed to the size-selective and covalent chemical binding of SOD1 to the nanoholes. With a lower detection limit of 1.0 ng/ml, the method can be used to selectively detect SOD1 in the presence of aggregates at the molecular level.

  14. Combined Use of Absolute and Differential Seismic Arrival Time Data to Improve Absolute Event Location

    NASA Astrophysics Data System (ADS)

    Myers, S.; Johannesson, G.

    2012-12-01

    Arrival time measurements based on waveform cross correlation are becoming more common as advanced signal processing methods are applied to seismic data archives and real-time data streams. Waveform correlation can precisely measure the time difference between the arrival of two phases, and differential time data can be used to constrain relative location of events. Absolute locations are needed for many applications, which generally requires the use of absolute time data. Current methods for measuring absolute time data are approximately two orders of magnitude less precise than differential time measurements. To exploit the strengths of both absolute and differential time data, we extend our multiple-event location method Bayesloc, which previously used absolute time data only, to include the use of differential time measurements that are based on waveform cross correlation. Fundamentally, Bayesloc is a formulation of the joint probability over all parameters comprising the multiple event location system. The Markov-Chain Monte Carlo method is used to sample from the joint probability distribution given arrival data sets. The differential time component of Bayesloc includes scaling a stochastic estimate of differential time measurement precision based the waveform correlation coefficient for each datum. For a regional-distance synthetic data set with absolute and differential time measurement error of 0.25 seconds and 0.01 second, respectively, epicenter location accuracy is improved from and average of 1.05 km when solely absolute time data are used to 0.28 km when absolute and differential time data are used jointly (73% improvement). The improvement in absolute location accuracy is the result of conditionally limiting absolute location probability regions based on the precise relative position with respect to neighboring events. Bayesloc estimates of data precision are found to be accurate for the synthetic test, with absolute and differential time measurement

  15. Influence of out-of-plane defects on vibration analysis of graphene: Molecular Dynamics and Non-local Elasticity approaches

    NASA Astrophysics Data System (ADS)

    Jalali, S. K.; Jomehzadeh, E.; Pugno, N. M.

    2016-03-01

    Out-of-plane defects may exist in graphene inevitably or purposely. The present study aims at investigating the influence of out-of-plane defects on vibrational analysis of single layered graphene sheets (SLGSs) implementing both nonlocal elasticity and molecular dynamics (MD) simulations. In nonlocal elasticity analysis, the defect is considered as an initial curvature which is modeled by an analytical function having controllable parameters for the amplitude, extension, and location. In molecular dynamics analysis, defects are simulated by inserting inverse Stone-Wales defects in the perfect structure of SLGSs. Both nonlocal continuum and MD simulation results reveal that the defects increase the vibrational frequency. It is shown that classical elasticity overestimates frequencies with a considerable error while the nonlocal plate model can fit MD results by implementing a proper small scale parameter.

  16. Vibrational properties of a Σ5( 3 1 0 )[ 0 0 1 ] NiO grain boundary: a local analysis by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Karakasidis, Theodoros E.

    2002-08-01

    Using molecular dynamics and a rigid ion potential we studied the vibrational properties of a Σ5(3 1 0)[0 0 1] tilt grain boundary in NiO. We calculated the local density of states and the mean square displacement (MSD) of the cation and ion sublattice for a wide temperature range. We examined their behaviour in the directions parallel and normal to the boundary as a function from the grain boundary plane. We found that the local phonon density of states of the sites of the boundary are altered with comparison to the bulk presenting in general a shift towards lower frequencies in the direction normal to the boundary and toward higher frequencies in the direction parallel to the grain boundary. This anisotropy, which is conformed by the results of the MSDs, is maintained up to high temperatures. We have also observed that the increase of temperature leads to the gradual loosening of the binding of atoms.

  17. Pleiades Absolute Calibration : Inflight Calibration Sites and Methodology

    NASA Astrophysics Data System (ADS)

    Lachérade, S.; Fourest, S.; Gamet, P.; Lebègue, L.

    2012-07-01

    In-flight calibration of space sensors once in orbit is a decisive step to be able to fulfil the mission objectives. This article presents the methods of the in-flight absolute calibration processed during the commissioning phase. Four In-flight calibration methods are used: absolute calibration, cross-calibration with reference sensors such as PARASOL or MERIS, multi-temporal monitoring and inter-bands calibration. These algorithms are based on acquisitions over natural targets such as African deserts, Antarctic sites, La Crau (Automatic calibration station) and Oceans (Calibration over molecular scattering) or also new extra-terrestrial sites such as the Moon and selected stars. After an overview of the instrument and a description of the calibration sites, it is pointed out how each method is able to address one or several aspects of the calibration. We focus on how these methods complete each other in their operational use, and how they help building a coherent set of information that addresses all aspects of in-orbit calibration. Finally, we present the perspectives that the high level of agility of PLEIADES offers for the improvement of its calibration and a better characterization of the calibration sites.

  18. An absolute measure for a key currency

    NASA Astrophysics Data System (ADS)

    Oya, Shunsuke; Aihara, Kazuyuki; Hirata, Yoshito

    It is generally considered that the US dollar and the euro are the key currencies in the world and in Europe, respectively. However, there is no absolute general measure for a key currency. Here, we investigate the 24-hour periodicity of foreign exchange markets using a recurrence plot, and define an absolute measure for a key currency based on the strength of the periodicity. Moreover, we analyze the time evolution of this measure. The results show that the credibility of the US dollar has not decreased significantly since the Lehman shock, when the Lehman Brothers bankrupted and influenced the economic markets, and has increased even relatively better than that of the euro and that of the Japanese yen.

  19. Absolute radiometry and the solar constant

    NASA Technical Reports Server (NTRS)

    Willson, R. C.

    1974-01-01

    A series of active cavity radiometers (ACRs) are described which have been developed as standard detectors for the accurate measurement of irradiance in absolute units. It is noted that the ACR is an electrical substitution calorimeter, is designed for automatic remote operation in any environment, and can make irradiance measurements in the range from low-level IR fluxes up to 30 solar constants with small absolute uncertainty. The instrument operates in a differential mode by chopping the radiant flux to be measured at a slow rate, and irradiance is determined from two electrical power measurements together with the instrumental constant. Results are reported for measurements of the solar constant with two types of ACRs. The more accurate measurement yielded a value of 136.6 plus or minus 0.7 mW/sq cm (1.958 plus or minus 0.010 cal/sq cm per min).

  20. From Hubble's NGSL to Absolute Fluxes

    NASA Technical Reports Server (NTRS)

    Heap, Sara R.; Lindler, Don

    2012-01-01

    Hubble's Next Generation Spectral Library (NGSL) consists of R-l000 spectra of 374 stars of assorted temperature, gravity, and metallicity. Each spectrum covers the wavelength range, 0.18-1.00 microns. The library can be viewed and/or downloaded from the website, http://archive.stsci.edu/prepds/stisngsll. Stars in the NGSL are now being used as absolute flux standards at ground-based observatories. However, the uncertainty in the absolute flux is about 2%, which does not meet the requirements of dark-energy surveys. We are therefore developing an observing procedure that should yield fluxes with uncertainties less than 1 % and will take part in an HST proposal to observe up to 15 stars using this new procedure.

  1. Impact of Winko on absolute discharges.

    PubMed

    Balachandra, Krishna; Swaminath, Sam; Litman, Larry C

    2004-01-01

    In Canada, case laws have had a significant impact on the way mentally ill offenders are managed, both in the criminal justice system and in the forensic mental health system. The Supreme Court of Canada's decision with respect to Winko has set a major precedent in the application of the test of significant risk to the safety of the public in making dispositions by the Ontario Review Board and granting absolute discharges to the mentally ill offenders in the forensic health system. Our study examines the impact of the Supreme Court of Canada's decision before and after Winko. The results show that the numbers of absolute discharges have increased post-Winko, which was statistically significant, but there could be other factors influencing this increase.

  2. Asteroid absolute magnitudes and slope parameters

    NASA Technical Reports Server (NTRS)

    Tedesco, Edward F.

    1991-01-01

    A new listing of absolute magnitudes (H) and slope parameters (G) has been created and published in the Minor Planet Circulars; this same listing will appear in the 1992 Ephemerides of Minor Planets. Unlike previous listings, the values of the current list were derived from fits of data at the V band. All observations were reduced in the same fashion using, where appropriate, a single basis default value of 0.15 for the slope parameter. Distances and phase angles were computed for each observation. The data for 113 asteroids was of sufficiently high quality to permit derivation of their H and G. These improved absolute magnitudes and slope parameters will be used to deduce the most reliable bias-corrected asteroid size-frequency distribution yet made.

  3. Absolute-magnitude distributions of supernovae

    SciTech Connect

    Richardson, Dean; Wright, John; Jenkins III, Robert L.; Maddox, Larry

    2014-05-01

    The absolute-magnitude distributions of seven supernova (SN) types are presented. The data used here were primarily taken from the Asiago Supernova Catalogue, but were supplemented with additional data. We accounted for both foreground and host-galaxy extinction. A bootstrap method is used to correct the samples for Malmquist bias. Separately, we generate volume-limited samples, restricted to events within 100 Mpc. We find that the superluminous events (M{sub B} < –21) make up only about 0.1% of all SNe in the bias-corrected sample. The subluminous events (M{sub B} > –15) make up about 3%. The normal Ia distribution was the brightest with a mean absolute blue magnitude of –19.25. The IIP distribution was the dimmest at –16.75.

  4. Absolute and relative dosimetry for ELIMED

    SciTech Connect

    Cirrone, G. A. P.; Schillaci, F.; Scuderi, V.; Cuttone, G.; Candiano, G.; Musumarra, A.; Pisciotta, P.; Romano, F.; Carpinelli, M.; Presti, D. Lo; Raffaele, L.; Tramontana, A.; Cirio, R.; Sacchi, R.; Monaco, V.; Marchetto, F.; Giordanengo, S.

    2013-07-26

    The definition of detectors, methods and procedures for the absolute and relative dosimetry of laser-driven proton beams is a crucial step toward the clinical use of this new kind of beams. Hence, one of the ELIMED task, will be the definition of procedures aiming to obtain an absolute dose measure at the end of the transport beamline with an accuracy as close as possible to the one required for clinical applications (i.e. of the order of 5% or less). Relative dosimetry procedures must be established, as well: they are necessary in order to determine and verify the beam dose distributions and to monitor the beam fluence and the energetic spectra during irradiations. Radiochromic films, CR39, Faraday Cup, Secondary Emission Monitor (SEM) and transmission ionization chamber will be considered, designed and studied in order to perform a fully dosimetric characterization of the ELIMED proton beam.

  5. Absolute photoionization cross sections of atomic oxygen

    NASA Technical Reports Server (NTRS)

    Samson, J. A. R.; Pareek, P. N.

    1985-01-01

    The absolute values of photoionization cross sections of atomic oxygen were measured from the ionization threshold to 120 A. An auto-ionizing resonance belonging to the 2S2P4(4P)3P(3Do, 3So) transition was observed at 479.43 A and another line at 389.97 A. The experimental data is in excellent agreement with rigorous close-coupling calculations that include electron correlations in both the initial and final states.

  6. Absolute photoionization cross sections of atomic oxygen

    NASA Technical Reports Server (NTRS)

    Samson, J. A. R.; Pareek, P. N.

    1982-01-01

    The absolute values of photoionization cross sections of atomic oxygen were measured from the ionization threshold to 120 A. An auto-ionizing resonance belonging to the 2S2P4(4P)3P(3Do, 3So) transition was observed at 479.43 A and another line at 389.97 A. The experimental data is in excellent agreement with rigorous close-coupling calculations that include electron correlations in both the initial and final states.

  7. Relative errors can cue absolute visuomotor mappings.

    PubMed

    van Dam, Loes C J; Ernst, Marc O

    2015-12-01

    When repeatedly switching between two visuomotor mappings, e.g. in a reaching or pointing task, adaptation tends to speed up over time. That is, when the error in the feedback corresponds to a mapping switch, fast adaptation occurs. Yet, what is learned, the relative error or the absolute mappings? When switching between mappings, errors with a size corresponding to the relative difference between the mappings will occur more often than other large errors. Thus, we could learn to correct more for errors with this familiar size (Error Learning). On the other hand, it has been shown that the human visuomotor system can store several absolute visuomotor mappings (Mapping Learning) and can use associated contextual cues to retrieve them. Thus, when contextual information is present, no error feedback is needed to switch between mappings. Using a rapid pointing task, we investigated how these two types of learning may each contribute when repeatedly switching between mappings in the absence of task-irrelevant contextual cues. After training, we examined how participants changed their behaviour when a single error probe indicated either the often-experienced error (Error Learning) or one of the previously experienced absolute mappings (Mapping Learning). Results were consistent with Mapping Learning despite the relative nature of the error information in the feedback. This shows that errors in the feedback can have a double role in visuomotor behaviour: they drive the general adaptation process by making corrections possible on subsequent movements, as well as serve as contextual cues that can signal a learned absolute mapping. PMID:26280315

  8. The absolute spectrophotometric catalog by Anita Cochran

    NASA Astrophysics Data System (ADS)

    Burnashev, V. I.; Burnasheva, B. A.; Ruban, E. V.; Hagen-Torn, E. I.

    2014-06-01

    The absolute spectrophotometric catalog by Anita Cochran is presented in a machine-readable form. The catalog systematizes observations acquired at the McDonald Observatory in 1977-1978. The data are compared with other sources, in particular, the calculated broadband stellar magnitudes are compared with photometric observations by other authors, to show that the observational data given in the catalog are reliable and suitable for a variety of applications. Observations of variable stars of different types make Cochran's catalog especially valuable.

  9. Absolute magnitudes and kinematics of barium stars.

    NASA Astrophysics Data System (ADS)

    Gomez, A. E.; Luri, X.; Grenier, S.; Prevot, L.; Mennessier, M. O.; Figueras, F.; Torra, J.

    1997-03-01

    The absolute magnitude of barium stars has been obtained from kinematical data using a new algorithm based on the maximum-likelihood principle. The method allows to separate a sample into groups characterized by different mean absolute magnitudes, kinematics and z-scale heights. It also takes into account, simultaneously, the censorship in the sample and the errors on the observables. The method has been applied to a sample of 318 barium stars. Four groups have been detected. Three of them show a kinematical behaviour corresponding to disk population stars. The fourth group contains stars with halo kinematics. The luminosities of the disk population groups spread a large range. The intrinsically brightest one (M_v_=-1.5mag, σ_M_=0.5mag) seems to be an inhomogeneous group containing barium binaries as well as AGB single stars. The most numerous group (about 150 stars) has a mean absolute magnitude corresponding to stars in the red giant branch (M_v_=0.9mag, σ_M_=0.8mag). The third group contains barium dwarfs, the obtained mean absolute magnitude is characteristic of stars on the main sequence or on the subgiant branch (M_v_=3.3mag, σ_M_=0.5mag). The obtained mean luminosities as well as the kinematical results are compatible with an evolutionary link between barium dwarfs and classical barium giants. The highly luminous group is not linked with these last two groups. More high-resolution spectroscopic data will be necessary in order to better discriminate between barium and non-barium stars.

  10. Chemical composition of French mimosa absolute oil.

    PubMed

    Perriot, Rodolphe; Breme, Katharina; Meierhenrich, Uwe J; Carenini, Elise; Ferrando, Georges; Baldovini, Nicolas

    2010-02-10

    Since decades mimosa (Acacia dealbata) absolute oil has been used in the flavor and perfume industry. Today, it finds an application in over 80 perfumes, and its worldwide industrial production is estimated five tons per year. Here we report on the chemical composition of French mimosa absolute oil. Straight-chain analogues from C6 to C26 with different functional groups (hydrocarbons, esters, aldehydes, diethyl acetals, alcohols, and ketones) were identified in the volatile fraction. Most of them are long-chain molecules: (Z)-heptadec-8-ene, heptadecane, nonadecane, and palmitic acid are the most abundant, and constituents such as 2-phenethyl alcohol, methyl anisate, and ethyl palmitate are present in smaller amounts. The heavier constituents were mainly triterpenoids such as lupenone and lupeol, which were identified as two of the main components. (Z)-Heptadec-8-ene, lupenone, and lupeol were quantified by GC-MS in SIM mode using external standards and represents 6%, 20%, and 7.8% (w/w) of the absolute oil. Moreover, odorant compounds were extracted by SPME and analyzed by GC-sniffing leading to the perception of 57 odorant zones, of which 37 compounds were identified by their odorant description, mass spectrum, retention index, and injection of the reference compound. PMID:20070087

  11. A Methodology for Absolute Isotope Composition Measurement

    NASA Astrophysics Data System (ADS)

    Shen, J. J.; Lee, D.; Liang, W.

    2007-12-01

    Double spike technique was a well defined method for isotope composition measurement by TIMS of samples which have natural mass fractionation effect, but it is still a problem to define the isotope composition for double spike itself. In this study, we modified the old double spike technique and found that we could use the modified technique to solve the ¡§true¡¨ isotope composition of double spike itself. According the true isotope composition of double spike, we can measure the absolute isotope composition if the sample has natural fractionation effect. A new vector analytical method has been developed in order to obtain the true isotopic composition of a 42Ca-48Ca double spike, and this is achieved by using two different sample-spike mixtures combined with the double spike and the natural Ca data. Because the natural sample, the two mixtures, and the spike should all lie on a single mixing line, we are able to constrain the true isotopic composition of our double spike using this new approach. This method not only can be used in Ca system but also in Ti, Cr, Fe, Ni, Zn, Mo, Ba and Pb systems. The absolute double spike isotopic ratio is important, which can save a lot of time to check different reference standards. Especially for Pb, radiogenic isotope system, the decay systems embodied in three of four naturally occurring isotopes induce difficult to obtain true isotopic ratios for absolute dating.

  12. Chemical composition of French mimosa absolute oil.

    PubMed

    Perriot, Rodolphe; Breme, Katharina; Meierhenrich, Uwe J; Carenini, Elise; Ferrando, Georges; Baldovini, Nicolas

    2010-02-10

    Since decades mimosa (Acacia dealbata) absolute oil has been used in the flavor and perfume industry. Today, it finds an application in over 80 perfumes, and its worldwide industrial production is estimated five tons per year. Here we report on the chemical composition of French mimosa absolute oil. Straight-chain analogues from C6 to C26 with different functional groups (hydrocarbons, esters, aldehydes, diethyl acetals, alcohols, and ketones) were identified in the volatile fraction. Most of them are long-chain molecules: (Z)-heptadec-8-ene, heptadecane, nonadecane, and palmitic acid are the most abundant, and constituents such as 2-phenethyl alcohol, methyl anisate, and ethyl palmitate are present in smaller amounts. The heavier constituents were mainly triterpenoids such as lupenone and lupeol, which were identified as two of the main components. (Z)-Heptadec-8-ene, lupenone, and lupeol were quantified by GC-MS in SIM mode using external standards and represents 6%, 20%, and 7.8% (w/w) of the absolute oil. Moreover, odorant compounds were extracted by SPME and analyzed by GC-sniffing leading to the perception of 57 odorant zones, of which 37 compounds were identified by their odorant description, mass spectrum, retention index, and injection of the reference compound.

  13. The Carina Project: Absolute and Relative Calibrations

    NASA Astrophysics Data System (ADS)

    Corsi, C. E.; Bono, G.; Walker, A. R.; Brocato, E.; Buonanno, R.; Caputo, F.; Castellani, M.; Castellani, V.; Dall'Ora, M.; Marconi, M.; Monelli, M.; Nonino, M.; Pulone, L.; Ripepi, V.; Smith, H. A.

    We discuss the reduction strategy adopted to perform the relative and the absolute calibration of the Wide Field Imager (WFI) available at the 2.2m ESO/MPI telescope and of the Mosaic Camera (MC) available at the 4m CTIO Blanco telescope. To properly constrain the occurrence of deceptive systematic errors in the relative calibration we observed with each chip the same set of stars. Current photometry seems to suggest that the WFI shows a positional effect when moving from the top to the bottom of individual chips. Preliminary results based on an independent data set collected with the MC suggest that this camera is only marginally affected by the same problem. To perform the absolute calibration we observed with each chip the same set of standard stars. The sample covers a wide color range and the accuracy both in the B and in the V-band appears to be of the order of a few hundredths of magnitude. Finally, we briefly outline the observing strategy to improve both relative and absolute calibrations of mosaic CCD cameras.

  14. What's the meaning of local? Using molecular markers to define seed transfer zones for ecological restoration in Norway.

    PubMed

    Jørgensen, Marte Holten; Elameen, Abdelhameed; Hofman, Nadine; Klemsdal, Sonja; Malaval, Sandra; Fjellheim, Siri

    2016-06-01

    According to the Norwegian Diversity Act, practitioners of restoration in Norway are instructed to use seed mixtures of local provenance. However, there are no guidelines for how local seed should be selected. In this study, we use genetic variation in a set of alpine species (Agrostis mertensii, Avenella flexuosa, Carex bigelowii, Festuca ovina, Poa alpina and Scorzoneroides autumnalis) to define seed transfer zones to reduce confusion about the definition of 'local seeds'. The species selected for the study are common in all parts of Norway and suitable for commercial seed production. The sampling covered the entire alpine region (7-20 populations per species, 3-15 individuals per population). We characterised genetic diversity using amplified fragment length polymorphisms. We identified different spatial genetic diversity structures in the species, most likely related to differences in reproductive strategies, phylogeographic factors and geographic distribution. Based on results from all species, we suggest four general seed transfer zones for alpine Norway. This is likely more conservative than needed for all species, given that no species show more than two genetic groups. Even so, the approach is practical as four seed mixtures will serve the need for restoration of vegetation in alpine regions in Norway. PMID:27247618

  15. What's the meaning of local? Using molecular markers to define seed transfer zones for ecological restoration in Norway.

    PubMed

    Jørgensen, Marte Holten; Elameen, Abdelhameed; Hofman, Nadine; Klemsdal, Sonja; Malaval, Sandra; Fjellheim, Siri

    2016-06-01

    According to the Norwegian Diversity Act, practitioners of restoration in Norway are instructed to use seed mixtures of local provenance. However, there are no guidelines for how local seed should be selected. In this study, we use genetic variation in a set of alpine species (Agrostis mertensii, Avenella flexuosa, Carex bigelowii, Festuca ovina, Poa alpina and Scorzoneroides autumnalis) to define seed transfer zones to reduce confusion about the definition of 'local seeds'. The species selected for the study are common in all parts of Norway and suitable for commercial seed production. The sampling covered the entire alpine region (7-20 populations per species, 3-15 individuals per population). We characterised genetic diversity using amplified fragment length polymorphisms. We identified different spatial genetic diversity structures in the species, most likely related to differences in reproductive strategies, phylogeographic factors and geographic distribution. Based on results from all species, we suggest four general seed transfer zones for alpine Norway. This is likely more conservative than needed for all species, given that no species show more than two genetic groups. Even so, the approach is practical as four seed mixtures will serve the need for restoration of vegetation in alpine regions in Norway.

  16. Molecular Mechanism of Local Drug Delivery with Paclitaxel-Eluting Membranes in Biliary and Pancreatic Cancer: New Application for an Old Drug

    PubMed Central

    Bang, Sookhee; Lee, Su Yeon; Baek, Yi-Yong; Yun, Jieun; Oh, Soo Jin; Lee, Chang Woo; Jo, Eun Ae; Yang, Sugeun; Lee, Don Haeng; Lee, Dong Ki

    2015-01-01

    Implantation of self-expanding metal stents (SEMS) is palliation for patients suffering from inoperable malignant obstructions associated with biliary and pancreatic cancers. Chemotherapeutic agent-eluting stents have been developed because SEMS are susceptible to occlusion by tumor in-growth. We reported recently that paclitaxel-eluting SEMS provide enhanced local drug delivery in an animal model. However, little is known about the molecular mechanisms by which paclitaxel-eluting stents attenuate tumor growth. We investigated the signal transduction pathways underlying the antiproliferative effects of a paclitaxel-eluting membrane (PEM) implanted in pancreatic/cholangiocarcinoma tumor bearing nude mice. Molecular and cellular alterations were analyzed in the PEM-implanted pancreatic/cholangiocarcinoma xenograft tumors by Western blot, immunoprecipitation, and immunofluorescence. The quantities of paclitaxel released into the tumor and plasma were determined by liquid chromatography-tandem mass spectroscopy. Paclitaxel from the PEM and its diffusion into the tumor inhibited angiogenesis, which involved suppression of mammalian target of rapamycin (mTOR) through regulation of hypoxia inducible factor (HIF-1) and increased apoptosis. Moreover, implantation of the PEM inhibited tumor-stromal interaction-related expression of proteins such as CD44, SPARC, matrix metalloproteinase-2, and vimentin. Local delivery of paclitaxel from a PEM inhibited growth of pancreatic/cholangiocarcinoma tumors in nude mice by suppressing angiogenesis via the mTOR and inducing apoptosis signal pathway. PMID:25983747

  17. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

    PubMed

    Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-01

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

  18. Selenium Incorporated Cationic Organochalcogen: Live Cell Compatible and Highly Photostable Molecular Stain for Imaging and Localization of Intracellular DNA.

    PubMed

    Gaur, Pankaj; Kumar, Ajay; Dey, Gourab; Kumar, Rajendra; Bhattacharyya, Shalmoli; Ghosh, Subrata

    2016-05-01

    Successful integration of selenium unit into a newly designed cationic chemical architecture led to the development of a highly photostable molecular maker PA5 to be used in fluorescence microscopy as cellular nucleus staining agent for longer duration imaging under continuous laser illumination. Adaptation of a targeted single-atom modification strategy led to the development of a series of proficient DNA light-up probes (PA1-PA5). Further, their comparative photophysical studies in the presence of DNA revealed the potential of electron rich heteroatoms of chalcogen family in improving binding efficiency and specificity of molecular probes toward DNA. The findings of cell studies confirmed the outstanding cell compatibility of probe PA5 in terms of cell permeability, biostability, and extremely low cytotoxicity. Moreover, the photostability experiment employing continuous laser illumination in solution phase as well as in cell assay (both fixed and live cells) revealed the admirable photobleaching resistance of PA5. Finally, while investigating the phototoxicity of PA5, the probe was found not to exhibit light-induced toxicity even when irradiated for longer duration. All these experimental results demonstrated the promising standing of PA5 as a futuristic cell compatible potential stain for bioimaging and temporal profiling of DNA. PMID:27066840

  19. Prediction of the dissociation constant pKa of organic acids from local molecular parameters of their electronic ground state.

    PubMed

    Yu, Haiying; Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

    2011-09-26

    A quantum chemical method has been developed to estimate the dissociation constant pK(a) of organic acids from their neutral molecular structures by employing electronic structure properties. The data set covers 219 phenols (including 29 phenols with intramolecular H-bonding), 150 aromatic carboxylic acids, 190 aliphatic carboxylic acids, and 138 alcohols, with pK(a) varying by 16 units (0.38-16.80). Optimized ground-state geometries employing the semiempirical AM1 Hamiltonian have been used to quantify the site-specific molecular readiness to donate or accept electron charge in terms of both charge-associated energies and energy-associated charges, augmented by an ortho substitution indicator for aromatic compounds. The resultant regression models yield squared correlation coefficients (r(2)) from 0.82 to 0.90 and root-mean-square errors (rms) from 0.39 to 0.70 pK(a) units, corresponding to an overall (subset-weighted) r(2) of 0.86. Simulated external validation, leave-10%-out cross-validation and target value scrambling demonstrate the statistical robustness and prediction power of the derived model suite. The low intercorrelation with prediction errors from the commercial ACD package provides opportunity for a consensus model approach, offering a pragmatic way for further increasing the confidence in prediction significantly. Interestingly, inclusion of calculated free energies of aqueous solvation does not improve the prediction performance, probably because of the limited precision provided by available continuum-solvation models.

  20. Absolute photoionization cross-section of the methyl radical.

    SciTech Connect

    Taatjes, C. A.; Osborn, D. L.; Selby, T.; Meloni, G.; Fan, H.; Pratt, S. T.; Chemical Sciences and Engineering Division; SNL

    2008-01-01

    The absolute photoionization cross-section of the methyl radical has been measured using two completely independent methods. The CH{sub 3} photoionization cross-section was determined relative to that of acetone and methyl vinyl ketone at photon energies of 10.2 and 11.0 eV by using a pulsed laser-photolysis/time-resolved synchrotron photoionization mass spectrometry method. The time-resolved depletion of the acetone or methyl vinyl ketone precursor and the production of methyl radicals following 193 nm photolysis are monitored simultaneously by using time-resolved synchrotron photoionization mass spectrometry. Comparison of the initial methyl signal with the decrease in precursor signal, in combination with previously measured absolute photoionization cross-sections of the precursors, yields the absolute photoionization cross-section of the methyl radical; {sigma}{sub CH}(10.2 eV) = (5.7 {+-} 0.9) x 10{sup -18} cm{sup 2} and {sigma}{sub CH{sub 3}}(11.0 eV) = (6.0 {+-} 2.0) x 10{sup -18} cm{sup 2}. The photoionization cross-section for vinyl radical determined by photolysis of methyl vinyl ketone is in good agreement with previous measurements. The methyl radical photoionization cross-section was also independently measured relative to that of the iodine atom by comparison of ionization signals from CH{sub 3} and I fragments following 266 nm photolysis of methyl iodide in a molecular-beam ion-imaging apparatus. These measurements gave a cross-section of (5.4 {+-} 2.0) x 10{sup -18} cm{sup 2} at 10.460 eV, (5.5 {+-} 2.0) x 10{sup -18} cm{sup 2} at 10.466 eV, and (4.9 {+-} 2.0) x 10{sup -18} cm{sup 2} at 10.471 eV. The measurements allow relative photoionization efficiency spectra of methyl radical to be placed on an absolute scale and will facilitate quantitative measurements of methyl concentrations by photoionization mass spectrometry.

  1. Novel serine-based gemini surfactants as chemical permeation enhancers of local anesthetics: A comprehensive study on structure-activity relationships, molecular dynamics and dermal delivery.

    PubMed

    Teixeira, Raquel S; Cova, Tânia F G G; Silva, Sérgio M C; Oliveira, Rita; do Vale, M Luísa C; Marques, Eduardo F; Pais, Alberto A C C; Veiga, Francisco J B

    2015-06-01

    This work aims at studying the efficacy of a series of novel biocompatible, serine-based surfactants as chemical permeation enhancers for two different local anesthetics, tetracaine and ropivacaine, combining an experimental and computational approach. The surfactants consist of gemini molecules structurally related, but with variations in headgroup charge (nonionic vs. cationic) and in the hydrocarbon chain lengths (main and spacer chains). In vitro permeation and molecular dynamics studies combined with cytotoxicity profiles were performed to investigate the permeation of both drugs, probe skin integrity, and rationalize the interactions at molecular level. Results show that these enhancers do not have significant deleterious effects on the skin structure and do not cause relevant changes on cell viability. Permeation across the skin is clearly improved using some of the selected serine-based gemini surfactants, namely the cationic ones with long alkyl chains and shorter spacer. This is noteworthy in the case of ropivacaine hydrochloride, which is not easily administered through the stratum corneum. Molecular dynamics results provide a mechanistic view of the surfactant action on lipid membranes that essentially corroborate the experimental observations. Overall, this study suggests the viability of these serine-based surfactants as suitable and promising delivery agents in pharmaceutical formulations.

  2. Absolute Quantitative MALDI Imaging Mass Spectrometry: A Case of Rifampicin in Liver Tissues.

    PubMed

    Chumbley, Chad W; Reyzer, Michelle L; Allen, Jamie L; Marriner, Gwendolyn A; Via, Laura E; Barry, Clifton E; Caprioli, Richard M

    2016-02-16

    Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) elucidates molecular distributions in thin tissue sections. Absolute pixel-to-pixel quantitation has remained a challenge, primarily lacking validation of the appropriate analytical methods. In the present work, isotopically labeled internal standards are applied to tissue sections to maximize quantitative reproducibility and yield accurate quantitative results. We have developed a tissue model for rifampicin (RIF), an antibiotic used to treat tuberculosis, and have tested different methods of applying an isotopically labeled internal standard for MALDI IMS analysis. The application of the standard and subsequently the matrix onto tissue sections resulted in quantitation that was not statistically significantly different from results obtained using HPLC-MS/MS of tissue extracts. Quantitative IMS experiments were performed on liver tissue from an animal dosed in vivo. Each microspot in the quantitative images measures the local concentration of RIF in the thin tissue section. Lower concentrations were detected from the blood vessels and around the portal tracts. The quantitative values obtained from these measurements were comparable (>90% similarity) to HPLC-MS/MS results obtained from extracts of the same tissue.

  3. MOLECULAR CHARACTERIZATION AND SEQUENCE PHYLOGENETIC ANALYSIS OF SURFACE ANTIGEN 3 (SAG3) GENE OF LOCAL INDIAN ISOLATES (CHENNAI AND IZATNAGAR) OF Toxoplasma gondii

    PubMed Central

    SUDAN, Vikrant; TEWARI, Anup Kumar; SINGH, Harkirat

    2015-01-01

    Context and objective: The molecular characterization of local isolates of Toxoplasma gondii is considered significant so as to assess the homologous variations between the different loci of various strains of parasites. Design and setting: The present communication deals with the molecular cloning and sequence analysis of the 1158 bp entire open reading frame (ORF) of surface antigen 3 (SAG3) of two Indian T. gondii isolates (Chennai and Izatnagar) being maintained as cryostock at the IVRI. Method: The surface antigen 3 (SAG3) of two local Indian isolates were cloned and sequenced before being compared with the available published sequences. Results: The sequence comparison analysis revealed 99.9% homology with the standard published RH strain sequence of T. gondii. The strains were also compared with other established published sequences and found to be most related to the P-Br strain and CEP strain (both 99.3%), and least with PRU strain (98.4%). However, the two Indian isolates had 100% homology between them. Conclusion: Finally, it was concluded that the Indian isolates were closer to the RH strain than to the P-Br strain (Brazilian strain), the CEP strain and the PRU strains (USA), with respect to nucleotide homology. The two Indian isolates used in the present study are known to vary between themselves, as far as homologies related to other genes are concerned, but they were found to be 100% homologous as far as SAG3 locus is concerned. This could be attributed to the fact that this SAG3 might be a conserved locus and thereby, further detailed studies are thereby warranted to exploit the use of this particular molecule in diagnostics and immunoprophylactics. The findings are important from the point of view of molecular phylogeny. PMID:26200959

  4. Network models provide insights into how oriens–lacunosum-moleculare and bistratified cell interactions influence the power of local hippocampal CA1 theta oscillations

    PubMed Central

    Ferguson, Katie A.; Huh, Carey Y. L.; Amilhon, Bénédicte; Manseau, Frédéric; Williams, Sylvain; Skinner, Frances K.

    2015-01-01

    Hippocampal theta is a 4–12 Hz rhythm associated with episodic memory, and although it has been studied extensively, the cellular mechanisms underlying its generation are unclear. The complex interactions between different interneuron types, such as those between oriens–lacunosum-moleculare (OLM) interneurons and bistratified cells (BiCs), make their contribution to network rhythms difficult to determine experimentally. We created network models that are tied to experimental work at both cellular and network levels to explore how these interneuron interactions affect the power of local oscillations. Our cellular models were constrained with properties from patch clamp recordings in the CA1 region of an intact hippocampus preparation in vitro. Our network models are composed of three different types of interneurons: parvalbumin-positive (PV+) basket and axo-axonic cells (BC/AACs), PV+ BiCs, and somatostatin-positive OLM cells. Also included is a spatially extended pyramidal cell model to allow for a simplified local field potential representation, as well as experimentally-constrained, theta frequency synaptic inputs to the interneurons. The network size, connectivity, and synaptic properties were constrained with experimental data. To determine how the interactions between OLM cells and BiCs could affect local theta power, we explored how the number of OLM-BiC connections and connection strength affected local theta power. We found that our models operate in regimes that could be distinguished by whether OLM cells minimally or strongly affected the power of network theta oscillations due to balances that, respectively, allow compensatory effects or not. Inactivation of OLM cells could result in no change or even an increase in theta power. We predict that the dis-inhibitory effect of OLM cells to BiCs to pyramidal cell interactions plays a critical role in the resulting power of network theta oscillations. Overall, our network models reveal a dynamic interplay

  5. Principles and procedures for determining absolute differential electron-molecule (atom) scattering cross sections

    NASA Technical Reports Server (NTRS)

    Nickel, J. C.; Zetner, P. W.; Shen, G.; Trajmar, S.

    1989-01-01

    Procedures and calibration techniques for measuring the absolute elastic and inelastic differential cross sections (DCS) for electron impact on molecular (atomic) species are described and illustrated by examples. The elastic DCS for the molecule under study is first determined by calibration against helium using the relative flow technique. The second step involves the production of energy-loss spectra for the instrument response function, the unfolding of overlapping inelastic structures and the normalization of inelastic intensities to the elastic cross sections. It is concluded that this method of determining absolute differential electron-molecule (atom) scattering cross sections is generally applicable and provides reliable results.

  6. Electron Localization in Molecular Fragmentation of H{sub 2} by Carrier-Envelope Phase Stabilized Laser Pulses

    SciTech Connect

    Kremer, Manuel; Fischer, Bettina; Feuerstein, Bernold; Sharma, Vandana; Hofrichter, Christian; Schroeter, Claus Dieter; Moshammer, Robert; Ullrich, Joachim; Jesus, Vitor L. B. de; Rudenko, Artem; Thumm, Uwe

    2009-11-20

    Fully differential data for H{sub 2} dissociation in ultrashort (6 fs, 760 nm), linearly polarized, intense (0.44 PW/cm{sup 2}) laser pulses with a stabilized carrier-envelope phase (CEP) were recorded with a reaction microscope. Depending on the CEP, the molecular orientation, and the kinetic energy release (KER), we find asymmetric proton emission at low KERs (0-3 eV), basically predicted by Roudnev and Esry, and much stronger than reported by Kling et al. Wave packet propagation calculations reproduce the salient features and discard, together with the observed KER-independent electron asymmetry, the first ionization step to be the reason for the asymmetric proton emission.

  7. Modeling Biophysical and Biological Properties From the Characteristics of the Molecular Electron Density, Electron Localization and Delocalization Matrices, and the Electrostatic Potential

    PubMed Central

    Matta*, Chérif F

    2014-01-01

    The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pKa's, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme–substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as “interacting quantum atoms (IQA)” energies which are expressible into an interaction matrix of two body terms (and diagonal one body “self” terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established. © 2014 The Author and the Journal of Computational Chemistry Published

  8. Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential.

    PubMed

    Matta, Chérif F

    2014-06-15

    The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pK(a)'s, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme-substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as "interacting quantum atoms (IQA)" energies which are expressible into an interaction matrix of two body terms (and diagonal one body "self" terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established.

  9. Molecular characterization, tissue distribution, and ultrastructural localization of adipokinetic hormones in the CNS of the firebug Pyrrhocoris apterus (Heteroptera, Insecta).

    PubMed

    Kodrík, Dalibor; Stašková, Tereza; Jedličková, Veronika; Weyda, František; Závodská, Radka; Pflegerová, Jitka

    2015-01-01

    Adipokinetic hormones (AKHs) are a group of insect metabolic neurohormones, synthesized and released from an endocrine retrocerebral gland, the corpus cardiacum (CC). Small amounts of AKH have also been identified in the brain, although their role in this organ is not clear. To address this gap in the knowledge about insect brain biology, we studied the nucleotide sequence, tissue distribution, and subcellular localization of AKHs in the brain and CC of the firebug Pyrrhocoris apterus. This insect expresses two AKHs; the octapeptides Pyrap-AKH and Peram-CAH-II, the presence of which was documented in the both studied organs. In situ hybridization and quantitative reverse-transcription (q-RT)-PCR revealed the expression of the genes encoding for both AKHs not only in the CC, but also in brain. Electron microscopy analysis of the brain revealed the presence of these hormones in specialized secretory granules localized predominantly in the cellular bodies of neurons. The hormones might be transported from the granules into the axons, where they could play a role in neuronal signaling. Under acute stress induced by the injection of 3μmol KCl, the level of AKHs in the brain increased to a greater extent than that in the CC. These results might indicate an enhanced role of brain-derived AKHs in defence reaction under acute stress situations. PMID:25449136

  10. Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO{sub 2}–H{sub 2}O systems

    SciTech Connect

    Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang

    2014-01-28

    In view of the important implications of excess electrons (EEs) interacting with CO{sub 2}–H{sub 2}O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO{sub 2}–H{sub 2}O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO{sub 2} molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO{sub 2}, an EE can stably reside in the empty, low-lying π{sup *} orbital of a CO{sub 2} molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO{sub 2}{sup −} oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO{sub 2}-bound solvated EE in [CO{sub 2}(H{sub 2}O){sub n}]{sup −} systems. Interestingly, hydration occurs not only on the O atoms of the core CO{sub 2}{sup −} through formation of O⋯H–O H–bond(s), but also on the C atom, through formation of a C⋯H–O H–bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H–O H–bonds, and vice versa. The number of water molecules associated with the CO{sub 2}{sup −} anion in the first hydration shell is about 4∼7. No dimer-core (C{sub 2}O{sub 4}{sup −}) and core-switching were observed in the double CO{sub 2} aqueous media. This work provides molecular dynamics

  11. Genuine multipartite entanglement of symmetric Gaussian states: Strong monogamy, unitary localization, scaling behavior, and molecular sharing structure

    NASA Astrophysics Data System (ADS)

    Adesso, Gerardo; Illuminati, Fabrizio

    2008-10-01

    We investigate the structural aspects of genuine multipartite entanglement in Gaussian states of continuous variable systems. Generalizing the results of Adesso and Illuminati [Phys. Rev. Lett. 99, 150501 (2007)], we analyze whether the entanglement shared by blocks of modes distributes according to a strong monogamy law. This property, once established, allows us to quantify the genuine N -partite entanglement not encoded into 2,…,K,…,(N-1) -partite quantum correlations. Strong monogamy is numerically verified, and the explicit expression of the measure of residual genuine multipartite entanglement is analytically derived, by a recursive formula, for a subclass of Gaussian states. These are fully symmetric (permutation-invariant) states that are multipartitioned into blocks, each consisting of an arbitrarily assigned number of modes. We compute the genuine multipartite entanglement shared by the blocks of modes and investigate its scaling properties with the number and size of the blocks, the total number of modes, the global mixedness of the state, and the squeezed resources needed for state engineering. To achieve the exact computation of the block entanglement, we introduce and prove a general result of symplectic analysis: Correlations among K blocks in N -mode multisymmetric and multipartite Gaussian states, which are locally invariant under permutation of modes within each block, can be transformed by a local (with respect to the partition) unitary operation into correlations shared by K single modes, one per block, in effective nonsymmetric states where N-K modes are completely uncorrelated. Due to this theorem, the above results, such as the derivation of the explicit expression for the residual multipartite entanglement, its nonnegativity, and its scaling properties, extend to the subclass of non-symmetric Gaussian states that are obtained by the unitary localization of the multipartite entanglement of symmetric states. These findings provide strong

  12. Absolute Radiometric Calibration of EUNIS-06

    NASA Technical Reports Server (NTRS)

    Thomas, R. J.; Rabin, D. M.; Kent, B. J.; Paustian, W.

    2007-01-01

    The Extreme-Ultraviolet Normal-Incidence Spectrometer (EUNIS) is a soundingrocket payload that obtains imaged high-resolution spectra of individual solar features, providing information about the Sun's corona and upper transition region. Shortly after its successful initial flight last year, a complete end-to-end calibration was carried out to determine the instrument's absolute radiometric response over its Longwave bandpass of 300 - 370A. The measurements were done at the Rutherford-Appleton Laboratory (RAL) in England, using the same vacuum facility and EUV radiation source used in the pre-flight calibrations of both SOHO/CDS and Hinode/EIS, as well as in three post-flight calibrations of our SERTS sounding rocket payload, the precursor to EUNIS. The unique radiation source provided by the Physikalisch-Technische Bundesanstalt (PTB) had been calibrated to an absolute accuracy of 7% (l-sigma) at 12 wavelengths covering our bandpass directly against the Berlin electron storage ring BESSY, which is itself a primary radiometric source standard. Scans of the EUNIS aperture were made to determine the instrument's absolute spectral sensitivity to +- 25%, considering all sources of error, and demonstrate that EUNIS-06 was the most sensitive solar E W spectrometer yet flown. The results will be matched against prior calibrations which relied on combining measurements of individual optical components, and on comparisons with theoretically predicted 'insensitive' line ratios. Coordinated observations were made during the EUNIS-06 flight by SOHO/CDS and EIT that will allow re-calibrations of those instruments as well. In addition, future EUNIS flights will provide similar calibration updates for TRACE, Hinode/EIS, and STEREO/SECCHI/EUVI.

  13. Clock time is absolute and universal

    NASA Astrophysics Data System (ADS)

    Shen, Xinhang

    2015-09-01

    A critical error is found in the Special Theory of Relativity (STR): mixing up the concepts of the STR abstract time of a reference frame and the displayed time of a physical clock, which leads to use the properties of the abstract time to predict time dilation on physical clocks and all other physical processes. Actually, a clock can never directly measure the abstract time, but can only record the result of a physical process during a period of the abstract time such as the number of cycles of oscillation which is the multiplication of the abstract time and the frequency of oscillation. After Lorentz Transformation, the abstract time of a reference frame expands by a factor gamma, but the frequency of a clock decreases by the same factor gamma, and the resulting multiplication i.e. the displayed time of a moving clock remains unchanged. That is, the displayed time of any physical clock is an invariant of Lorentz Transformation. The Lorentz invariance of the displayed times of clocks can further prove within the framework of STR our earth based standard physical time is absolute, universal and independent of inertial reference frames as confirmed by both the physical fact of the universal synchronization of clocks on the GPS satellites and clocks on the earth, and the theoretical existence of the absolute and universal Galilean time in STR which has proved that time dilation and space contraction are pure illusions of STR. The existence of the absolute and universal time in STR has directly denied that the reference frame dependent abstract time of STR is the physical time, and therefore, STR is wrong and all its predictions can never happen in the physical world.

  14. Achieving Climate Change Absolute Accuracy in Orbit

    NASA Technical Reports Server (NTRS)

    Wielicki, Bruce A.; Young, D. F.; Mlynczak, M. G.; Thome, K. J; Leroy, S.; Corliss, J.; Anderson, J. G.; Ao, C. O.; Bantges, R.; Best, F.; Bowman, K.; Brindley, H.; Butler, J. J.; Collins, W.; Dykema, J. A.; Doelling, D. R.; Feldman, D. R.; Fox, N.; Huang, X.; Holz, R.; Huang, Y.; Jennings, D.; Jin, Z.; Johnson, D. G.; Jucks, K.; Kato, S.; Kratz, D. P.; Liu, X.; Lukashin, C.; Mannucci, A. J.; Phojanamongkolkij, N.; Roithmayr, C. M.; Sandford, S.; Taylor, P. C.; Xiong, X.

    2013-01-01

    The Climate Absolute Radiance and Refractivity Observatory (CLARREO) mission will provide a calibration laboratory in orbit for the purpose of accurately measuring and attributing climate change. CLARREO measurements establish new climate change benchmarks with high absolute radiometric accuracy and high statistical confidence across a wide range of essential climate variables. CLARREO's inherently high absolute accuracy will be verified and traceable on orbit to Système Internationale (SI) units. The benchmarks established by CLARREO will be critical for assessing changes in the Earth system and climate model predictive capabilities for decades into the future as society works to meet the challenge of optimizing strategies for mitigating and adapting to climate change. The CLARREO benchmarks are derived from measurements of the Earth's thermal infrared spectrum (5-50 micron), the spectrum of solar radiation reflected by the Earth and its atmosphere (320-2300 nm), and radio occultation refractivity from which accurate temperature profiles are derived. The mission has the ability to provide new spectral fingerprints of climate change, as well as to provide the first orbiting radiometer with accuracy sufficient to serve as the reference transfer standard for other space sensors, in essence serving as a "NIST [National Institute of Standards and Technology] in orbit." CLARREO will greatly improve the accuracy and relevance of a wide range of space-borne instruments for decadal climate change. Finally, CLARREO has developed new metrics and methods for determining the accuracy requirements of climate observations for a wide range of climate variables and uncertainty sources. These methods should be useful for improving our understanding of observing requirements for most climate change observations.

  15. Molecular characterization of the gonadal kisspeptin system: Cloning, tissue distribution, gene expression analysis and localization in sablefish (Anoplopoma fimbria).

    PubMed

    Fairgrieve, Marian R; Shibata, Yasushi; Smith, Elizabeth K; Hayman, Edward S; Luckenbach, J Adam

    2016-01-01

    The kisspeptin system plays pivotal roles in the regulation of vertebrate reproduction. Classically, kisspeptin produced in the brain stimulates brain gonadotropin-releasing hormone signaling, which in turn activates the pituitary-gonad axis. Expression of the kisspeptin system has also been documented in peripheral tissues, including gonads of mammals and fishes. However, the fish gonadal kisspeptin system remained uncharacterized. Herein we report identification and characterization of four kisspeptin system mRNAs (kisspeptin 1 (kiss1), kiss2, and G protein-coupled receptor 54-1 (gpr54-1) and gpr54-2) in sablefish, Anoplopoma fimbria. Sablefish predicted protein sequences were highly similar to those of other marine teleosts, but less so to freshwater teleosts. Tissue distribution analyses revealed that all four kisspeptin-system transcripts were expressed in both brain and gonad. However, kiss2 was the predominant transcript in the gonads and the only transcript detected in ovulated eggs. Ontogenetic analysis of kiss2 expression in juvenile sablefish gonads demonstrated that levels were low during sex differentiation but increased with fish size and gonadal development. Dramatic increases in kiss2 mRNA occurred during primary oocyte growth, while levels remained relatively low in testes. In situ hybridization revealed that kiss2 mRNA was localized to cytoplasm of perinucleolus stage oocytes, suggesting it could play a local role in oogenesis or could be synthesized and stored within oocytes as maternal mRNA. This represents the first study to focus on the gonadal kisspeptin system in fishes and provides important tools for further investigation of both the gonadal and brain kisspeptin systems in sablefish.

  16. Molecular characterization of the gonadal kisspeptin system: Cloning, tissue distribution, gene expression analysis and localization in sablefish (Anoplopoma fimbria).

    PubMed

    Fairgrieve, Marian R; Shibata, Yasushi; Smith, Elizabeth K; Hayman, Edward S; Luckenbach, J Adam

    2016-01-01

    The kisspeptin system plays pivotal roles in the regulation of vertebrate reproduction. Classically, kisspeptin produced in the brain stimulates brain gonadotropin-releasing hormone signaling, which in turn activates the pituitary-gonad axis. Expression of the kisspeptin system has also been documented in peripheral tissues, including gonads of mammals and fishes. However, the fish gonadal kisspeptin system remained uncharacterized. Herein we report identification and characterization of four kisspeptin system mRNAs (kisspeptin 1 (kiss1), kiss2, and G protein-coupled receptor 54-1 (gpr54-1) and gpr54-2) in sablefish, Anoplopoma fimbria. Sablefish predicted protein sequences were highly similar to those of other marine teleosts, but less so to freshwater teleosts. Tissue distribution analyses revealed that all four kisspeptin-system transcripts were expressed in both brain and gonad. However, kiss2 was the predominant transcript in the gonads and the only transcript detected in ovulated eggs. Ontogenetic analysis of kiss2 expression in juvenile sablefish gonads demonstrated that levels were low during sex differentiation but increased with fish size and gonadal development. Dramatic increases in kiss2 mRNA occurred during primary oocyte growth, while levels remained relatively low in testes. In situ hybridization revealed that kiss2 mRNA was localized to cytoplasm of perinucleolus stage oocytes, suggesting it could play a local role in oogenesis or could be synthesized and stored within oocytes as maternal mRNA. This represents the first study to focus on the gonadal kisspeptin system in fishes and provides important tools for further investigation of both the gonadal and brain kisspeptin systems in sablefish. PMID:26386183

  17. Absolute calibration of the Auger fluorescence detectors

    SciTech Connect

    Bauleo, P.; Brack, J.; Garrard, L.; Harton, J.; Knapik, R.; Meyhandan, R.; Rovero, A.C.; Tamashiro, A.; Warner, D.

    2005-07-01

    Absolute calibration of the Pierre Auger Observatory fluorescence detectors uses a light source at the telescope aperture. The technique accounts for the combined effects of all detector components in a single measurement. The calibrated 2.5 m diameter light source fills the aperture, providing uniform illumination to each pixel. The known flux from the light source and the response of the acquisition system give the required calibration for each pixel. In the lab, light source uniformity is studied using CCD images and the intensity is measured relative to NIST-calibrated photodiodes. Overall uncertainties are presently 12%, and are dominated by systematics.

  18. Absolute rate theories of epigenetic stability

    NASA Astrophysics Data System (ADS)

    Walczak, Aleksandra M.; Onuchic, José N.; Wolynes, Peter G.

    2005-12-01

    Spontaneous switching events in most characterized genetic switches are rare, resulting in extremely stable epigenetic properties. We show how simple arguments lead to theories of the rate of such events much like the absolute rate theory of chemical reactions corrected by a transmission factor. Both the probability of the rare cellular states that allow epigenetic escape and the transmission factor depend on the rates of DNA binding and unbinding events and on the rates of protein synthesis and degradation. Different mechanisms of escape from the stable attractors occur in the nonadiabatic, weakly adiabatic, and strictly adiabatic regimes, characterized by the relative values of those input rates. rate theory | stochastic gene expression | gene switches

  19. Characterization of the DARA solar absolute radiometer

    NASA Astrophysics Data System (ADS)

    Finsterle, W.; Suter, M.; Fehlmann, A.; Kopp, G.

    2011-12-01

    The Davos Absolute Radiometer (DARA) prototype is an Electrical Substitution Radiometer (ESR) which has been developed as a successor of the PMO6 type on future space missions and ground based TSI measurements. The DARA implements an improved thermal design of the cavity detector and heat sink assembly to minimize air-vacuum differences and to maximize thermal symmetry of measuring and compensating cavity. The DARA also employs an inverted viewing geometry to reduce internal stray light. We will report on the characterization and calibration experiments which were carried out at PMOD/WRC and LASP (TRF).

  20. Absolute Priority for a Vehicle in VANET

    NASA Astrophysics Data System (ADS)

    Shirani, Rostam; Hendessi, Faramarz; Montazeri, Mohammad Ali; Sheikh Zefreh, Mohammad

    In today's world, traffic jams waste hundreds of hours of our life. This causes many researchers try to resolve the problem with the idea of Intelligent Transportation System. For some applications like a travelling ambulance, it is important to reduce delay even for a second. In this paper, we propose a completely infrastructure-less approach for finding shortest path and controlling traffic light to provide absolute priority for an emergency vehicle. We use the idea of vehicular ad-hoc networking to reduce the imposed travelling time. Then, we simulate our proposed protocol and compare it with a centrally controlled traffic light system.

  1. Absolute method of measuring magnetic susceptibility

    USGS Publications Warehouse

    Thorpe, A.; Senftle, F.E.

    1959-01-01

    An absolute method of standardization and measurement of the magnetic susceptibility of small samples is presented which can be applied to most techniques based on the Faraday method. The fact that the susceptibility is a function of the area under the curve of sample displacement versus distance of the magnet from the sample, offers a simple method of measuring the susceptibility without recourse to a standard sample. Typical results on a few substances are compared with reported values, and an error of less than 2% can be achieved. ?? 1959 The American Institute of Physics.

  2. Low molecular weight heparin seems to improve local capillary circulation and healing of chronic foot ulcers in diabetic patients.

    PubMed

    Jörneskog, G; Brismar, K; Fagrell, B

    1993-01-01

    Ten diabetic patients with peripheral arterial occlusive disease, peripheral polyneuropathy and chronic foot ulcers were given 2500 U low molecular weight heparin (Fragmin, Kabi-Pharmacia AB, Sweden) subcutaneously once a day during 8 weeks. The mean age was 63 (47-80) years and the mean duration of foot ulcers 8 (4-12) months. All patients had previously received conventional treatment during 12 weeks, without any noticeable improvement on ulcer healing. The ulcer area was measured, and the skin microcirculation of the forefoot and around the ulcers was investigated before, during and after treatment with Fragmin. The total skin microcirculation was measured by laser Doppler fluxmetry, the nutritional skin microcirculation by vital capillaroscopy and the macrocirculation by determination of the ankle/arm pressure ratio. The ulcer area decreased significantly in eight patients of which four healed the ulcers completely. Of the remaining two patients one deteriorated, whereas one showed a decrease of the ulcer area during treatment, but an increase when treatment was stopped. The macro- and total microcirculation were unchanged in all patients, whereas the nutritional capillary circulation improved in seven out of nine patients, concomitantly with clinical improvement. The biological zero value (a flow-independent part of the LD signal) was high in 4 patients before treatment, but decreased during treatment and remained low even after treatment with Fragmin.-The results indicate that Fragmin positively influences the healing process of chronic foot ulcers in diabetic patients, possibly by improving the capillary circulation in the ulcer margin, in spite of an unchanged arterial and total skin microcirculation of the region.

  3. Interplay between spin-density wave and 3 d local moments with random exchange in a molecular conductor

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Genta; Maesato, Mitsuhiko; Komatsu, Tokutaro; Imakubo, Tatsuro; Kitagawa, Hiroshi

    2016-02-01

    We present the results of high-pressure transport measurements on the anion-mixed molecular conductors (DIETSe)2M Br2Cl2 [DIETSe = diiodo(ethylenedithio)tetraselenafulvalene; M =Fe , Ga]. They undergo a metal-insulator (M-I) transition below 9 K at ambient pressure, which is suppressed by applying pressure, indicating a spin-density-wave (SDW) transition caused by a nesting instability of the quasi-one-dimensional (Q1D) Fermi surface, as observed in the parent compounds (DIETSe)2M Cl4 (M =Fe , Ga). In the metallic state, the existence of the Q1D Fermi surface is confirmed by observing the Lebed resonance. The critical pressures of the SDW, Pc, of the M Br2Cl2 (M =Fe , Ga) salts are significantly lower than those of the the M Cl4 (M = Fe, Ga) salts, suggesting chemical pressure effects. Above Pc, field-induced SDW transitions appear, as evidenced by kink structures in the magnetoresistance (MR) in both salts. The FeBr2Cl2 salt also shows antiferromagnetic (AF) ordering of d spins at 4 K, below which significant spin-charge coupling is observed. A large positive MR change up to 150% appears above the spin-flop field at high pressure. At low pressure, in particular below Pc, a dip or kink structure appears in MR at the spin-flop field, which shows unconventionally large hysteresis at low temperature (T <1 K). The hysteresis region clearly decreases with increasing pressure towards Pc, strongly indicating that the coexisting SDW plays an important role in the enhancement of magnetic hysteresis besides the random exchange interaction.

  4. PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

    PubMed Central

    Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G.; Kihara, Daisuke

    2014-01-01

    Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets. PMID:25167137

  5. Sentinel-2/MSI absolute calibration: first results

    NASA Astrophysics Data System (ADS)

    Lonjou, V.; Lachérade, S.; Fougnie, B.; Gamet, P.; Marcq, S.; Raynaud, J.-L.; Tremas, T.

    2015-10-01

    Sentinel-2 is an optical imaging mission devoted to the operational monitoring of land and coastal areas. It is developed in partnership between the European Commission and the European Space Agency. The Sentinel-2 mission is based on a satellites constellation deployed in polar sun-synchronous orbit. It will offer a unique combination of global coverage with a wide field of view (290km), a high revisit (5 days with two satellites), a high resolution (10m, 20m and 60m) and multi-spectral imagery (13 spectral bands in visible and shortwave infra-red domains). CNES is involved in the instrument commissioning in collaboration with ESA. This paper reviews all the techniques that will be used to insure an absolute calibration of the 13 spectral bands better than 5% (target 3%), and will present the first results if available. First, the nominal calibration technique, based on an on-board sun diffuser, is detailed. Then, we show how vicarious calibration methods based on acquisitions over natural targets (oceans, deserts, and Antarctica during winter) will be used to check and improve the accuracy of the absolute calibration coefficients. Finally, the verification scheme, exploiting photometer in-situ measurements over Lacrau plain, is described. A synthesis, including spectral coherence, inter-methods agreement and temporal evolution, will conclude the paper.

  6. Experimental results for absolute cylindrical wavefront testing

    NASA Astrophysics Data System (ADS)

    Reardon, Patrick J.; Alatawi, Ayshah

    2014-09-01

    Applications for Cylindrical and near-cylindrical surfaces are ever-increasing. However, fabrication of high quality cylindrical surfaces is limited by the difficulty of accurate and affordable metrology. Absolute testing of such surfaces represents a challenge to the optical testing community as cylindrical reference wavefronts are difficult to produce. In this paper, preliminary results for a new method of absolute testing of cylindrical wavefronts are presented. The method is based on the merging of the random ball test method with the fiber optic reference test. The random ball test assumes a large number of interferograms of a good quality sphere with errors that are statistically distributed such that the average of the errors goes to zero. The fiber optic reference test utilizes a specially processed optical fiber to provide a clean high quality reference wave from an incident line focus from the cylindrical wave under test. By taking measurements at different rotation and translations of the fiber, an analogous procedure can be employed to determine the quality of the converging cylindrical wavefront with high accuracy. This paper presents and discusses the results of recent tests of this method using a null optic formed by a COTS cylindrical lens and a free-form polished corrector element.

  7. Absolute Electron Extraction Efficiency of Liquid Xenon

    NASA Astrophysics Data System (ADS)

    Kamdin, Katayun; Mizrachi, Eli; Morad, James; Sorensen, Peter

    2016-03-01

    Dual phase liquid/gas xenon time projection chambers (TPCs) currently set the world's most sensitive limits on weakly interacting massive particles (WIMPs), a favored dark matter candidate. These detectors rely on extracting electrons from liquid xenon into gaseous xenon, where they produce proportional scintillation. The proportional scintillation from the extracted electrons serves to internally amplify the WIMP signal; even a single extracted electron is detectable. Credible dark matter searches can proceed with electron extraction efficiency (EEE) lower than 100%. However, electrons systematically left at the liquid/gas boundary are a concern. Possible effects include spontaneous single or multi-electron proportional scintillation signals in the gas, or charging of the liquid/gas interface or detector materials. Understanding EEE is consequently a serious concern for this class of rare event search detectors. Previous EEE measurements have mostly been relative, not absolute, assuming efficiency plateaus at 100%. I will present an absolute EEE measurement with a small liquid/gas xenon TPC test bed located at Lawrence Berkeley National Laboratory.

  8. Absolute Proper Motions of Southern Globular Clusters

    NASA Astrophysics Data System (ADS)

    Dinescu, D. I.; Girard, T. M.; van Altena, W. F.

    1996-05-01

    Our program involves the determination of absolute proper motions with respect to galaxies for a sample of globular clusters situated in the southern sky. The plates cover a 6(deg) x 6(deg) area and are taken with the 51-cm double astrograph at Cesco Observatory in El Leoncito, Argentina. We have developed special methods to deal with the modelling error of the plate transformation and we correct for magnitude equation using the cluster stars. This careful astrometric treatment leads to accuracies of from 0.5 to 1.0 mas/yr for the absolute proper motion of each cluster, depending primarily on the number of measurable cluster stars which in turn is related to the cluster's distance. Space velocities are then derived which, in association with metallicities, provide key information for the formation scenario of the Galaxy, i.e. accretion and/or dissipational collapse. Here we present results for NGC 1851, NGC 6752, NGC 6584, NGC 6362 and NGC 288.

  9. Relational versus absolute representation in categorization.

    PubMed

    Edwards, Darren J; Pothos, Emmanuel M; Perlman, Amotz

    2012-01-01

    This study explores relational-like and absolute-like representations in categorization. Although there is much evidence that categorization processes can involve information about both the particular physical properties of studied instances and abstract (relational) properties, there has been little work on the factors that lead to one kind of representation as opposed to the other. We tested 370 participants in 6 experiments, in which participants had to classify new items into predefined artificial categories. In 4 experiments, we observed a predominantly relational-like mode of classification, and in 2 experiments we observed a shift toward an absolute-like mode of classification. These results suggest 3 factors that promote a relational-like mode of classification: fewer items per group, more training groups, and the presence of a time delay. Overall, we propose that less information about the distributional properties of a category or weaker memory traces for the category exemplars (induced, e.g., by having smaller categories or a time delay) can encourage relational-like categorization.

  10. Transient absolute robustness in stochastic biochemical networks.

    PubMed

    Enciso, German A

    2016-08-01

    Absolute robustness allows biochemical networks to sustain a consistent steady-state output in the face of protein concentration variability from cell to cell. This property is structural and can be determined from the topology of the network alone regardless of rate parameters. An important question regarding these systems is the effect of discrete biochemical noise in the dynamical behaviour. In this paper, a variable freezing technique is developed to show that under mild hypotheses the corresponding stochastic system has a transiently robust behaviour. Specifically, after finite time the distribution of the output approximates a Poisson distribution, centred around the deterministic mean. The approximation becomes increasingly accurate, and it holds for increasingly long finite times, as the total protein concentrations grow to infinity. In particular, the stochastic system retains a transient, absolutely robust behaviour corresponding to the deterministic case. This result contrasts with the long-term dynamics of the stochastic system, which eventually must undergo an extinction event that eliminates robustness and is completely different from the deterministic dynamics. The transiently robust behaviour may be sufficient to carry out many forms of robust signal transduction and cellular decision-making in cellular organisms. PMID:27581485

  11. Localization and molecular interactions of mitoxantrone within living K562 cells as probed by confocal spectral imaging analysis.

    PubMed Central

    Feofanov, A; Sharonov, S; Kudelina, I; Fleury, F; Nabiev, I

    1997-01-01

    Studying mechanisms of drug antitumor action is complicated by the lack of noninvasive methods enabling direct monitoring of the state and interactions of the drugs within intact viable cells. Here we present a confocal spectral imaging (CSI) technique as a method of overcoming this problem. We applied this method to the examination of localization and interactions of mitoxantrone (1, 4-dihydroxy-5, 8-bis-[([2-(2-hydroxyethyl)-amino]ethyl)amino]-9,10-anthracenedione dihydrochloride), a potent antitumor drug, in living K562 cells. A two-dimensional set of fluorescence spectra of mitoxantrone (MITOX) recorded with micron resolution within a drug-treated cell was analyzed to reveal formation of drug-target complexes and to create the maps of their intracellular distribution. The analysis was based on detailed in vitro modeling of drug-target (DNA, RNA, DNA topoisomerase II) interactions and environmental effects affecting drug fluorescence. MITOX exposed to aqueous intracellular environment, MITOX bound to hydrophobic cellular structures, complexes of MITOX with nucleic acids, as well as the naphtoquinoxaline metabolite of MITOX were simultaneously detected and mapped in K562 cells. These states and complexes are known to be immediately related to the antitumor action of the drug. The results obtained present a basis for the subsequent quantitative analysis of concentration and time-dependent accumulation of free and bound MITOX within different compartments of living cancer cells. Images FIGURE 3 FIGURE 5 FIGURE 6 PMID:9414242

  12. Molecular cloning and characterization of a surface-localized adhesion protein in Mycoplasma bovis Hubei-1 strain.

    PubMed

    Zou, Xiaohui; Li, Yuan; Wang, Yang; Zhou, Yumei; Liu, Yang; Xin, Jiuqing

    2013-01-01

    Mycoplasma bovis (M. bovis) is an important pathogen that causes various bovine diseases, such as mastitis in cows and pneumonia in calves. The surface proteins are generally thought to play a central role in the pathogenesis of this organism. We screened the entire genome of M. bovis Hubei-1 and discovered a gene named vpmaX that encodes the 25 kDa variable surface lipoprotein A (VpmaX). Sequence analysis revealed that VpmaX contains several repetitive units and a typical bacterial lipoprotein signal sequence. The vpmaX gene was cloned and expressed in E. coli to obtain recombinant VpmaX (rVpmaX). Western blot analysis using a rabbit antibody against rVpmaX demonstrated that VpmaX is a membrane protein. Immunostaining visualized via confocal laser scanning microscopy showed that rVpmaX was able to adhere to embryonic bovine lung cells (EBL), and this was also confirmed by a sandwich ELISA. In summary, a surface-localized adhesion protein was identified in M. bovis Hubei-1.

  13. Molecular cloning, sequencing analysis, and chromosomal localization of the human protease inhibitor 4 (Kallistatin) gene (P14)

    SciTech Connect

    Chai, K.X.; Chao, J.; Chao, L.; Ward, D.C.

    1994-09-15

    The gene encoding human protease inhibitor 4 (kallistatin; gene symbol PI4), a novel serine proteinase inhibitor (serpin), has been isolated and completely sequenced. The kallistatin gene is 9618 bp in length and contains five exons and four introns. The structure and organization of the kallistatin gene are similar to those of the genes encoding {alpha}{sub 1}-antichymotrypsin. The kallistatin gene is also similar to the genes encoding rat and mouse kallikrein-binding proteins. The first exon of the kallistatin gene is a noncoding 89-bp fragment, as determined by primer extension. The fifth exon, which contains 308 bp of noncoding sequence, encodes the reactive center of kallistatin. In the 5`-flanking region of the kallistatin gene, 1125 bp have been sequenced and a consensus promoter segment with potential transcription regulatory sites, including CAAT and TATA boxes, an AP-2 binding site, a GC-rich region, a cAMP response element, and an AP-1 binding site, has been identified within this region. The kallistatin gene was localized by in situ hybridization to human chromosome 14q31-132.1, close to the serpin genes encoding {alpha}{sub 1}-antichymotrypsin, protein C inhibitor, {alpha}{sub 1}-antitrypsin, and corticosteroid-binding globulin. In a genomic DNA Southern blot, kallistatin-related genes were identified in monkey, mouse, rat, bovine, dog, cat, and a ground mole. The patterns of hybridization revealed clues of human serpin evolution. 34 refs., 6 figs.

  14. Identification, molecular characterization, and chromosomal localization of the cDNA encoding a novel leucine zipper motif-containing protein

    SciTech Connect

    Sun, Der-Shan; Chang, Nan-Chi A.; Chang, A.C.

    1996-08-15

    cDNA clones encoding a novel protein (LUZP) with three leucine zipper motifs were first identified from a murine bone marrow cDNA library. After screening two additional cDNA libraries of activated peritoneal exudate cells, 32 positive clones were obtained from 1.3 x 10{sup 7} phage plaques. Four overlapping clones constituting a total of 7399 hp were sequenced on both strands. The complete open reading frame of LUZP is 1067 amino acids. In addition to three leucine zipper motifs located at the NH2 terminus, there are three nuclear localization signals and a large number of putative Ser/Thr phosphorylation sites. Western blot analyses indicate that LUZP is predominantly expressed in brain, whereas immunocytochemistry data clearly reveal its presence in the nucleus of neutrons. Interspecific backcross analyses have mapped Luzp to mouse chromosome 4 in proximity to Gpcr14. Comparative mapping data suggest that the human homolog of Luzp will map to human chromosome 1p36. 32 refs., 4 figs.

  15. General characterization of Tityus fasciolatus scorpion venom. Molecular identification of toxins and localization of linear B-cell epitopes.

    PubMed

    Mendes, T M; Guimarães-Okamoto, P T C; Machado-de-Avila, R A; Oliveira, D; Melo, M M; Lobato, Z I; Kalapothakis, E; Chávez-Olórtegui, C

    2015-06-01

    This communication describes the general characteristics of the venom from the Brazilian scorpion Tityus fasciolatus, which is an endemic species found in the central Brazil (States of Goiás and Minas Gerais), being responsible for sting accidents in this area. The soluble venom obtained from this scorpion is toxic to mice being the LD50 is 2.984 mg/kg (subcutaneally). SDS-PAGE of the soluble venom resulted in 10 fractions ranged in size from 6 to 10-80 kDa. Sheep were employed for anti-T. fasciolatus venom serum production. Western blotting analysis showed that most of these venom proteins are immunogenic. T. fasciolatus anti-venom revealed consistent cross-reactivity with venom antigens from Tityus serrulatus. Using known primers for T. serrulatus toxins, we have identified three toxins sequences from T. fasciolatus venom. Linear epitopes of these toxins were localized and fifty-five overlapping pentadecapeptides covering complete amino acid sequence of the three toxins were synthesized in cellulose membrane (spot-synthesis technique). The epitopes were located on the 3D structures and some important residues for structure/function were identified.

  16. Molecular characterization and genetic diversity in an avocado collection of cultivars and local Spanish genotypes using SSRs.

    PubMed

    Alcaraz, M L; Hormaza, J I

    2007-12-01

    In this work, 75 avocado accessions maintained in an ex situ germplasm collection at the E.E. la Mayora in Málaga (Spain) were characterized with 16 microsatellites previously developed in this species. This avocado collection includes both local Spanish genotypes obtained through prospection and genotypes obtained by exchange with different countries. A total of 156 different amplification fragments were detected ranging from 4 to 16 per locus with an average of 9.75 alleles per locus. All the microsatellites were highly informative with an expected heterozygosity higher than 0.5 and a probability of identity below 0.36. The total probability of identity was 2.85x10(-14). Fifteen of the 16 loci studied showed a positive Wright's fixation index (F) indicating a deficit of heterozygotes with an average over all the SSRs of 0.18. A dendrogram was generated using UPGMA (unweighted pair group method with arithmetic averages) based on the Nei and Li similarity index. This dendrogram classified most of the genotypes analyzed into three major groups which mainly differed in racial origin although with low bootstrap support probably due to the presence of many interracial hybrids in the collection. All the genotypes studied could be unequivocally distinguished with the combination of SSRs used except some putative mutations of 'Hass' and an additional group of two cultivars. The results obtained indicate that the set of SSRs used is highly informative and are discussed in terms of their implications for avocado germplasm characterization and management.

  17. General characterization of Tityus fasciolatus scorpion venom. Molecular identification of toxins and localization of linear B-cell epitopes.

    PubMed

    Mendes, T M; Guimarães-Okamoto, P T C; Machado-de-Avila, R A; Oliveira, D; Melo, M M; Lobato, Z I; Kalapothakis, E; Chávez-Olórtegui, C

    2015-06-01

    This communication describes the general characteristics of the venom from the Brazilian scorpion Tityus fasciolatus, which is an endemic species found in the central Brazil (States of Goiás and Minas Gerais), being responsible for sting accidents in this area. The soluble venom obtained from this scorpion is toxic to mice being the LD50 is 2.984 mg/kg (subcutaneally). SDS-PAGE of the soluble venom resulted in 10 fractions ranged in size from 6 to 10-80 kDa. Sheep were employed for anti-T. fasciolatus venom serum production. Western blotting analysis showed that most of these venom proteins are immunogenic. T. fasciolatus anti-venom revealed consistent cross-reactivity with venom antigens from Tityus serrulatus. Using known primers for T. serrulatus toxins, we have identified three toxins sequences from T. fasciolatus venom. Linear epitopes of these toxins were localized and fifty-five overlapping pentadecapeptides covering complete amino acid sequence of the three toxins were synthesized in cellulose membrane (spot-synthesis technique). The epitopes were located on the 3D structures and some important residues for structure/function were identified. PMID:25817000

  18. A Conceptual Approach to Absolute Value Equations and Inequalities

    ERIC Educational Resources Information Center

    Ellis, Mark W.; Bryson, Janet L.

    2011-01-01

    The absolute value learning objective in high school mathematics requires students to solve far more complex absolute value equations and inequalities. When absolute value problems become more complex, students often do not have sufficient conceptual understanding to make any sense of what is happening mathematically. The authors suggest that the…

  19. Using, Seeing, Feeling, and Doing Absolute Value for Deeper Understanding

    ERIC Educational Resources Information Center

    Ponce, Gregorio A.

    2008-01-01

    Using sticky notes and number lines, a hands-on activity is shared that anchors initial student thinking about absolute value. The initial point of reference should help students successfully evaluate numeric problems involving absolute value. They should also be able to solve absolute value equations and inequalities that are typically found in…

  20. Molecular identification of the first local dengue fever outbreak in Shenzhen city, China: a potential imported vertical transmission from Southeast Asia?

    PubMed

    Yang, F; Guo, G Z; Chen, J Q; Ma, H W; Liu, T; Huang, D N; Yao, C H; Zhang, R L; Xue, C F; Zhang, L

    2014-02-01

    A suspected dengue fever outbreak occurred in 2010 at a solitary construction site in Shenzhen city, China. To investigate this epidemic, we used serological, molecular biological, and bioinformatics techniques. Of nine serum samples from suspected patients, we detected seven positive for dengue virus (DENV) antibodies, eight for DENV-1 RNA, and three containing live viruses. The isolated virus, SZ1029 strain, was sequenced and confirmed as DENV-1, showing the highest E-gene homology to D1/Malaysia/36000/05 and SG(EHI)DED142808 strains recently reported in Southeast Asia. Further phylogenetic tree analysis confirmed their close relationship. At the epidemic site, we also detected 14 asymptomatic co-workers (out of 291) positive for DENV antibody, and DENV-1-positive mosquitoes. Thus, we concluded that DENV-1 caused the first local dengue fever outbreak in Shenzhen. Because no imported case was identified, the molecular fingerprints of the SZ1029 strain suggest this outbreak may be due to vertical transmission imported from Southeast Asia.

  1. Localization of specialized intestinal metaplasia and the molecular alterations in Barrett esophagus in a Japanese population: an analysis of biopsy samples based on the "Seattle" biopsy protocol.

    PubMed

    Fukui, Shota; Watari, Jiro; Tomita, Toshihiko; Yamasaki, Takahisa; Okugawa, Takuya; Kondo, Takashi; Kono, Tomoaki; Tozawa, Katsuyuki; Ikehara, Hisatomo; Ohda, Yoshio; Oshima, Tadayuki; Fukui, Hirokazu; Das, Kiron M; Miwa, Hiroto

    2016-05-01

    It remains unclear why Barrett esophagus (BE)-associated adenocarcinoma (EAC) frequently occurs in the 0 to 3 o'clock area of the BE. The aims of this study were to clarify the localization of specialized intestinal metaplasia (SIM) as a precancerous lesion and of molecular alterations among different locations using 4-quadrant biopsies based on the "Seattle" protocol. We prospectively evaluated microsatellite instability; methylation status at the APC, CDKN2A, hMLH1, RUNX3, and MGMT genes; the immunoreactivity of the monoclonal antibody Das-1 for the colonic phenotype; and Ki-67 staining in 10 early EACs and 128 biopsy samples from 32 BE patients. Among the molecular changes, only APC gene hypermethylation was an independent predictive marker of EAC (odds ratio, 24.4; P = .01). SIM was more frequently identified in the 0 to 3 o'clock quadrant than in the 6 to 9 o'clock quadrant (P = .08). The Ki-67 index was higher in SIM than in the columnar-lined epithelium (CLE) without goblet cells (P < .0001) and in both SIM and CLE with Das-1 reactivity than in those without (P = .04 and P = .06, respectively). Furthermore, the index was relatively higher in the 0 to 3 o'clock quadrant than in the 6 to 9 o'clock quadrant in cases with Das-1 reactivity. RUNX3 methylation was more frequently found in SIM than in CLE (P = .04), whereas the incidence of the other biomarkers did not show a significant difference between the 0 to 3 o'clock and 6 to 9 o'clock areas, nor between SIM and CLE. SIM with Das-1 reactivity, but not molecular alterations, in the 0 to 3 o'clock quadrant may have higher proliferative activity compared to the other areas of the BE. PMID:27067780

  2. Molecular cloning, functional characterization and localization of an annexin from a fish gill fluke Microcotyle sebastis (Platyhelminthes: Monogenea).

    PubMed

    Choi, Seung Hyuk; Kwon, Se Ryun; Lee, Eun Hye; Kim, Ki Hong

    2009-01-01

    The full cDNA of an annexin gene from Microcotyle sebastis (MsANX) was cloned for the first time in monogeneans. The cDNA of MsANX comprises 1199bp with a 29bp 5' untranslated region, an open reading frame of 1062bp, and a 108bp 3' untranslated region. The recombinantly produced MsANX bound phosphatidylserine vesicles in the presence of Ca2+, whereas no MsANX was precipitated in the absence of free Ca2+. Phylogenetically, MsANX formed a cluster with human annexin A13, known as the earliest annexin in vertebrates and expressed mainly in the intestine. The localization of MsANX in M. sebastis was analyzed by Western blotting and immunohistochemistry using the antiserum raised against the recombinant MsANX. In Western blot analysis, rat antiserum bound to a protein corresponding to the MsANX in size when worm crude extracts were used as antigens, but no bands were detected by the antiserum when the excretory/secretory proteins of worms were used as antigens. In immunohistochemistry analysis, significant antibody binding annexin was found in the ovarian region, the pharynx and the intestinal caecum of the worm. Interestingly, the alimentary canal location of MsANX was similar to the location of human annexin A13, and further research is needed to trace evolutionary relationship among helminthic annexins and human annexin A13. Also it remains to be investigated whether immunization of naïve fish with the recombinant MsANX can induce protective immune responses against M. sebastis infection.

  3. Molecular characterization, functional expression, tissue localization and protective potential of a Taenia solium fatty acid-binding protein.

    PubMed

    Illescas, Oscar; Carrero, Julio C; Bobes, Raúl J; Flisser, Ana; Rosas, Gabriela; Laclette, Juan P

    2012-12-01

    The fatty acid-binding proteins (FABPs) comprise a family of proteins that are widely expressed in animal cells and perform a variety of vital functions. Here, we report the identification, characterization, recombinant expression, tissue localization and protective potential of a Taenia solium FABP (TsFABP1). The TsFABP1 primary structure showed all the conserved residues characteristic of the subfamily iv of the intracellular Lipid-Binding Proteins (iLBPs), including those involved in the binding stabilization of the fatty acid molecule. Through a competitive binding assay we found that TsFABP1 is able to bind at least six different fatty acids with preference toward palmitic and stearic acid, suggesting that TsFABP1 is a member of the iLBP subfamily iv. Immunolocalization assays carried out on larval and adult tissues of four species of taeniids using anti-TsFABP1 hyperimmune sera produced in mice and rabbit, showed intense labeling in the tegument of the spiral canal and in subtegumental cytons of the larvae. These findings suggest that the spiral canal might be a major place for FA uptake in the developing scolex. In contrast, only subtegumental cytons in the adult worms stained positive. We propose that TsFABP1 is involved in the mechanism to mobilize fatty acids between compartments in the extensive syncytial tissue of taeniids. Protection assays carried out in a murine model of cysticercosis showed that subcutaneous immunization with TsFABP1 resulted in about 45% reduction of parasite load against an intraperitoneal challenge with Taenia crassiceps cysts. This reduction in parasite load correlated with the level of cellular and humoral immune responses against TsFABP1, as determined in spleen lymphocyte proliferation and ELISA testing.

  4. The Absolute Radiometric Calibration of Space - Sensors.

    NASA Astrophysics Data System (ADS)

    Holm, Ronald Gene

    1987-09-01

    The need for absolute radiometric calibration of space-based sensors will continue to increase as new generations of space sensors are developed. A reflectance -based in-flight calibration procedure is used to determine the radiance reaching the entrance pupil of the sensor. This procedure uses ground-based measurements coupled with a radiative transfer code to characterize the effects the atmosphere has on the signal reaching the sensor. The computed radiance is compared to the digital count output of the sensor associated with the image of a test site. This provides an update to the preflight calibration of the system and a check on the on-board internal calibrator. This calibration procedure was used to perform a series of five calibrations of the Landsat-5 Thematic Mapper (TM). For the 12 measurements made in TM bands 1-3, the RMS variation from the mean as a percentage of the mean is (+OR-) 1.9%, and for measurements in the IR, TM bands 4,5, and 7, the value is (+OR-) 3.4%. The RMS variation for all 23 measurements is (+OR-) 2.8%. The absolute calibration techniques were put to another test with a series of three calibration of the SPOT-1 High Resolution Visible, (HRV), sensors. The ratio, HRV-2/HRV-1, of absolute calibration coefficients compared very well with ratios of histogrammed data obtained when the cameras simultaneously imaged the same ground site. Bands PA, B1 and B3 agreed to within 3%, while band B2 showed a 7% difference. The procedure for performing a satellite calibration was then used to demonstrate how a calibrated satellite sensor can be used to quantitatively evaluate surface reflectance over a wide range of surface features. Predicted reflectance factors were compared to values obtained from aircraft -based radiometer data. This procedure was applied on four dates with two different surface conditions per date. A strong correlation, R('2) = .996, was shown between reflectance values determined from satellite imagery and low-flying aircraft

  5. Ring polymer molecular dynamics fast computation of rate coefficients on accurate potential energy surfaces in local configuration space: Application to the abstraction of hydrogen from methane

    NASA Astrophysics Data System (ADS)

    Meng, Qingyong; Chen, Jun; Zhang, Dong H.

    2016-04-01

    To fast and accurately compute rate coefficients of the H/D + CH4 → H2/HD + CH3 reactions, we propose a segmented strategy for fitting suitable potential energy surface (PES), on which ring-polymer molecular dynamics (RPMD) simulations are performed. On the basis of recently developed permutation invariant polynomial neural-network approach [J. Li et al., J. Chem. Phys. 142, 204302 (2015)], PESs in local configuration spaces are constructed. In this strategy, global PES is divided into three parts, including asymptotic, intermediate, and interaction parts, along the reaction coordinate. Since less fitting parameters are involved in the local PESs, the computational efficiency for operating the PES routine is largely enhanced by a factor of ˜20, comparing with that for global PES. On interaction part, the RPMD computational time for the transmission coefficient can be further efficiently reduced by cutting off the redundant part of the child trajectories. For H + CH4, good agreements among the present RPMD rates and those from previous simulations as well as experimental results are found. For D + CH4, on the other hand, qualitative agreement between present RPMD and experimental results is predicted.

  6. A Dual Modulated Homochiral Helical Nanofilament Phase with Local Columnar Ordering Formed by Bent Core Liquid Crystals: Effects of Molecular Chirality.

    PubMed

    Li, Lin; Salamonczyk, Miroslaw; Jákli, Antal; Hegmann, Torsten

    2016-08-01

    Helical nanofilament (HNF) phases form as a result of an intralayer mismatch between top and bottom molecular halves in bent-core liquid crystals (BC-LCs) that is relieved by local saddle-splay geometry. HNFs are immensely attractive for photovoltaic and chiral separation applications and as templates for the chiral spatial assembly of guest molecules. Here, the synthesis and characterization of two unichiral BC-LCs and one racemic mixture with tris-biphenyl-diester cores featuring chiral (R,R) and (S,S) or racemic 2-octyloxy aliphatic side chains are presented. In comparison to the achiral compound with linear side chains forming an intralayer modulated HNF phase (HNFmod ), synchrotron small angle X-ray diffraction indicates that the unichiral derivatives form a dual modulated HNF phase with intra- as well as interlayer modulations (HNFmod2 ) suggesting a columnar local structure of the nanofilaments. Transmission electron microscopy and circular dichroism spectropolarimetry confirm that the unichiral materials exclusively form homochiral HNFs with a twist sense-matching secondary twist. A contact preparation provides the first example of two identical chiral liquid crystal phases only differing in their handedness that do not mix and form an achiral liquid crystal phase with an entirely different structure in the contact zone.

  7. Molecular heterogeneity in the choroid plexus epithelium: the 22-member γ-protocadherin family is differentially expressed, apically localized, and implicated in CSF regulation

    PubMed Central

    Lobas, Mark A.; Helsper, Lindsey; Vernon, Claire G.; Schreiner, Dietmar; Zhang, Yong; Holtzman, Michael J.; Thedens, Daniel R.; Weiner, Joshua A.

    2011-01-01

    The choroid plexus (CP) epithelium develops from the ependyma that lines the ventricular system, and plays a critical role in the development and function of the brain. In addition to being the primary site of CSF production, the CP maintains the blood-CSF barrier via apical tight junctions between epithelial cells. Here we show that the 22-member γ-Protocadherin (γ-Pcdh) family of cell adhesion molecules, which we have implicated previously in synaptogenesis and neuronal survival, is highly expressed by both CP epithelial and ependymal cells, in which γ-Pcdh protein localization is, surprisingly, tightly restricted to the apical membrane. Multi-label immunostaining demonstrates that γ-Pcdhs are excluded from tight junctions, basolateral adherens junctions, and apical cilia tufts. RT-PCR analysis indicates that, as a whole, the CP expresses most members of the Pcdh-γ gene family. Immunostaining using novel monoclonal antibodies specific for single γ-Pcdh proteins shows that individual epithelial cells differ in their apically-localized γ-Pcdh repertoire. Restricted mutation of the Pcdh-γ locus in the choroid plexus and ependyma leads to significant reductions in ventricular volume, without obvious disruptions of epithelial apical-basal polarity. Together, these results suggest an unsuspected role for the γ-Pcdhs in CSF production and demonstrate a surprising molecular heterogeneity in the CP epithelium. PMID:22092001

  8. Base damage, local sequence context and TP53 mutation hotspots: a molecular dynamics study of benzo[a]pyrene induced DNA distortion and mutability

    PubMed Central

    Menzies, Georgina E.; Reed, Simon H.; Brancale, Andrea; Lewis, Paul D.

    2015-01-01

    The mutational pattern for the TP53 tumour suppressor gene in lung tumours differs to other cancer types by having a higher frequency of G:C>T:A transversions. The aetiology of this differing mutation pattern is still unknown. Benzo[a]pyrene,diol epoxide (BPDE) is a potent cigarette smoke carcinogen that forms guanine adducts at TP53 CpG mutation hotspot sites including codons 157, 158, 245, 248 and 273. We performed molecular modelling of BPDE-adducted TP53 duplex sequences to determine the degree of local distortion caused by adducts which could influence the ability of nucleotide excision repair. We show that BPDE adducted codon 157 has greater structural distortion than other TP53 G:C>T:A hotspot sites and that sequence context more distal to adjacent bases must influence local distortion. Using TP53 trinucleotide mutation signatures for lung cancer in smokers and non-smokers we further show that codons 157 and 273 have the highest mutation probability in smokers. Combining this information with adduct structural data we predict that G:C>T:A mutations at codon 157 in lung tumours of smokers are predominantly caused by BPDE. Our results provide insight into how different DNA sequence contexts show variability in DNA distortion at mutagen adduct sites that could compromise DNA repair at well characterized cancer related mutation hotspots. PMID:26400171

  9. A Dual Modulated Homochiral Helical Nanofilament Phase with Local Columnar Ordering Formed by Bent Core Liquid Crystals: Effects of Molecular Chirality.

    PubMed

    Li, Lin; Salamonczyk, Miroslaw; Jákli, Antal; Hegmann, Torsten

    2016-08-01

    Helical nanofilament (HNF) phases form as a result of an intralayer mismatch between top and bottom molecular halves in bent-core liquid crystals (BC-LCs) that is relieved by local saddle-splay geometry. HNFs are immensely attractive for photovoltaic and chiral separation applications and as templates for the chiral spatial assembly of guest molecules. Here, the synthesis and characterization of two unichiral BC-LCs and one racemic mixture with tris-biphenyl-diester cores featuring chiral (R,R) and (S,S) or racemic 2-octyloxy aliphatic side chains are presented. In comparison to the achiral compound with linear side chains forming an intralayer modulated HNF phase (HNFmod ), synchrotron small angle X-ray diffraction indicates that the unichiral derivatives form a dual modulated HNF phase with intra- as well as interlayer modulations (HNFmod2 ) suggesting a columnar local structure of the nanofilaments. Transmission electron microscopy and circular dichroism spectropolarimetry confirm that the unichiral materials exclusively form homochiral HNFs with a twist sense-matching secondary twist. A contact preparation provides the first example of two identical chiral liquid crystal phases only differing in their handedness that do not mix and form an achiral liquid crystal phase with an entirely different structure in the contact zone. PMID:27334846

  10. Use of Absolute and Comparative Performance Feedback in Absolute and Comparative Judgments and Decisions

    ERIC Educational Resources Information Center

    Moore, Don A.; Klein, William M. P.

    2008-01-01

    Which matters more--beliefs about absolute ability or ability relative to others? This study set out to compare the effects of such beliefs on satisfaction with performance, self-evaluations, and bets on future performance. In Experiment 1, undergraduate participants were told they had answered 20% correct, 80% correct, or were not given their…

  11. Absolute radiometric calibration of the CCRS SAR

    NASA Astrophysics Data System (ADS)

    Ulander, Lars M. H.; Hawkins, Robert K.; Livingstone, Charles E.; Lukowski, Tom I.

    1991-11-01

    Determining the radar scattering coefficients from SAR (synthetic aperture radar) image data requires absolute radiometric calibration of the SAR system. The authors describe an internal calibration methodology for the airborne Canada Centre for Remote Sensing (CCRS) SAR system, based on radar theory, a detailed model of the radar system, and measurements of system parameters. The methodology is verified by analyzing external calibration data acquired over a 6-month period in 1988 by the C-band radar using HH polarization. The results indicate that the overall error is +/- 0.8 dB (1-sigma) for incidence angles +/- 20 deg from antenna boresight. The dominant error contributions are due to the antenna radome and uncertainties in the elevation angle relative to the antenna boresight.

  12. Absolute calibration of ultraviolet filter photometry

    NASA Technical Reports Server (NTRS)

    Bless, R. C.; Fairchild, T.; Code, A. D.

    1972-01-01

    The essential features of the calibration procedure can be divided into three parts. First, the shape of the bandpass of each photometer was determined by measuring the transmissions of the individual optical components and also by measuring the response of the photometer as a whole. Secondly, each photometer was placed in the essentially-collimated synchrotron radiation bundle maintained at a constant intensity level, and the output signal was determined from about 100 points on the objective. Finally, two or three points on the objective were illuminated by synchrotron radiation at several different intensity levels covering the dynamic range of the photometers. The output signals were placed on an absolute basis by the electron counting technique described earlier.

  13. Absolute measurements of fast neutrons using yttrium

    SciTech Connect

    Roshan, M. V.; Springham, S. V.; Rawat, R. S.; Lee, P.; Krishnan, M.

    2010-08-15

    Yttrium is presented as an absolute neutron detector for pulsed neutron sources. It has high sensitivity for detecting fast neutrons. Yttrium has the property of generating a monoenergetic secondary radiation in the form of a 909 keV gamma-ray caused by inelastic neutron interaction. It was calibrated numerically using MCNPX and does not need periodic recalibration. The total yttrium efficiency for detecting 2.45 MeV neutrons was determined to be f{sub n}{approx}4.1x10{sup -4} with an uncertainty of about 0.27%. The yttrium detector was employed in the NX2 plasma focus experiments and showed the neutron yield of the order of 10{sup 8} neutrons per discharge.

  14. Absolute geostrophic currents in global tropical oceans

    NASA Astrophysics Data System (ADS)

    Yang, Lina; Yuan, Dongliang

    2016-11-01

    A set of absolute geostrophic current (AGC) data for the period January 2004 to December 2012 are calculated using the P-vector method based on monthly gridded Argo profiles in the world tropical oceans. The AGCs agree well with altimeter geostrophic currents, Ocean Surface Current Analysis-Real time currents, and moored current-meter measurements at 10-m depth, based on which the classical Sverdrup circulation theory is evaluated. Calculations have shown that errors of wind stress calculation, AGC transport, and depth ranges of vertical integration cannot explain non-Sverdrup transport, which is mainly in the subtropical western ocean basins and equatorial currents near the Equator in each ocean basin (except the North Indian Ocean, where the circulation is dominated by monsoons). The identified non-Sverdrup transport is thereby robust and attributed to the joint effect of baroclinicity and relief of the bottom (JEBAR) and mesoscale eddy nonlinearity.

  15. Absolute Measurement of Electron Cloud Density

    SciTech Connect

    Covo, M K; Molvik, A W; Cohen, R H; Friedman, A; Seidl, P A; Logan, G; Bieniosek, F; Baca, D; Vay, J; Orlando, E; Vujic, J L

    2007-06-21

    Beam interaction with background gas and walls produces ubiquitous clouds of stray electrons that frequently limit the performance of particle accelerator and storage rings. Counterintuitively we obtained the electron cloud accumulation by measuring the expelled ions that are originated from the beam-background gas interaction, rather than by measuring electrons that reach the walls. The kinetic ion energy measured with a retarding field analyzer (RFA) maps the depressed beam space-charge potential and provides the dynamic electron cloud density. Clearing electrode current measurements give the static electron cloud background that complements and corroborates with the RFA measurements, providing an absolute measurement of electron cloud density during a 5 {micro}s duration beam pulse in a drift region of the magnetic transport section of the High-Current Experiment (HCX) at LBNL.

  16. Micron Accurate Absolute Ranging System: Range Extension

    NASA Technical Reports Server (NTRS)

    Smalley, Larry L.; Smith, Kely L.

    1999-01-01

    The purpose of this research is to investigate Fresnel diffraction as a means of obtaining absolute distance measurements with micron or greater accuracy. It is believed that such a system would prove useful to the Next Generation Space Telescope (NGST) as a non-intrusive, non-contact measuring system for use with secondary concentrator station-keeping systems. The present research attempts to validate past experiments and develop ways to apply the phenomena of Fresnel diffraction to micron accurate measurement. This report discusses past research on the phenomena, and the basis of the use Fresnel diffraction distance metrology. The apparatus used in the recent investigations, experimental procedures used, preliminary results are discussed in detail. Continued research and equipment requirements on the extension of the effective range of the Fresnel diffraction systems is also described.

  17. Absolute calibration of remote sensing instruments

    NASA Astrophysics Data System (ADS)

    Biggar, S. F.; Bruegge, C. J.; Capron, B. A.; Castle, K. R.; Dinguirard, M. C.; Holm, R. G.; Lingg, L. J.; Mao, Y.; Palmer, J. M.; Phillips, A. L.

    1985-12-01

    Source-based and detector-based methods for the absolute radiometric calibration of a broadband field radiometer are described. Using such a radiometer, calibrated by both methods, the calibration of the integrating sphere used in the preflight calibration of the Thematic Mapper was redetermined. The results are presented. The in-flight calibration of space remote sensing instruments is discussed. A method which uses the results of ground-based reflectance and atmospheric measurements as input to a radiative transfer code to predict the radiance at the instrument is described. A calibrated, helicopter-mounted radiometer is used to determine the radiance levels at intermediate altitudes to check the code predictions. Results of such measurements for the calibration of the Thematic Mapper on Landsat 5 and an analysis that shows the value of such measurements are described.

  18. Absolute radiometric calibration of the Thematic Mapper

    NASA Technical Reports Server (NTRS)

    Slater, P. N.; Biggar, S. F.; Holm, R. G.; Jackson, R. D.; Mao, Y.

    1986-01-01

    Calibration data for the solar reflective bands of the Landsat-5 TM obtained from five in-flight absolute radiometric calibrations from July 1984-November 1985 at White Sands, New Mexico are presented and analyzed. Ground reflectance and atmospheric data were utilized to predict the spectral radiance at the entrance pupil of the TM and the average number of digital counts in each TM band. The calibration of each of the TM solar reflective bands was calculated in terms of average digital counts/unit spectral radiance for each band. It is observed that for the 12 reflectance-based measurements the rms variation from the means as a percentage of the mean is + or - 1.9 percent; for the 11 measurements in the IR bands, it is + or - 3.4 percent; and the rms variation for all 23 measurements is + or - 2.8 percent.

  19. Swarm's Absolute Scalar Magnetometer metrological performances

    NASA Astrophysics Data System (ADS)

    Leger, J.; Fratter, I.; Bertrand, F.; Jager, T.; Morales, S.

    2012-12-01

    The Absolute Scalar Magnetometer (ASM) has been developed for the ESA Earth Observation Swarm mission, planned for launch in November 2012. As its Overhauser magnetometers forerunners flown on Oersted and Champ satellites, it will deliver high resolution scalar measurements for the in-flight calibration of the Vector Field Magnetometer manufactured by the Danish Technical University. Latest results of the ground tests carried out to fully characterize all parameters that may affect its accuracy, both at instrument and satellite level, will be presented. In addition to its baseline function, the ASM can be operated either at a much higher sampling rate (burst mode at 250 Hz) or in a dual mode where it also delivers vector field measurements as a by-product. The calibration procedure and the relevant vector performances will be discussed.

  20. MAGSAT: Vector magnetometer absolute sensor alignment determination

    NASA Technical Reports Server (NTRS)

    Acuna, M. H.

    1981-01-01

    A procedure is described for accurately determining the absolute alignment of the magnetic axes of a triaxial magnetometer sensor with respect to an external, fixed, reference coordinate system. The method does not require that the magnetic field vector orientation, as generated by a triaxial calibration coil system, be known to better than a few degrees from its true position, and minimizes the number of positions through which a sensor assembly must be rotated to obtain a solution. Computer simulations show that accuracies of better than 0.4 seconds of arc can be achieved under typical test conditions associated with existing magnetic test facilities. The basic approach is similar in nature to that presented by McPherron and Snare (1978) except that only three sensor positions are required and the system of equations to be solved is considerably simplified. Applications of the method to the case of the MAGSAT Vector Magnetometer are presented and the problems encountered discussed.

  1. Application of the Absolute Nodal Co-Ordinate Formulation to Multibody System Dynamics

    NASA Astrophysics Data System (ADS)

    Escalona, J. L.; Hussien, H. A.; Shabana, A. A.

    1998-07-01

    The floating frame of reference formulation is currently the most widely used approach in flexible multibody simulations. The use of this approach, however, has been limited to small deformation problems. In this investigation, the computer implementation of the newabsolute nodal co-ordinate formulationand its use in the small and large deformation analysis of flexible multibody systems that consist of interconnected bodies are discussed. While in the floating frame of reference formulation a mixed set of absolute reference and local elastic co-ordinates are used, in the absolute nodal co-ordinate formulation only absolute co-ordinates are used. In the absolute nodal co-ordinate formulation, new interpretation of the nodal co-ordinates of the finite elements is used. No infinitesimal or finite rotations are used as nodal co-ordinates from beams and plates, instead, global slopes are used to define the element nodal co-ordinates. Using this interpretation of the element co-ordinates, beams and plates can be considered as isoparametric elements, and as a result, exact modelling of the rigid body dynamics can be obtained using the element shape function and the absolute nodal co-ordinates. Unlike the floating frame of reference approach, no co-ordinate transformation is required in order to determine the element inertia. The mass matrix of the finite elements is a constant matrix, and therefore, the centrifugal and Coriolis forces are equal to zero when the absolute nodal co-ordinate formulation is used. Another advantage of using the absolute nodal co-ordinate formulation in the dynamic simulation of multibody systems is its simplicity in imposing some of the joint constraints and also its simplicity in formulating the generalized forces due to spring-damper elements. The results obtained in this investigation show an excellent agreement with the results obtained using the floating frame of reference formulation when large rotation-small deformation problems are

  2. Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Schmitz, Christian; Bachert, Peter

    2004-12-01

    Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model

  3. Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum.

    PubMed

    Cheng, Dongmei; Hoogenraad, Casper C; Rush, John; Ramm, Elizabeth; Schlager, Max A; Duong, Duc M; Xu, Ping; Wijayawardana, Sameera R; Hanfelt, John; Nakagawa, Terunaga; Sheng, Morgan; Peng, Junmin

    2006-06-01

    The postsynaptic density (PSD) of central excitatory synapses is essential for postsynaptic signaling, and its components are heterogeneous among different neuronal subtypes and brain structures. Here we report large scale relative and absolute quantification of proteins in PSDs purified from adult rat forebrain and cerebellum. PSD protein profiles were determined using the cleavable ICAT strategy and LC-MS/MS. A total of 296 proteins were identified and quantified with 43 proteins exhibiting statistically significant abundance change between forebrain and cerebellum, indicating marked molecular heterogeneity of PSDs between different brain regions. Moreover we utilized absolute quantification strategy, in which synthetic isotope-labeled peptides were used as internal standards, to measure the molar abundance of 32 key PSD proteins in forebrain and cerebellum. These data confirm the abundance of calcium/calmodulin-dependent protein kinase II and PSD-95 and reveal unexpected stoichiometric ratios between glutamate receptors, scaffold proteins, and signaling molecules in the PSD. Our data also demonstrate that the absolute quantification method is well suited for targeted quantitative proteomic analysis. Overall this study delineates a crucial molecular difference between forebrain and cerebellar PSDs and provides a quantitative framework for measuring the molecular stoichiometry of the PSD. PMID:16507876

  4. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions.

    PubMed

    Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A

    2008-12-01

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

  5. The molecular systemic and local effects of intra-tendinous injection of Platelet Rich Plasma in tendinosis: preliminary results on a rat model with ELISA method

    PubMed Central

    Dallaudiere, Benjamin; Louedec, Liliane; Lenet, Marie Paule Jacob; Pesquer, Lionel; Blaise, Elvind; Perozziello, Anne; Michel, Jean Baptiste; Moinard, Maryse; Meyer, Philippe; Serfaty, Jean Michel

    2015-01-01

    Summary Purpose the aim of our study was thus to quantify the effect of Platelet Rich Plasma (PRP) injection on systemic and local growth factors and to identify molecular markers in a rat model of patellar and Achilles tendinosis treated with PRP. Material and method twenty two rats were used for the study. Two healthy rats were used as control (T−). We induced tendinosis (T+) in 20 rats (80 tendons by injecting under ultrasonography (US) guidance Collagenase 1® (day 0 = D0, patellar=40 and Achilles=40). At D3, these 20 rats with tendinosis were separated in treatment by either PRP (PRPT+, n=28), physiological serum (PST+, n=28, control) US-guided intratendinous injection, or without no PRP or PS (T+, n=24, control of natural evolution of tendinopathy). Follow-up at D7, D13, D18 and D25 using serum sample and local tendon removal with ELISA technics and comparison between the 3 groups were performed. Results during biological follow up, comparison of all serum samples of PRPT+, PST+ and T+ groups showed no significant modification of their biological markers at D7, D13, D18 and D25 (p>0.22). Comparison of immunological sample tendon markers of PRPT+, PST+ and T+ groups also showed no significant modification of markers at D7, D13, D18 and D25 (p>0.16) considering each biological marker and also all subgroups confounded. Conclusion our study strongly suggests that a single intratendinous US-guided injection of PRP in Achilles and patellar T+ doesn’t increase biological markers such as growth factors compared to a control group in mid-term and long-term follow-up. PMID:26261788

  6. On the absolute alignment of GONG images

    NASA Astrophysics Data System (ADS)

    Toner, C. G.

    2001-01-01

    In order to combine data from the six instruments in the GONG network the alignment of all of the images must be known to a fairly high precision (~0°.1 for GONG Classic and ~0°.01 for GONG+). The relative orientation is obtained using the angular cross-correlation method described by (Toner & Harvey, 1998). To obtain the absolute orientation the Project periodically records a day of drift scans, where the image of the Sun is allowed to drift across the CCD repeatedly throughout the day. These data are then analyzed to deduce the direction of Terrestrial East-West as a function of hour angle (i.e., time) for that instrument. The transit of Mercury on Nov. 15, 1999, which was recorded by three of the GONG instruments, provided an independent check on the current alignment procedures. Here we present a comparison of the alignment of GONG images as deduced from both drift scans and the Mercury transit for two GONG sites: Tucson (GONG+ camera) and Mauna Loa (GONG Classic camera). The agreement is within ~0°.01 for both cameras, however, the scatter is substantially larger for GONG Classic: ~0°.03 compared to ~0°.01 for GONG+.

  7. Climate Absolute Radiance and Refractivity Observatory (CLARREO)

    NASA Technical Reports Server (NTRS)

    Leckey, John P.

    2015-01-01

    The Climate Absolute Radiance and Refractivity Observatory (CLARREO) is a mission, led and developed by NASA, that will measure a variety of climate variables with an unprecedented accuracy to quantify and attribute climate change. CLARREO consists of three separate instruments: an infrared (IR) spectrometer, a reflected solar (RS) spectrometer, and a radio occultation (RO) instrument. The mission will contain orbiting radiometers with sufficient accuracy, including on orbit verification, to calibrate other space-based instrumentation, increasing their respective accuracy by as much as an order of magnitude. The IR spectrometer is a Fourier Transform spectrometer (FTS) working in the 5 to 50 microns wavelength region with a goal of 0.1 K (k = 3) accuracy. The FTS will achieve this accuracy using phase change cells to verify thermistor accuracy and heated halos to verify blackbody emissivity, both on orbit. The RS spectrometer will measure the reflectance of the atmosphere in the 0.32 to 2.3 microns wavelength region with an accuracy of 0.3% (k = 2). The status of the instrumentation packages and potential mission options will be presented.

  8. Absolute flux measurements for swift atoms

    NASA Technical Reports Server (NTRS)

    Fink, M.; Kohl, D. A.; Keto, J. W.; Antoniewicz, P.

    1987-01-01

    While a torsion balance in vacuum can easily measure the momentum transfer from a gas beam impinging on a surface attached to the balance, this measurement depends on the accommodation coefficients of the atoms with the surface and the distribution of the recoil. A torsion balance is described for making absolute flux measurements independent of recoil effects. The torsion balance is a conventional taut suspension wire design and the Young modulus of the wire determines the relationship between the displacement and the applied torque. A compensating magnetic field is applied to maintain zero displacement and provide critical damping. The unique feature is to couple the impinging gas beam to the torsion balance via a Wood's horn, i.e., a thin wall tube with a gradual 90 deg bend. Just as light is trapped in a Wood's horn by specular reflection from the curved surfaces, the gas beam diffuses through the tube. Instead of trapping the beam, the end of the tube is open so that the atoms exit the tube at 90 deg to their original direction. Therefore, all of the forward momentum of the gas beam is transferred to the torsion balance independent of the angle of reflection from the surfaces inside the tube.

  9. Gyrokinetic Statistical Absolute Equilibrium and Turbulence

    SciTech Connect

    Jian-Zhou Zhu and Gregory W. Hammett

    2011-01-10

    A paradigm based on the absolute equilibrium of Galerkin-truncated inviscid systems to aid in understanding turbulence [T.-D. Lee, "On some statistical properties of hydrodynamical and magnetohydrodynamical fields," Q. Appl. Math. 10, 69 (1952)] is taken to study gyrokinetic plasma turbulence: A finite set of Fourier modes of the collisionless gyrokinetic equations are kept and the statistical equilibria are calculated; possible implications for plasma turbulence in various situations are discussed. For the case of two spatial and one velocity dimension, in the calculation with discretization also of velocity v with N grid points (where N + 1 quantities are conserved, corresponding to an energy invariant and N entropy-related invariants), the negative temperature states, corresponding to the condensation of the generalized energy into the lowest modes, are found. This indicates a generic feature of inverse energy cascade. Comparisons are made with some classical results, such as those of Charney-Hasegawa-Mima in the cold-ion limit. There is a universal shape for statistical equilibrium of gyrokinetics in three spatial and two velocity dimensions with just one conserved quantity. Possible physical relevance to turbulence, such as ITG zonal flows, and to a critical balance hypothesis are also discussed.

  10. Issues in Absolute Spectral Radiometric Calibration: Intercomparison of Eight Sources

    NASA Technical Reports Server (NTRS)

    Goetz, Alexander F. H.; Kindel, Bruce; Pilewskie, Peter

    1998-01-01

    The application of atmospheric models to AVIRIS and other spectral imaging data to derive surface reflectance requires that the sensor output be calibrated to absolute radiance. Uncertainties in absolute calibration are to be expected, and claims of 92% accuracy have been published. Measurements of accurate surface albedos and cloud absorption to be used in radiative balance calculations depend critically on knowing the absolute spectral-radiometric response of the sensor. The Earth Observing System project is implementing a rigorous program of absolute radiometric calibration for all optical sensors. Since a number of imaging instruments that provide output in terms of absolute radiance are calibrated at different sites, it is important to determine the errors that can be expected among calibration sites. Another question exists about the errors in the absolute knowledge of the exoatmospheric spectral solar irradiance.

  11. Absolute nuclear material assay using count distribution (LAMBDA) space

    SciTech Connect

    Prasad, Mano K.; Snyderman, Neal J.; Rowland, Mark S.

    2015-12-01

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  12. Absolute nuclear material assay using count distribution (LAMBDA) space

    DOEpatents

    Prasad, Manoj K.; Snyderman, Neal J.; Rowland, Mark S.

    2012-06-05

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  13. Antifungal activity of tuberose absolute and some of its constituents.

    PubMed

    Nidiry, Eugene Sebastian J; Babu, C S Bujji

    2005-05-01

    The antifungal activity of the absolute of tuberose (Polianthes tuberosa ) and some of its constituents were evaluated against the mycelial growth of Colletotrichum gloeosporioides on potato-dextrose-agar medium. Tuberose absolute showed only mild activity at a concentration of 500 mg/L. However, three constituents present in the absolute, namely geraniol, indole and methyl anthranilate exhibited significant activity showing total inhibition of the mycelial growth at this concentration.

  14. Scanning micro-resonator direct-comb absolute spectroscopy

    PubMed Central

    Gambetta, Alessio; Cassinerio, Marco; Gatti, Davide; Laporta, Paolo; Galzerano, Gianluca

    2016-01-01

    Direct optical Frequency Comb Spectroscopy (DFCS) is proving to be a fundamental tool in many areas of science and technology thanks to its unique performance in terms of ultra-broadband, high-speed detection and frequency accuracy, allowing for high-fidelity mapping of atomic and molecular energy structure. Here we present a novel DFCS approach based on a scanning Fabry-Pérot micro-cavity resonator (SMART) providing a simple, compact and accurate method to resolve the mode structure of an optical frequency comb. The SMART approach, while drastically reducing system complexity, allows for a straightforward absolute calibration of the optical-frequency axis with an ultimate resolution limited by the micro-resonator resonance linewidth and can be used in any spectral region from UV to THz. We present an application to high-precision spectroscopy of acetylene at 1.54 μm, demonstrating performances comparable or even better than current state-of-the-art DFCS systems in terms of sensitivity, optical bandwidth and frequency-resolution. PMID:27752132

  15. Surface Characterization of pNIPAM Under Varying Absolute Humidity

    NASA Astrophysics Data System (ADS)

    Chhabra, Arnav; Kanapuram, Ravitej; Leva, Harrison; Trejo, Juan; Kim, Tae Jin; Hidrovo, Carlos

    2012-11-01

    Poly(N-isopropylacrylamide) has become ubiquitously known as a ``smart'' polymer, showing many promising applications in tissue engineering and drug delivery systems. These applications are particularly reliant on its trenchant, thermally induced hydrophilic-hydrophobic transition that occurs at the lower critical solution temperature (LCST). This feature imparts the pNIPAM programmable adsorption and release capabilities, thus eliminating the need for additional enzymes when removing cells from pNIPAM coated surfaces and leaving the extracellular matrix proteins of the cells largely untouched. The dependence of the LCST on molecular weight, solvent systems, and various salts has been studied extensively. However, what has not been explored is the effect of humidity on the characteristic properties of the polymer, specifically the LCST and the magnitude of the hydrophilic-hydrophobic transition. We studied the surface energy variation of pNIPAM as a function of humidity by altering the absolute humidity and keeping the ambient temperature constant. Our experiments were conducted inside a cuboidal environmental chamber with control over the temperature and humidity inside the chamber. A controlled needle was employed to dispense size-regulated droplets. Throughout this process, a CCD camera was used to image the droplet and the static contact angle was determined using image processing techniques. The behavior of pNIPAM as a function of humidity is presented and discussed.

  16. Absolute calibration for complex-geometry biomedical diffuse optical spectroscopy

    NASA Astrophysics Data System (ADS)

    Mastanduno, Michael A.; Jiang, Shudong; El-Ghussein, Fadi; diFlorio-Alexander, Roberta; Pogue, Brian W.; Paulsen, Keith D.

    2013-03-01

    We have presented methodology to calibrate data in NIRS/MRI imaging versus an absolute reference phantom and results in both phantoms and healthy volunteers. This method directly calibrates data to a diffusion-based model, takes advantage of patient specific geometry from MRI prior information, and generates an initial guess without the need for a large data set. This method of calibration allows for more accurate quantification of total hemoglobin, oxygen saturation, water content, scattering, and lipid concentration as compared with other, slope-based methods. We found the main source of error in the method to be derived from incorrect assignment of reference phantom optical properties rather than initial guess in reconstruction. We also present examples of phantom and breast images from a combined frequency domain and continuous wave MRI-coupled NIRS system. We were able to recover phantom data within 10% of expected contrast and within 10% of the actual value using this method and compare these results with slope-based calibration methods. Finally, we were able to use this technique to calibrate and reconstruct images from healthy volunteers. Representative images are shown and discussion is provided for comparison with existing literature. These methods work towards fully combining the synergistic attributes of MRI and NIRS for in-vivo imaging of breast cancer. Complete software and hardware integration in dual modality instruments is especially important due to the complexity of the technology and success will contribute to complex anatomical and molecular prognostic information that can be readily obtained in clinical use.

  17. Molecular and morphological variation of Paragonimus westermani in Vietnam with records of new second intermediate crab hosts and a new locality in a northern province.

    PubMed

    Doanh, N Pham; Tu, A Luu; Bui, T Dung; Loan, T Ho; Nonaka, Nariaki; Horii, Yoichiro; Blair, David; Nawa, Yukifumi

    2016-10-01

    Paragonimus westermani is one of the most medically important lung flukes and is widely distributed in Asia. It exhibits considerable variation in morphological, genetic and biological features. In central provinces of Vietnam, a high prevalence of metacercariae of this species has been reported from the crab intermediate host, Vietopotamon aluoiense. In this study, we detected P. westermani metacercariae in two additional crab hosts, Donopotamon haii in Quang Tri Province, central Vietnam and Indochinamon tannanti in Yen Bai Province in the north. The latter is a new locality for P. westermani in a northern region of Vietnam where P. heterotremus is the only species currently known to cause human paragonimiasis. Paragonimus westermani metacercariae found in Vietnam showed considerable morphological variation but slight genetic variation based on DNA sequences from the nuclear ribosomal ITS2 region and the mitochondrial 16S gene. Co-infection of the same individual crabs with P. westermani and P. heterotremus and/or some other Paragonimus species was found frequently, suggesting potential for co-infection in humans. The findings of the present study emphasize the need for highly specific molecular and immunodiagnostic methods to differentially diagnose between P. westermani and P. heterotremus infections.

  18. Molecular analysis of 24 Alagille syndrome families identifies a single submicroscopic deletion and further localizes the Alagille region within 20p12

    SciTech Connect

    Rand, E.B.; Piccoli, D.A.; Spinner, N.B.

    1995-11-01

    Alagille syndrome (AGS) is a clinically defined disorder characterized by cholestatic liver disease with bile duct paucity, peculiar facies, structural heart defects, vertebral anomalies, and ocular abnormalities. Multiple patients with various cytogenetic abnormalities involving 20p12 have been identified, allowing the assignment of AGS to this region. The presence of interstitial deletions of varying size led to the hypothesis that AGS is a contiguous gene deletion syndrome. This molecular analysis of cytogenetically normal AGS patients was performed in order to test this hypothesis and to refine the localization of the known AGS region. Investigation of inheritance of simple tandem repeat polymorphism alleles in 67 members of 24 cytogenetically normal Alagille families led to the identification of a single submicroscopic deletion. The deletion included loci D20S61, D20S41, D20S186, and D20S188 and presumably intervening uninformative loci D20S189 and D20S27. The six deleted loci are contained in a single YAC of 1.9 Mb. The additional finding of multiple unrelated probands who are heterozygous at each locus demonstrates that microdeletions at known loci within the AGS region are rare in cytogenetically normal patients with this disorder. This suggests that the majority of cases of AGS may be the result of a single gene defect rather than a contiguous gene deletion syndrome. 29 refs., 4 figs., 1 tab.

  19. Influence of longitudinal isotope substitution on the thermal conductivity of carbon nanotubes: Results of nonequilibrium molecular dynamics and local density functional calculations

    SciTech Connect

    Leroy, Frédéric Böhm, Michael C.; Schulte, Joachim; Balasubramanian, Ganesh

    2014-04-14

    We report reverse nonequilibrium molecular dynamics calculations of the thermal conductivity of isotope substituted (10,10) carbon nanotubes (CNTs) at 300 K. {sup 12}C and {sup 14}C isotopes both at 50% content were arranged either randomly, in bands running parallel to the main axis of the CNTs or in bands perpendicular to this axis. It is found that the systems with randomly distributed isotopes yield significantly reduced thermal conductivity. In contrast, the systems where the isotopes are organized in patterns parallel to the CNTs axis feature no reduction in thermal conductivity when compared with the pure {sup 14}C system. Moreover, a reduction of approximately 30% is observed in the system with the bands of isotopes running perpendicular to the CNT axis. The computation of phonon dispersion curves in the local density approximation and classical densities of vibrational states reveal that the phonon structure of carbon nanotubes is conserved in the isotope substituted systems with the ordered patterns, yielding high thermal conductivities in spite of the mass heterogeneity. In order to complement our conclusions on the {sup 12}C-{sup 14}C mixtures, we computed the thermal conductivity of systems where the {sup 14}C isotope was turned into pseudo-atoms of 20 and 40 atomic mass units.

  20. The absolute disparity anomaly and the mechanism of relative disparities.

    PubMed

    Chopin, Adrien; Levi, Dennis; Knill, David; Bavelier, Daphne

    2016-06-01

    There has been a long-standing debate about the mechanisms underlying the perception of stereoscopic depth and the computation of the relative disparities that it relies on. Relative disparities between visual objects could be computed in two ways: (a) using the difference in the object's absolute disparities (Hypothesis 1) or (b) using relative disparities based on the differences in the monocular separations between objects (Hypothesis 2). To differentiate between these hypotheses, we measured stereoscopic discrimination thresholds for lines with different absolute and relative disparities. Participants were asked to judge the depth of two lines presented at the same distance from the fixation plane (absolute disparity) or the depth between two lines presented at different distances (relative disparity). We used a single stimulus method involving a unique memory component for both conditions, and no extraneous references were available. We also measured vergence noise using Nonius lines. Stereo thresholds were substantially worse for absolute disparities than for relative disparities, and the difference could not be explained by vergence noise. We attribute this difference to an absence of conscious readout of absolute disparities, termed the absolute disparity anomaly. We further show that the pattern of correlations between vergence noise and absolute and relative disparity acuities can be explained jointly by the existence of the absolute disparity anomaly and by the assumption that relative disparity information is computed from absolute disparities (Hypothesis 1).

  1. The absolute disparity anomaly and the mechanism of relative disparities

    PubMed Central

    Chopin, Adrien; Levi, Dennis; Knill, David; Bavelier, Daphne

    2016-01-01

    There has been a long-standing debate about the mechanisms underlying the perception of stereoscopic depth and the computation of the relative disparities that it relies on. Relative disparities between visual objects could be computed in two ways: (a) using the difference in the object's absolute disparities (Hypothesis 1) or (b) using relative disparities based on the differences in the monocular separations between objects (Hypothesis 2). To differentiate between these hypotheses, we measured stereoscopic discrimination thresholds for lines with different absolute and relative disparities. Participants were asked to judge the depth of two lines presented at the same distance from the fixation plane (absolute disparity) or the depth between two lines presented at different distances (relative disparity). We used a single stimulus method involving a unique memory component for both conditions, and no extraneous references were available. We also measured vergence noise using Nonius lines. Stereo thresholds were substantially worse for absolute disparities than for relative disparities, and the difference could not be explained by vergence noise. We attribute this difference to an absence of conscious readout of absolute disparities, termed the absolute disparity anomaly. We further show that the pattern of correlations between vergence noise and absolute and relative disparity acuities can be explained jointly by the existence of the absolute disparity anomaly and by the assumption that relative disparity information is computed from absolute disparities (Hypothesis 1). PMID:27248566

  2. Absolute Plate Velocities from Seismic Anisotropy

    NASA Astrophysics Data System (ADS)

    Kreemer, Corné; Zheng, Lin; Gordon, Richard

    2015-04-01

    The orientation of seismic anisotropy inferred beneath plate interiors may provide a means to estimate the motions of the plate relative to the sub-asthenospheric mantle. Here we analyze two global sets of shear-wave splitting data, that of Kreemer [2009] and an updated and expanded data set, to estimate plate motions and to better understand the dispersion of the data, correlations in the errors, and their relation to plate speed. We also explore the effect of using geologically current plate velocities (i.e., the MORVEL set of angular velocities [DeMets et al. 2010]) compared with geodetically current plate velocities (i.e., the GSRM v1.2 angular velocities [Kreemer et al. 2014]). We demonstrate that the errors in plate motion azimuths inferred from shear-wave splitting beneath any one tectonic plate are correlated with the errors of other azimuths from the same plate. To account for these correlations, we adopt a two-tier analysis: First, find the pole of rotation and confidence limits for each plate individually. Second, solve for the best fit to these poles while constraining relative plate angular velocities to consistency with the MORVEL relative plate angular velocities. The SKS-MORVEL absolute plate angular velocities (based on the Kreemer [2009] data set) are determined from the poles from eight plates weighted proportionally to the root-mean-square velocity of each plate. SKS-MORVEL indicates that eight plates (Amur, Antarctica, Caribbean, Eurasia, Lwandle, Somalia, Sundaland, and Yangtze) have angular velocities that differ insignificantly from zero. The net rotation of the lithosphere is 0.25±0.11° Ma-1 (95% confidence limits) right-handed about 57.1°S, 68.6°E. The within-plate dispersion of seismic anisotropy for oceanic lithosphere (σ=19.2° ) differs insignificantly from that for continental lithosphere (σ=21.6° ). The between-plate dispersion, however, is significantly smaller for oceanic lithosphere (σ=7.4° ) than for continental

  3. Evaluation of the Absolute Regional Temperature Potential

    NASA Technical Reports Server (NTRS)

    Shindell, D. T.

    2012-01-01

    The Absolute Regional Temperature Potential (ARTP) is one of the few climate metrics that provides estimates of impacts at a sub-global scale. The ARTP presented here gives the time-dependent temperature response in four latitude bands (90-28degS, 28degS-28degN, 28-60degN and 60-90degN) as a function of emissions based on the forcing in those bands caused by the emissions. It is based on a large set of simulations performed with a single atmosphere-ocean climate model to derive regional forcing/response relationships. Here I evaluate the robustness of those relationships using the forcing/response portion of the ARTP to estimate regional temperature responses to the historic aerosol forcing in three independent climate models. These ARTP results are in good accord with the actual responses in those models. Nearly all ARTP estimates fall within +/-20%of the actual responses, though there are some exceptions for 90-28degS and the Arctic, and in the latter the ARTP may vary with forcing agent. However, for the tropics and the Northern Hemisphere mid-latitudes in particular, the +/-20% range appears to be roughly consistent with the 95% confidence interval. Land areas within these two bands respond 39-45% and 9-39% more than the latitude band as a whole. The ARTP, presented here in a slightly revised form, thus appears to provide a relatively robust estimate for the responses of large-scale latitude bands and land areas within those bands to inhomogeneous radiative forcing and thus potentially to emissions as well. Hence this metric could allow rapid evaluation of the effects of emissions policies at a finer scale than global metrics without requiring use of a full climate model.

  4. Absolute Radiometric Calibration of KOMPSAT-3A

    NASA Astrophysics Data System (ADS)

    Ahn, H. Y.; Shin, D. Y.; Kim, J. S.; Seo, D. C.; Choi, C. U.

    2016-06-01

    This paper presents a vicarious radiometric calibration of the Korea Multi-Purpose Satellite-3A (KOMPSAT-3A) performed by the Korea Aerospace Research Institute (KARI) and the Pukyong National University Remote Sensing Group (PKNU RSG) in 2015.The primary stages of this study are summarized as follows: (1) A field campaign to determine radiometric calibrated target fields was undertaken in Mongolia and South Korea. Surface reflectance data obtained in the campaign were input to a radiative transfer code that predicted at-sensor radiance. Through this process, equations and parameters were derived for the KOMPSAT-3A sensor to enable the conversion of calibrated DN to physical units, such as at-sensor radiance or TOA reflectance. (2) To validate the absolute calibration coefficients for the KOMPSAT-3A sensor, we performed a radiometric validation with a comparison of KOMPSAT-3A and Landsat-8 TOA reflectance using one of the six PICS (Libya 4). Correlations between top-of-atmosphere (TOA) radiances and the spectral band responses of the KOMPSAT-3A sensors at the Zuunmod, Mongolia and Goheung, South Korea sites were significant for multispectral bands. The average difference in TOA reflectance between KOMPSAT-3A and Landsat-8 image over the Libya 4, Libya site in the red-green-blue (RGB) region was under 3%, whereas in the NIR band, the TOA reflectance of KOMPSAT-3A was lower than the that of Landsat-8 due to the difference in the band passes of two sensors. The KOMPSAT-3Aensor includes a band pass near 940 nm that can be strongly absorbed by water vapor and therefore displayed low reflectance. Toovercome this, we need to undertake a detailed analysis using rescale methods, such as the spectral bandwidth adjustment factor.

  5. Orion Absolute Navigation System Progress and Challenge

    NASA Technical Reports Server (NTRS)

    Holt, Greg N.; D'Souza, Christopher

    2012-01-01

    The absolute navigation design of NASA's Orion vehicle is described. It has undergone several iterations and modifications since its inception, and continues as a work-in-progress. This paper seeks to benchmark the current state of the design and some of the rationale and analysis behind it. There are specific challenges to address when preparing a timely and effective design for the Exploration Flight Test (EFT-1), while still looking ahead and providing software extensibility for future exploration missions. The primary onboard measurements in a Near-Earth or Mid-Earth environment consist of GPS pseudo-range and delta-range, but for future explorations missions the use of star-tracker and optical navigation sources need to be considered. Discussions are presented for state size and composition, processing techniques, and consider states. A presentation is given for the processing technique using the computationally stable and robust UDU formulation with an Agee-Turner Rank-One update. This allows for computational savings when dealing with many parameters which are modeled as slowly varying Gauss-Markov processes. Preliminary analysis shows up to a 50% reduction in computation versus a more traditional formulation. Several state elements are discussed and evaluated, including position, velocity, attitude, clock bias/drift, and GPS measurement biases in addition to bias, scale factor, misalignment, and non-orthogonalities of the accelerometers and gyroscopes. Another consideration is the initialization of the EKF in various scenarios. Scenarios such as single-event upset, ground command, and cold start are discussed as are strategies for whole and partial state updates as well as covariance considerations. Strategies are given for dealing with latent measurements and high-rate propagation using multi-rate architecture. The details of the rate groups and the data ow between the elements is discussed and evaluated.

  6. Absolute calibration in the 1750 A-3350 A region. [revisions for air extinction

    NASA Technical Reports Server (NTRS)

    Strongylis, G. J.; Bohlin, R. C.

    1979-01-01

    The absolute flux measurements in the rocket ultraviolet made by Bohlin, Frimout, and Lillie (BFL) are revised using a more correct treatment of the air extinction that enters the air calibration of their instrument. The absorption by molecular oxygen and ozone, Rayleigh scattering, and extinction by aerosols is tabulated for general use in ultraviolet calibrations performed in air. The revised absolute flux of Eta UMa and final fluxes for Alpha Lyr and Zeta Oph are presented in the 1750 A-3350 A region. The absolute flux of the star Eta UMa (B3 V) is compared to four other independent determinations in the 1200 A-3400 A region and a maximum difference of 35% is found near 1500 A between the OAO-2 and Apollo 17 fluxes. Longward of 1700 A the typical scatter in the different determinations is only plus or minus 5%. The rocket measurements of BFL, the ANS and TD-1 satellite data, and the Apollo 17 data are compared to the ultraviolet fluxes from the OAO-2, demonstrating a photometric reproducibility of about plus or minus 3%. Therefore, all four sets of spectrophotometry can be reduced to a common absolute scale.

  7. Mid-infrared absolute spectral responsivity scale based on an absolute cryogenic radiometer and an optical parametric oscillator laser

    NASA Astrophysics Data System (ADS)

    Zhao, Kun; Shi, Xueshun; Chen, Haidong; Liu, Yulong; Liu, Changming; Chen, Kunfeng; Li, Ligong; Gan, Haiyong; Ma, Chong

    2016-06-01

    We are reporting on a laser-based absolute spectral responsivity scale in the mid-infrared spectral range. By using a mid-infrared tunable optical parametric oscillator as the laser source, the absolute responsivity scale has been established by calibrating thin-film thermopile detectors against an absolute cryogenic radiometer. The thin-film thermopile detectors can be then used as transfer standard detectors. The extended uncertainty of the absolute spectral responsivity measurement has been analyzed to be 0.58%–0.68% (k  =  2).

  8. Mid-infrared absolute spectral responsivity scale based on an absolute cryogenic radiometer and an optical parametric oscillator laser

    NASA Astrophysics Data System (ADS)

    Zhao, Kun; Shi, Xueshun; Chen, Haidong; Liu, Yulong; Liu, Changming; Chen, Kunfeng; Li, Ligong; Gan, Haiyong; Ma, Chong

    2016-06-01

    We are reporting on a laser-based absolute spectral responsivity scale in the mid-infrared spectral range. By using a mid-infrared tunable optical parametric oscillator as the laser source, the absolute responsivity scale has been established by calibrating thin-film thermopile detectors against an absolute cryogenic radiometer. The thin-film thermopile detectors can be then used as transfer standard detectors. The extended uncertainty of the absolute spectral responsivity measurement has been analyzed to be 0.58%-0.68% (k  =  2).

  9. Alignment and absolute wavelength calibration of imaging Bragg spectrometers

    NASA Astrophysics Data System (ADS)

    Bertschinger, G.; Marchuk, O.; Barnsley, R.

    2016-11-01

    In the present and the next generation of fusion devices, imaging Bragg spectrometers are key diagnostics to measure plasma parameters in the hot core, especially ion temperature and plasma rotation. The latter quantities are routinely obtained using the Doppler-width and -shift of the emitted spectral lines, respectively. Line shift measurements require absolute accuracies Δλ/λ of about 10 ppm, where λ-is the observed wavelength. For ITER and the present fusion devices, spectral lines of He-and H-like argon, iron, and krypton as well as Ne-like tungsten are foreseen for the measurements. For these lines, Kα lines can be found, some in higher order, which fit into the narrow energy window of the spectrometers. For arbitrary wavelength settings, Kα lines are also used to measure the miscut of the spherical crystals; afterwards the spectrometers can be set according to the geometrical imaging properties using coordinate measurement machines. For the spectrometers measuring Lyα lines of H-like ions, fluorescence targets can provide in situ localized calibration lines on the spectra. The fluorescence targets are used best in transmission and are excited by the thermal x-ray radiation of the plasma. An analytic theory of fluorescence is worked out.

  10. Weighted Wilcoxon-type Smoothly Clipped Absolute Deviation Method

    PubMed Central

    Wang, Lan; Li, Runze

    2009-01-01

    Summary Shrinkage-type variable selection procedures have recently seen increasing applications in biomedical research. However, their performance can be adversely influenced by outliers in either the response or the covariate space. This paper proposes a weighted Wilcoxon-type smoothly clipped absolute deviation (WW-SCAD) method, which deals with robust variable selection and robust estimation simultaneously. The new procedure can be conveniently implemented with the statistical software R. We establish that the WW-SCAD correctly identifies the set of zero coefficients with probability approaching one and estimates the nonzero coefficients with the rate n−1/2. Moreover, with appropriately chosen weights the WW-SCAD is robust with respect to outliers in both the x and y directions. The important special case with constant weights yields an oracle-type estimator with high efficiency at the presence of heavier-tailed random errors. The robustness of the WW-SCAD is partly justified by its asymptotic performance under local shrinking contamination. We propose a BIC-type tuning parameter selector for the WW-SCAD. The performance of the WW-SCAD is demonstrated via simulations and by an application to a study that investigates the effects of personal characteristics and dietary factors on plasma beta-carotene level. PMID:18647294

  11. An Absolute Phase Space for the Physicality of Matter

    SciTech Connect

    Valentine, John S.

    2010-12-22

    We define an abstract and absolute phase space (''APS'') for sub-quantum intrinsic wave states, in three axes, each mapping directly to a duality having fundamental ontological basis. Many aspects of quantum physics emerge from the interaction algebra and a model deduced from principles of 'unique solvability' and 'identifiable entity', and we reconstruct previously abstract fundamental principles and phenomena from these new foundations. The physical model defines bosons as virtual continuous waves pairs in the APS, and fermions as real self-quantizing snapshots of those waves when simple conditions are met. The abstraction and physical model define a template for the constitution of all fermions, a template for all the standard fundamental bosons and their local interactions, in a common framework and compactified phase space for all forms of real matter and virtual vacuum energy, and a distinct algebra for observables and unobservables. To illustrate our scheme's potential, we provide examples of slit experiment variations (where the model finds theoretical basis for interference only occurring between two final sources), QCD (where we may model most attributes known to QCD, and a new view on entanglement), and we suggest approaches for other varied applications. We believe this is a viable candidate for further exploration as a foundational proposition for physics.

  12. An Absolute Phase Space for the Physicality of Matter

    NASA Astrophysics Data System (ADS)

    Valentine, John S.

    2010-12-01

    We define an abstract and absolute phase space ("APS") for sub-quantum intrinsic wave states, in three axes, each mapping directly to a duality having fundamental ontological basis. Many aspects of quantum physics emerge from the interaction algebra and a model deduced from principles of `unique solvability' and `identifiable entity', and we reconstruct previously abstract fundamental principles and phenomena from these new foundations. The physical model defines bosons as virtual continuous waves pairs in the APS, and fermions as real self-quantizing snapshots of those waves when simple conditions are met. The abstraction and physical model define a template for the constitution of all fermions, a template for all the standard fundamental bosons and their local interactions, in a common framework and compactified phase space for all forms of real matter and virtual vacuum energy, and a distinct algebra for observables and unobservables. To illustrate our scheme's potential, we provide examples of slit experiment variations (where the model finds theoretical basis for interference only occurring between two final sources), QCD (where we may model most attributes known to QCD, and a new view on entanglement), and we suggest approaches for other varied applications. We believe this is a viable candidate for further exploration as a foundational proposition for physics.

  13. Absolute Ligand Discrimination by Dimeric Signaling Receptors.

    PubMed

    Fathi, Sepehr; Nayak, Chitra R; Feld, Jordan J; Zilman, Anton G

    2016-09-01

    Many signaling pathways act through shared components, where different ligand molecules bind the same receptors or activate overlapping sets of response regulators downstream. Nevertheless, different ligands acting through cross-wired pathways often lead to different outcomes in terms of the target cell behavior and function. Although a number of mechanisms have been proposed, it still largely remains unclear how cells can reliably discriminate different molecular ligands under such circumstances. Here we show that signaling via ligand-induced receptor dimerization-a very common motif in cellular signaling-naturally incorporates a mechanism for the discrimination of ligands acting through the same receptor. PMID:27602720

  14. Novalis' Poetic Uncertainty: A "Bildung" with the Absolute

    ERIC Educational Resources Information Center

    Mika, Carl

    2016-01-01

    Novalis, the Early German Romantic poet and philosopher, had at the core of his work a mysterious depiction of the "absolute." The absolute is Novalis' name for a substance that defies precise knowledge yet calls for a tentative and sensitive speculation. How one asserts a truth, represents an object, and sets about encountering things…

  15. Absolute Pitch in Infant Auditory Learning: Evidence for Developmental Reorganization.

    ERIC Educational Resources Information Center

    Saffran, Jenny R.; Griepentrog, Gregory J.

    2001-01-01

    Two experiments examined 8-month-olds' use of absolute and relative pitch cues in a tone-sequence statistical learning task. Results suggest that, given unsegmented stimuli that do not conform to rules of musical composition, infants are more likely to track patterns of absolute pitches than of relative pitches. A third experiment found that adult…

  16. Supplementary and Enrichment Series: Absolute Value. Teachers' Commentary. SP-25.

    ERIC Educational Resources Information Center

    Bridgess, M. Philbrick, Ed.

    This is one in a series of manuals for teachers using SMSG high school supplementary materials. The pamphlet includes commentaries on the sections of the student's booklet, answers to the exercises, and sample test questions. Topics covered include addition and multiplication in terms of absolute value, graphs of absolute value in the Cartesian…

  17. Supplementary and Enrichment Series: Absolute Value. SP-24.

    ERIC Educational Resources Information Center

    Bridgess, M. Philbrick, Ed.

    This is one in a series of SMSG supplementary and enrichment pamphlets for high school students. This series is designed to make material for the study of topics of special interest to students readily accessible in classroom quantity. Topics covered include absolute value, addition and multiplication in terms of absolute value, graphs of absolute…

  18. Absolute dimensions of unevolved O type close binaries

    SciTech Connect

    Doom, C.; de Loore, C.

    1984-03-15

    A method is presented to derive the absolute dimensions of early-type detached binaries by combining the observed parameters with results of evolutionary computations. The method is used to obtain the absolute dimensions of nine close binaries. We find that most systems have an initial masss ratio near 1.

  19. Absolute Humidity and the Seasonality of Influenza (Invited)

    NASA Astrophysics Data System (ADS)

    Shaman, J. L.; Pitzer, V.; Viboud, C.; Grenfell, B.; Goldstein, E.; Lipsitch, M.

    2010-12-01

    Much of the observed wintertime increase of mortality in temperate regions is attributed to seasonal influenza. A recent re-analysis of laboratory experiments indicates that absolute humidity strongly modulates the airborne survival and transmission of the influenza virus. Here we show that the onset of increased wintertime influenza-related mortality in the United States is associated with anomalously low absolute humidity levels during the prior weeks. We then use an epidemiological model, in which observed absolute humidity conditions temper influenza transmission rates, to successfully simulate the seasonal cycle of observed influenza-related mortality. The model results indicate that direct modulation of influenza transmissibility by absolute humidity alone is sufficient to produce this observed seasonality. These findings provide epidemiological support for the hypothesis that absolute humidity drives seasonal variations of influenza transmission in temperate regions. In addition, we show that variations of the basic and effective reproductive numbers for influenza, caused by seasonal changes in absolute humidity, are consistent with the general timing of pandemic influenza outbreaks observed for 2009 A/H1N1 in temperate regions. Indeed, absolute humidity conditions correctly identify the region of the United States vulnerable to a third, wintertime wave of pandemic influenza. These findings suggest that the timing of pandemic influenza outbreaks is controlled by a combination of absolute humidity conditions, levels of susceptibility and changes in population mixing and contact rates.

  20. Determination of Absolute Zero Using a Computer-Based Laboratory

    ERIC Educational Resources Information Center

    Amrani, D.

    2007-01-01

    We present a simple computer-based laboratory experiment for evaluating absolute zero in degrees Celsius, which can be performed in college and undergraduate physical sciences laboratory courses. With a computer, absolute zero apparatus can help demonstrators or students to observe the relationship between temperature and pressure and use…

  1. Absolute configuration assignment of a chiral molecule in the gas phase using foil-induced Coulomb explosion imaging

    NASA Astrophysics Data System (ADS)

    Herwig, Philipp; Zawatzky, Kerstin; Schwalm, Dirk; Grieser, Manfred; Heber, Oded; Jordon-Thaden, Brandon; Krantz, Claude; Novotný, Oldřich; Repnow, Roland; Schurig, Volker; Vager, Zeev; Wolf, Andreas; Trapp, Oliver; Kreckel, Holger

    2014-11-01

    Chiral molecules exist in two configurations that are nonsuperposable mirror images of one another. The underlying molecular structure is referred to as the absolute configuration. In chiral environments, the handedness of molecules influences their chemical characteristics dramatically, and therefore the determination of absolute configurations is of fundamental interest in organic chemistry and biology. Commonly applied techniques to assign absolute configuration are anomalous single-crystal x-ray diffraction and vibrational circular dichroism. However, these techniques become increasingly more challenging when applied to molecules that are made out of light atoms exclusively. Furthermore, there is no established method to determine the absolute handedness of gas-phase molecules that are not optically active. In this work, we apply the foil-induced Coulomb explosion imaging technique to determine directly the absolute configuration of the chiral molecule trans-2,3-dideuterooxirane (C2OD2H2) in the gas phase. The experiment leads to the definitive assignment of the (R ,R ) configuration to an enantio-selected dideuterooxirane sample with a statistical confidence of 5 σ . As the handedness of trans-2,3-dideuterooxirane is unambiguously linked by chemical synthesis to the stereochemical key reference glyceraldehyde, our results provide an independent verification of the absolute configuration of the stereochemical reference standard.

  2. Absolute radiometric calibration of advanced remote sensing systems

    NASA Technical Reports Server (NTRS)

    Slater, P. N.

    1982-01-01

    The distinction between the uses of relative and absolute spectroradiometric calibration of remote sensing systems is discussed. The advantages of detector-based absolute calibration are described, and the categories of relative and absolute system calibrations are listed. The limitations and problems associated with three common methods used for the absolute calibration of remote sensing systems are addressed. Two methods are proposed for the in-flight absolute calibration of advanced multispectral linear array systems. One makes use of a sun-illuminated panel in front of the sensor, the radiance of which is monitored by a spectrally flat pyroelectric radiometer. The other uses a large, uniform, high-radiance reference ground surface. The ground and atmospheric measurements required as input to a radiative transfer program to predict the radiance level at the entrance pupil of the orbital sensor are discussed, and the ground instrumentation is described.

  3. Fully distributed absolute blood flow velocity measurement for middle cerebral arteries using Doppler optical coherence tomography

    PubMed Central

    Qi, Li; Zhu, Jiang; Hancock, Aneeka M.; Dai, Cuixia; Zhang, Xuping; Frostig, Ron D.; Chen, Zhongping

    2016-01-01

    Doppler optical coherence tomography (DOCT) is considered one of the most promising functional imaging modalities for neuro biology research and has demonstrated the ability to quantify cerebral blood flow velocity at a high accuracy. However, the measurement of total absolute blood flow velocity (BFV) of major cerebral arteries is still a difficult problem since it is related to vessel geometry. In this paper, we present a volumetric vessel reconstruction approach that is capable of measuring the absolute BFV distributed along the entire middle cerebral artery (MCA) within a large field-of-view. The Doppler angle at each point of the MCA, representing the vessel geometry, is derived analytically by localizing the artery from pure DOCT images through vessel segmentation and skeletonization. Our approach could achieve automatic quantification of the fully distributed absolute BFV across different vessel branches. Experiments on rodents using swept-source optical coherence tomography showed that our approach was able to reveal the consequences of permanent MCA occlusion with absolute BFV measurement. PMID:26977365

  4. Critical inclination for absolute/convective instability transition in inverted falling films

    NASA Astrophysics Data System (ADS)

    Scheid, Benoit; Kofman, Nicolas; Rohlfs, Wilko

    2016-04-01

    Liquid films flowing down the underside of inclined plates are subject to the interaction between the hydrodynamic and the Rayleigh-Taylor (R-T) instabilities causing a patterned and wavy topology at the free surface. The R-T instability results from the denser liquid film being located above a less dense ambient gas, and deforming into an array of droplets, which eventually drip if no saturation mechanism arises. Such saturation mechanism can actually be provided by a fluid motion along the inclined plate. Using a weighted integral boundary layer model, this study examines the critical inclination angle, measured from the vertical, that separates regimes of absolute and convective instability. If the instability is of absolute type, growing perturbations stay localized in space potentially leading to dripping. If the instability is of convective type, growing perturbations move downwards the inclined plate, forming waves and eventually, but not necessarily, droplets. Remarkably, there is a minimum value of the critical angle below which a regime of absolute instability cannot exist. This minimum angle decreases with viscosity: it is about 85° for water, about 70° for silicon oil 20 times more viscous than water, and reaches a limiting value for liquid with a viscosity larger than about 1000 times the one of water. It results that for any fluid, absolute dripping can only exist for inclination angle (taken from the vertical) larger than 57.4°.

  5. A localized and propagating SPR, and molecular imprinting based fiber-optic ascorbic acid sensor using an in situ polymerized polyaniline–Ag nanocomposite

    NASA Astrophysics Data System (ADS)

    Shrivastav, Anand M.; Usha, Sruthi P.; Gupta, Banshi D.

    2016-08-01

    We report a successful approach for the fabrication and characterization of a fiber-optic sensor for ascorbic acid (AA) detection, using a molecularly imprinted polyaniline–Ag (PANI–Ag) nanocomposite layer based on the combined phenomena of surface plasmon resonance (SPR) and localized SPR (LSPR). The PANI–Ag nanocomposite is synthesized by an in situ polymerization process and AA imprints are prepared on the polymeric composite. The confirmation of the PANI–Ag nanocomposite and AA imprinting is performed using various characterization methods such as x-ray diffraction (XRD), UV–vis, Fourier transform infrared spectroscopy and scanning electron microscopy. From XRD, the size of Ag nanoparticles is analyzed. The absorbance spectra are recorded for samples of different concentrations of AA around the sensing region of the probe. An increase in peak absorbance wavelength with the increase in AA concentration is observed with a linear response for the concentration range from 10‑8 M to 10‑6 M. The sensor possesses a high sensitivity of 45.1 nm log‑1 M near an AA concentration of 10‑8 M. The limit of detection (LOD) and limit of quantification of the sensor are found to be 7.383 × 10‑11 M and 4.16 × 10‑10 M, respectively. The LOD of the sensor is compared to studies reported in the literature and is found to be the lowest. The sensor possesses several other advantages such as cost effectiveness, selectivity, and low response time (<5 s), along with abilities of remote sensing and online monitoring.

  6. Molecular cloning, genomic organization, chromosomal mapping and subcellular localization of mouse PAP7: a PBR and PKA-RIalpha associated protein.

    PubMed

    Liu, Jun; Cavalli, Luciane R; Haddad, Bassem R; Papadopoulos, Vassilios

    2003-04-10

    A mouse protein that interacts with the peripheral-type benzodiazepine receptor (PBR) and the cAMP-dependent protein kinase A (PKA) regulatory subunit RIalpha (PKA-RIalpha), named PBR and PKA associated protein 7 (PAP7) was identified and shown to be involved in hormone-induced steroid biosynthesis in testicular Leydig cells. In the present study, mouse PAP7 cDNA was extended by 5'-rapid amplification of cDNA ends; and a 3432 bp sequence, encoding a 525-amino-acid protein with a calculated molecular weight of 60 kDa, was re-assembled. Mouse and human PAP7 share an 85% amino acid identity and contain a conserved acyl-CoA-binding protein/diazepam binding inhibitor (ACBP/DBI) motif. ACBP/DBI has been identified as the endogenous PBR ligand able to stimulate mitochondrial steroid formation in all steroidogenic cells. The full-length mouse PAP7 gene was cloned and assembled by screening a BAC clone, polymerase chain reaction and searching the mouse genome database. The gene is approximately 29 kb in length and includes eight exons and seven introns. Although it is shorter than the human PAP7 gene, all exons are conserved between the mouse and human. The mouse PAP7 gene was mapped to chromosome 1H3-5 by fluorescence in situ hybridization in agreement with in silico search of the mouse genome database that mapped the PAP7 cDNA sequence to the 1H4 area. Immunofluorescence confocal microscopy demonstrated that PAP7 is mainly localized in the trans-Golgi apparatus and mitochondria in mouse tumor Leydig cells, in agreement with its proposed function in targeting the PKA isoenzyme to organelles rich in PBR, i.e. mitochondria, where phosphorylation of specific protein substrates mediates the hormone-induced steroid formation.

  7. Uroporphyrinogen-III synthase: Molecular cloning, nucleotide sequence, expression of a mouse full-length cDNA, and its localization on mouse chromosome 7

    SciTech Connect

    Xu, W.; Desnick, R.J.; Kozak, C.A.

    1995-04-10

    Uroporphyrinogen-III synthase, the fourth enzyme in the heme biosynthetic pathway, is responsible for the conversion of hydroxymethylbilane to the cyclic tetrapyrrole, uroporphyrinogen III. The deficient activity of URO-S is the enzymatic defect in congenital erythropoietic porphyria (CEP), an autosomal recessive disorder. For the generation of a mouse model of CEP, the human URO-S cDNA was used to screen 2 X 10{sup 6} recombinants from a mouse adult liver cDNA library. Ten positive clones were isolated, and dideoxy sequencing of the entire 1.6-kb insert of clone pmUROS-1 revealed 5{prime} and 3{prime} untranslated sequences of 144 and 623 bp, respectively, and an open reading frame of 798 bp encoding a 265-amino-acid polypeptide with a predicted molecular mass of 28,501 Da. The mouse and human coding sequences had 80.5 and 77.8% nucleotide and amino acid identity, respectively. The authenticity of the mouse cDNA was established by expression of the active monomeric enzyme in Escherichia coli. In addition, the analysis of two multilocus genetic crosses localized the mouse gene on chromosome 7, consistent with the mapping of the human gene to a position of conserved synteny on chromosome 10. The isolation, expression, and chromosomal mapping of this full-length cDNA should facilitate studies of the structure and organization of the mouse genomic sequence and the development of a mouse model of CEP for characterization of the disease pathogenesis and evaluation of gene therapy. 38 refs., 1 tab.

  8. Molecular epidemiology of Cryptococcus neoformans in Brazil and the United States: evidence for both local genetic differences and a global clonal population structure.

    PubMed Central

    Franzot, S P; Hamdan, J S; Currie, B P; Casadevall, A

    1997-01-01

    Little is known about the global molecular epidemiology of the human pathogenic fungus Cryptococcus neoformans. We studied 51 clinical and environmental (pigeon excreta) isolates from two cities in Brazil (Belo Horizonte and Rio de Janeiro) by analyzing their carbon assimilation patterns, electrophoretic karyotypes, restriction fragment length polymorphisms (RFLPs) with the C. neoformans repetitive element-1 (CNRE-1), and URA5 sequences. Results were compared to those previously obtained for isolates from New York City by the same DNA typing methods. Computer-assisted analysis of RFLPs and contour-clamped homogeneous electrophoresis (CHEF) patterns and URA5 sequences was performed to generate dendrograms. Some environmental and clinical isolates were found to be indistinguishable by CHEF, CNRE-1 RFLP, and URA5 sequence analyses. Similarly, some isolates from Rio de Janeiro and Belo Horizonte were indistinguishable by the three DNA typing techniques. Overall, Brazilian isolates appeared to be less heterogeneous by DNA analysis than isolates from other regions. Several Brazilian isolates were highly related to New York City isolates. Phylogenetic analysis of the sequences obtained for the Brazilian isolates and those obtained for New York City isolates was congruent with the dendrogram generated from the CNRE-1 RFLP data. In summary our results indicate (i) that the discriminatory power of the DNA typing method differs for Brazilian and New York City strains, with the order being CNRE-1 RFLP analysis > URA5 sequence analysis > CHEF analysis and CHEF analysis > URA5 sequence analysis > CNRE-1 RFLP analysis, respectively; (ii) that there are differences in local genetic diversity for Brazilian and New York City isolates; (iii) that there is additional evidence linking clinical isolates to those in pigeon excreta; and (iv) that some isolates from Brazil and New York City are closely related, consistent with the global dispersal of certain pathogenic strains. PMID

  9. A localized and propagating SPR, and molecular imprinting based fiber-optic ascorbic acid sensor using an in situ polymerized polyaniline-Ag nanocomposite

    NASA Astrophysics Data System (ADS)

    Shrivastav, Anand M.; Usha, Sruthi P.; Gupta, Banshi D.

    2016-08-01

    We report a successful approach for the fabrication and characterization of a fiber-optic sensor for ascorbic acid (AA) detection, using a molecularly imprinted polyaniline-Ag (PANI-Ag) nanocomposite layer based on the combined phenomena of surface plasmon resonance (SPR) and localized SPR (LSPR). The PANI-Ag nanocomposite is synthesized by an in situ polymerization process and AA imprints are prepared on the polymeric composite. The confirmation of the PANI-Ag nanocomposite and AA imprinting is performed using various characterization methods such as x-ray diffraction (XRD), UV-vis, Fourier transform infrared spectroscopy and scanning electron microscopy. From XRD, the size of Ag nanoparticles is analyzed. The absorbance spectra are recorded for samples of different concentrations of AA around the sensing region of the probe. An increase in peak absorbance wavelength with the increase in AA concentration is observed with a linear response for the concentration range from 10-8 M to 10-6 M. The sensor possesses a high sensitivity of 45.1 nm log-1 M near an AA concentration of 10-8 M. The limit of detection (LOD) and limit of quantification of the sensor are found to be 7.383 × 10-11 M and 4.16 × 10-10 M, respectively. The LOD of the sensor is compared to studies reported in the literature and is found to be the lowest. The sensor possesses several other advantages such as cost effectiveness, selectivity, and low response time (<5 s), along with abilities of remote sensing and online monitoring.

  10. A localized and propagating SPR, and molecular imprinting based fiber-optic ascorbic acid sensor using an in situ polymerized polyaniline-Ag nanocomposite.

    PubMed

    Shrivastav, Anand M; Usha, Sruthi P; Gupta, Banshi D

    2016-08-26

    We report a successful approach for the fabrication and characterization of a fiber-optic sensor for ascorbic acid (AA) detection, using a molecularly imprinted polyaniline-Ag (PANI-Ag) nanocomposite layer based on the combined phenomena of surface plasmon resonance (SPR) and localized SPR (LSPR). The PANI-Ag nanocomposite is synthesized by an in situ polymerization process and AA imprints are prepared on the polymeric composite. The confirmation of the PANI-Ag nanocomposite and AA imprinting is performed using various characterization methods such as x-ray diffraction (XRD), UV-vis, Fourier transform infrared spectroscopy and scanning electron microscopy. From XRD, the size of Ag nanoparticles is analyzed. The absorbance spectra are recorded for samples of different concentrations of AA around the sensing region of the probe. An increase in peak absorbance wavelength with the increase in AA concentration is observed with a linear response for the concentration range from 10(-8) M to 10(-6) M. The sensor possesses a high sensitivity of 45.1 nm log(-1) M near an AA concentration of 10(-8) M. The limit of detection (LOD) and limit of quantification of the sensor are found to be 7.383 × 10(-11) M and 4.16 × 10(-10) M, respectively. The LOD of the sensor is compared to studies reported in the literature and is found to be the lowest. The sensor possesses several other advantages such as cost effectiveness, selectivity, and low response time (<5 s), along with abilities of remote sensing and online monitoring. PMID:27405256

  11. Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints.

    PubMed

    Laub, P B; Khorasanizadeh, S; Roder, H

    1995-05-01

    The local structure within an 8-A radius around residue 45 of a recombinant F45W variant of human ubiquitin has been determined using 67 interproton distance restraints measured by two-dimensional proton NMR. Proton chemical shift evidence indicates that structural perturbations due to the F45W mutation are minimal and limited to the immediate vicinity of the site of mutation. Simulated annealing implemented with stochastic boundary molecular dynamics was applied to refine the structure of Trp 45 and 10 neighboring residues. The stochastic boundary method allowed the entire protein to be reassembled from the refined coordinates and the outlying unrefined coordinates with little distortion at the boundary. Refinement began with four low-energy indole ring orientations of F45W-substituted wild-type (WT) ubiquitin crystal coordinates. Distance restraints were derived from mostly long-range NOE cross peaks with 51 restraints involving the Trp 45 indole ring. Tandem refinements of 64 structures were done using either (1) upper and lower bounds derived from qualitative inspection of NOE crosspeak intensities or (2) quantitative analysis of cross-peak heights using the program MARDIGRAS. Though similar to those based on qualitative restraint, structures obtained using quantitative NOE analysis were superior in terms of precision and accuracy as measured by back-calculated sixth-root R factors. The six-membered portion of the indole ring is nearly coincident with the phenyl ring of the WT and the indole NH is exposed to solvent. Accommodation of the larger ring is accompanied by small perturbations in the backbone and a 120 degrees rotation of the chi 2 dihedral angle of Leu 50.

  12. Absolute Thermal SST Measurements over the Deepwater Horizon Oil Spill

    NASA Astrophysics Data System (ADS)

    Good, W. S.; Warden, R.; Kaptchen, P. F.; Finch, T.; Emery, W. J.

    2010-12-01

    Climate monitoring and natural disaster rapid assessment require baseline measurements that can be tracked over time to distinguish anthropogenic versus natural changes to the Earth system. Disasters like the Deepwater Horizon Oil Spill require constant monitoring to assess the potential environmental and economic impacts. Absolute calibration and validation of Earth-observing sensors is needed to allow for comparison of temporally separated data sets and provide accurate information to policy makers. The Ball Experimental Sea Surface Temperature (BESST) radiometer was designed and built by Ball Aerospace to provide a well calibrated measure of sea surface temperature (SST) from an unmanned aerial system (UAS). Currently, emissive skin SST observed by satellite infrared radiometers is validated by shipborne instruments that are expensive to deploy and can only take a few data samples along the ship track to overlap within a single satellite pixel. Implementation on a UAS will allow BESST to map the full footprint of a satellite pixel and perform averaging to remove any local variability due to the difference in footprint size of the instruments. It also enables the capability to study this sub-pixel variability to determine if smaller scale effects need to be accounted for in models to improve forecasting of ocean events. In addition to satellite sensor validation, BESST can distinguish meter scale variations in SST which could be used to remotely monitor and assess thermal pollution in rivers and coastal areas as well as study diurnal and seasonal changes to bodies of water that impact the ocean ecosystem. BESST was recently deployed on a conventional Twin Otter airplane for measurements over the Gulf of Mexico to access the thermal properties of the ocean surface being affected by the oil spill. Results of these measurements will be presented along with ancillary sensor data used to eliminate false signals including UV and Synthetic Aperture Radar (SAR

  13. Communication: Probing the absolute configuration of chiral molecules at aqueous interfaces

    SciTech Connect

    Lotze, Stephan Versluis, Jan; Olijve, Luuk L. C.; Schijndel, Luuk van; Milroy, Lech G.; Voets, Ilja K.; Bakker, Huib J.

    2015-11-28

    We demonstrate that the enantiomers of chiral macromolecules at an aqueous interface can be distinguished with monolayer sensitivity using heterodyne-detected vibrational sum-frequency generation (VSFG). We perform VSFG spectroscopy with a polarization combination that selectively probes chiral molecular structures. By using frequencies far detuned from electronic resonances, we probe the chiral macromolecular structures with high surface specificity. The phase of the sum-frequency light generated by the chiral molecules is determined using heterodyne detection. With this approach, we can distinguish right-handed and left-handed helical peptides at a water-air interface. We thus show that heterodyne-detected VSFG is sensitive to the absolute configuration of complex, interfacial macromolecules and has the potential to determine the absolute configuration of enantiomers at interfaces.

  14. Absolute Binding Free Energy Calculations: On the Accuracy of Computational Scoring of Protein-ligand Interactions

    PubMed Central

    Singh, Nidhi; Warshel, Arieh

    2010-01-01

    Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer-aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic Linear Response Approximation (LRA/β version) and its variants including the Linear Interaction Energy (LIE) to the more approximated and considerably faster scaled Protein Dipoles Langevin Dipoles (PDLD/S-LRA version), as well as the less rigorous Molecular Mechanics Poisson–Boltzmann/Surface Area (MM/PBSA) and Generalized Born/Surface Area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/β, the LIE, the PDLD/S-LRA/β and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the non-electrostatic term. On the average, the PDLD/S-LRA/β performs effectively. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies due to its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S-LRA/β appears to offer an appealing option for the final stages of massive screening approaches. PMID:20186976

  15. Mini-implants and miniplates generate sub-absolute and absolute anchorage

    PubMed Central

    Consolaro, Alberto

    2014-01-01

    The functional demand imposed on bone promotes changes in the spatial properties of osteocytes as well as in their extensions uniformly distributed throughout the mineralized surface. Once spatial deformation is established, osteocytes create the need for structural adaptations that result in bone formation and resorption that happen to meet the functional demands. The endosteum and the periosteum are the effectors responsible for stimulating adaptive osteocytes in the inner and outer surfaces.Changes in shape, volume and position of the jaws as a result of skeletal correction of the maxilla and mandible require anchorage to allow bone remodeling to redefine morphology, esthetics and function as a result of spatial deformation conducted by orthodontic appliances. Examining the degree of changes in shape, volume and structural relationship of areas where mini-implants and miniplates are placed allows us to classify mini-implants as devices of subabsolute anchorage and miniplates as devices of absolute anchorage. PMID:25162561

  16. An All Fiber White Light Interferometric Absolute Temperature Measurement System

    PubMed Central

    Kim, Jeonggon Harrison

    2008-01-01

    Recently the author of this article proposed a new signal processing algorithm for an all fiber white light interferometer. In this article, an all fiber white light interferometric absolute temperature measurement system is presented using the previously proposed signal processing algorithm. Stability and absolute temperature measurement were demonstrated. These two tests demonstrated the feasibility of absolute temperature measurement with an accuracy of 0.015 fringe and 0.0005 fringe, respectively. A hysteresis test from 373K to 873K was also presented. Finally, robustness of the sensor system towards laser diode temperature drift, AFMZI temperature drift and PZT non-linearity was demonstrated.

  17. Measurement of Disintegration Rates and Absolute {gamma}-ray Intensities

    SciTech Connect

    DeVries, Daniel J.; Griffin, Henry C.

    2006-03-13

    The majority of practical radioactive materials decay by modes that include {gamma}-ray emission. For questions of 'how much' or 'how pure', one must know the absolute intensities of the major radiations. We are using liquid scintillation counting (LSC) to measurements of disintegration rates, coupled with {gamma}-ray spectroscopy to measure absolute {gamma}-ray emission probabilities. Described is a study of the 227Th chain yielding absolute {gamma}-ray intensities with {approx}0.5% accuracy and information on LSC efficiencies.

  18. Absolute Antenna Calibration at the US National Geodetic Survey

    NASA Astrophysics Data System (ADS)

    Mader, G. L.; Bilich, A. L.

    2012-12-01

    Geodetic GNSS applications routinely demand millimeter precision and extremely high levels of accuracy. To achieve these accuracies, measurement and instrument biases at the centimeter to millimeter level must be understood. One of these biases is the antenna phase center, the apparent point of signal reception for a GNSS antenna. It has been well established that phase center patterns differ between antenna models and manufacturers; additional research suggests that the addition of a radome or the choice of antenna mount can significantly alter those a priori phase center patterns. For the more demanding GNSS positioning applications and especially in cases of mixed-antenna networks, it is all the more important to know antenna phase center variations as a function of both elevation and azimuth in the antenna reference frame and incorporate these models into analysis software. Determination of antenna phase center behavior is known as "antenna calibration". Since 1994, NGS has computed relative antenna calibrations for more than 350 antennas. In recent years, the geodetic community has moved to absolute calibrations - the IGS adopted absolute antenna phase center calibrations in 2006 for use in their orbit and clock products, and NGS's CORS group began using absolute antenna calibration upon the release of the new CORS coordinates in IGS08 epoch 2005.00 and NAD 83(2011,MA11,PA11) epoch 2010.00. Although NGS relative calibrations can be and have been converted to absolute, it is considered best practice to independently measure phase center characteristics in an absolute sense. Consequently, NGS has developed and operates an absolute calibration system. These absolute antenna calibrations accommodate the demand for greater accuracy and for 2-dimensional (elevation and azimuth) parameterization. NGS will continue to provide calibration values via the NGS web site www.ngs.noaa.gov/ANTCAL, and will publish calibrations in the ANTEX format as well as the legacy ANTINFO

  19. Cholesterol biosynthesis from lanosterol. Molecular cloning, tissue distribution, expression, chromosomal localization, and regulation of rat 7-dehydrocholesterol reductase, a Smith-Lemli-Opitz syndrome-related protein.

    PubMed

    Bae, S H; Lee, J N; Fitzky, B U; Seong, J; Paik, Y K

    1999-05-21

    The cDNA encoding the 471-amino acid rat 7-dehydrocholesterol reductase (DHCR), an enzyme that has been implicated in both cholesterol biosynthesis and developmental abnormalities (e.g. Smith-Lemli-Opitz syndrome) in mammals, has been cloned and sequenced, and the primary structure of the enzyme has been deduced. The DHCR gene was mapped to chromosome 8q2.1 by fluorescence in situ hybridization. Rat DHCR, calculated molecular mass of 54.15-kDa polypeptide, shares a close amino acid identity with mouse and human DHCRs (96 and 87%, respectively) as compared with its other related proteins (e.g. fungal sterol Delta14-reductase) and exhibits high hydrophobicity (>68%) with 9 transmembrane domains. Five putative sterol-sensing domains were predicted to be localized in transmembrane domains 4-8, which are highly homologous to those found in 3-hydroxymethylglutaryl-CoA reductase, sterol regulatory element-binding protein cleavage-activating protein, and patched protein. The polypeptide encoded by DHCR cDNA was expressed in yeast as a 55.45-kDa myc-tagged fusion protein, which was recognized with anti-myc monoclonal antibody 9E10 and shown to possess full DHCR activity with respect to dependence on NADPH and sensitivity to DHCR inhibitors. Northern blot analysis indicates that the highest expression of DHCR mRNA was detected in liver, followed by kidney and brain. In rat brains, the highest level of mRNA encoding DHCR was detected in the midbrain, followed by the spinal cord and medulla. Feeding rats 5% cholestyramine plus 0.1% lovastatin in chow resulted in both approximately a 3-fold induction of DHCR mRNA and a 5-fold increase of the enzymic activity in the liver. When rats were fed 0.1% (w/w) AY-9944 (in chow) for 14-days, a complete inhibition of DHCR activity and a significant reduction in serum total cholesterol level were observed. However, the level of hepatic DHCR mRNA fell only slightly, suggesting that AY-9944 may act more rapidly at the protein level than at

  20. Absolute frequency measurement at 10-16 level based on the international atomic time

    NASA Astrophysics Data System (ADS)

    Hachisu, H.; Fujieda, M.; Kumagai, M.; Ido, T.

    2016-06-01

    Referring to International Atomic Time (TAI), we measured the absolute frequency of the 87Sr lattice clock with its uncertainty of 1.1 x 10-15. Unless an optical clock is continuously operated for the five days of the TAI grid, it is required to evaluate dead time uncertainty in order to use the available five-day average of the local frequency reference. We homogeneously distributed intermittent measurements over the five-day grid of TAI, by which the dead time uncertainty was reduced to low 10-16 level. Three campaigns of the five (or four)-day consecutive measurements have resulted in the absolute frequency of the 87Sr clock transition of 429 228 004 229 872.85 (47) Hz, where the systematic uncertainty of the 87Sr optical frequency standard amounts to 8.6 x 10-17.

  1. Absolute pitch in infant auditory learning: evidence for developmental reorganization.

    PubMed

    Saffran, J R; Griepentrog, G J

    2001-01-01

    To what extent do infants represent the absolute pitches of complex auditory stimuli? Two experiments with 8-month-old infants examined the use of absolute and relative pitch cues in a tone-sequence statistical learning task. The results suggest that, given unsegmented stimuli that do not conform to the rules of musical composition, infants are more likely to track patterns of absolute pitches than of relative pitches. A 3rd experiment tested adults with or without musical training on the same statistical learning tasks used in the infant experiments. Unlike the infants, adult listeners relied primarily on relative pitch cues. These results suggest a shift from an initial focus on absolute pitch to the eventual dominance of relative pitch, which, it is argued, is more useful for both music and speech processing.

  2. Absolute calibration of sniffer probes on Wendelstein 7-X

    NASA Astrophysics Data System (ADS)

    Moseev, D.; Laqua, H. P.; Marsen, S.; Stange, T.; Braune, H.; Erckmann, V.; Gellert, F.; Oosterbeek, J. W.

    2016-08-01

    Here we report the first measurements of the power levels of stray radiation in the vacuum vessel of Wendelstein 7-X using absolutely calibrated sniffer probes. The absolute calibration is achieved by using calibrated sources of stray radiation and the implicit measurement of the quality factor of the Wendelstein 7-X empty vacuum vessel. Normalized absolute calibration coefficients agree with the cross-calibration coefficients that are obtained by the direct measurements, indicating that the measured absolute calibration coefficients and stray radiation levels in the vessel are valid. Close to the launcher, the stray radiation in the empty vessel reaches power levels up to 340 kW/m2 per MW injected beam power. Furthest away from the launcher, i.e., half a toroidal turn, still 90 kW/m2 per MW injected beam power is measured.

  3. Temporal Dynamics of Microbial Rhodopsin Fluorescence Reports Absolute Membrane Voltage

    PubMed Central

    Hou, Jennifer H.; Venkatachalam, Veena; Cohen, Adam E.

    2014-01-01

    Plasma membrane voltage is a fundamentally important property of a living cell; its value is tightly coupled to membrane transport, the dynamics of transmembrane proteins, and to intercellular communication. Accurate measurement of the membrane voltage could elucidate subtle changes in cellular physiology, but existing genetically encoded fluorescent voltage reporters are better at reporting relative changes than absolute numbers. We developed an Archaerhodopsin-based fluorescent voltage sensor whose time-domain response to a stepwise change in illumination encodes the absolute membrane voltage. We validated this sensor in human embryonic kidney cells. Measurements were robust to variation in imaging parameters and in gene expression levels, and reported voltage with an absolute accuracy of 10 mV. With further improvements in membrane trafficking and signal amplitude, time-domain encoding of absolute voltage could be applied to investigate many important and previously intractable bioelectric phenomena. PMID:24507604

  4. Absolute Value Boundedness, Operator Decomposition, and Stochastic Media and Equations

    NASA Technical Reports Server (NTRS)

    Adomian, G.; Miao, C. C.

    1973-01-01

    The research accomplished during this period is reported. Published abstracts and technical reports are listed. Articles presented include: boundedness of absolute values of generalized Fourier coefficients, propagation in stochastic media, and stationary conditions for stochastic differential equations.

  5. Absolute calibration of sniffer probes on Wendelstein 7-X.

    PubMed

    Moseev, D; Laqua, H P; Marsen, S; Stange, T; Braune, H; Erckmann, V; Gellert, F; Oosterbeek, J W

    2016-08-01

    Here we report the first measurements of the power levels of stray radiation in the vacuum vessel of Wendelstein 7-X using absolutely calibrated sniffer probes. The absolute calibration is achieved by using calibrated sources of stray radiation and the implicit measurement of the quality factor of the Wendelstein 7-X empty vacuum vessel. Normalized absolute calibration coefficients agree with the cross-calibration coefficients that are obtained by the direct measurements, indicating that the measured absolute calibration coefficients and stray radiation levels in the vessel are valid. Close to the launcher, the stray radiation in the empty vessel reaches power levels up to 340 kW/m(2) per MW injected beam power. Furthest away from the launcher, i.e., half a toroidal turn, still 90 kW/m(2) per MW injected beam power is measured. PMID:27587121

  6. Preparation of an oakmoss absolute with reduced allergenic potential.

    PubMed

    Ehret, C; Maupetit, P; Petrzilka, M; Klecak, G

    1992-06-01

    Synopsis Oakmoss absolute, an extract of the lichen Evernia prunastri, is known to cause allergenic skin reactions due to the presence of certain aromatic aldehydes such as atranorin, chloratranorin, ethyl hematommate and ethyl chlorohematommate. In this paper it is shown that treatment of Oakmoss absolute with amino acids such as lysine and/or leucine, lowers considerably the content of these allergenic constituents including atranol and chloratranol. The resulting Oakmoss absolute, which exhibits an excellent olfactive quality, was tested extensively in comparative studies on guinea pigs and on man. The results of the Guinea Pig Maximization Test (GPMT) and Human Repeated Insult Patch Test (HRIPT) indicate that, in comparison with the commercial test sample, the allergenicity of this new quality of Oakmoss absolute was considerably reduced, and consequently better skin tolerance of this fragrance for man was achieved. PMID:19272096

  7. Absolute Free Energies for Biomolecules in Implicit or Explicit Solvent

    NASA Astrophysics Data System (ADS)

    Berryman, Joshua T.; Schilling, Tanja

    Methods for absolute free energy calculation by alchemical transformation of a quantitative model to an analytically tractable one are discussed. These absolute free energy methods are placed in the context of other methods, and an attempt is made to describe the best practice for such calculations given the current state of the art. Calculations of the equilibria between the four free energy basins of the dialanine molecule and the two right- and left-twisted basins of DNA are discussed as examples.

  8. Heat capacity and absolute entropy of iron phosphides

    SciTech Connect

    Dobrokhotova, Z.V.; Zaitsev, A.I.; Litvina, A.D.

    1994-09-01

    There is little or no data on the thermodynamic properties of iron phosphides despite their importance for several areas of science and technology. The information available is of a qualitative character and is based on assessments of the heat capacity and absolute entropy. In the present work, we measured the heat capacity over the temperature range of 113-873 K using a differential scanning calorimeter (DSC) and calculated the absolute entropy.

  9. Microfabricated Collector-Generator Electrode Sensor for Measuring Absolute pH and Oxygen Concentrations.

    PubMed

    Dengler, Adam K; Wightman, R Mark; McCarty, Gregory S

    2015-10-20

    Fast-scan cyclic voltammetry (FSCV) has attracted attention for studying in vivo neurotransmission due to its subsecond temporal resolution, selectivity, and sensitivity. Traditional FSCV measurements use background subtraction to isolate changes in the local electrochemical environment, providing detailed information on fluctuations in the concentration of electroactive species. This background subtraction removes information about constant or slowly changing concentrations. However, determination of background concentrations is still important for understanding functioning brain tissue. For example, neural activity is known to consume oxygen and produce carbon dioxide which affects local levels of oxygen and pH. Here, we present a microfabricated microelectrode array which uses FSCV to detect the absolute levels of oxygen and pH in vitro. The sensor is a collector-generator electrode array with carbon microelectrodes spaced 5 μm apart. In this work, a periodic potential step is applied at the generator producing transient local changes in the electrochemical environment. The collector electrode continuously performs FSCV enabling these induced changes in concentration to be recorded with the sensitivity and selectivity of FSCV. A negative potential step applied at the generator produces a transient local pH shift at the collector. The generator-induced pH signal is detected using FSCV at the collector and correlated to absolute solution pH by postcalibration of the anodic peak position. In addition, in oxygenated solutions a negative potential step at the generator produces hydrogen peroxide by reducing oxygen. Hydrogen peroxide is detected with FSCV at the collector electrode, and the magnitude of the oxidative peak is proportional to absolute oxygen concentrations. Oxygen interference on the pH signal is minimal and can be accounted for with a postcalibration.

  10. Separation of Betti Reaction Product Enantiomers: Absolute Configuration and Inhibition of Botulinum Neurotoxin A

    PubMed Central

    2011-01-01

    The racemic product of the Betti reaction of 5-chloro-8-hydroxyquinoline, benzaldehyde, and 2-aminopyridine was separated by chiral HPLC to determine which enantiomer inhibited botulinum neurotoxin serotype A. When the enantiomers unexpectedly proved to have comparable activity, the absolute structures of (+)-(R)-1 and (−)-(S)-1 were determined by comparison of calculated and observed circular dichroism spectra. Molecular modeling studies were undertaken in an effort to understand the observed bioactivity and revealed different ensembles of binding modes, with roughly equal binding energies, for the two enantiomers. PMID:22102940

  11. Determination of the Absolute Configurations of Chiral Drugs Using Chiroptical Spectroscopy.

    PubMed

    Polavarapu, Prasad L

    2016-01-01

    Chiroptical spectroscopy has emerged as a promising tool for the determination of absolute configurations and predominant conformations of chiral molecules in academic laboratories. This promise has led to the adaption of chiroptical spectroscopic methods as valuable tools in chiral drug discovery research programs of the pharmaceutical industry. Most major pharmaceutical companies have invested in in-house chiroptical spectroscopy applications and reported successful outcomes. In the context of continuously increasing applications of chiroptical spectroscopy for chiral molecular structure determination, a review of recent developments and applications for chiral drugs is presented in this manuscript. PMID:27529201

  12. Global absolut gravity reference system as replacement of IGSN 71

    NASA Astrophysics Data System (ADS)

    Wilmes, Herbert; Wziontek, Hartmut; Falk, Reinhard

    2015-04-01

    The determination of precise gravity field parameters is of great importance in a period in which earth sciences are achieving the necessary accuracy to monitor and document global change processes. This is the reason why experts from geodesy and metrology joined in a successful cooperation to make absolute gravity observations traceable to SI quantities, to improve the metrological kilogram definition and to monitor mass movements and smallest height changes for geodetic and geophysical applications. The international gravity datum is still defined by the International Gravity Standardization Net adopted in 1971 (IGSN 71). The network is based upon pendulum and spring gravimeter observations taken in the 1950s and 60s supported by the early free fall absolute gravimeters. Its gravity values agreed in every case to better than 0.1 mGal. Today, more than 100 absolute gravimeters are in use worldwide. The series of repeated international comparisons confirms the traceability of absolute gravity measurements to SI quantities and confirm the degree of equivalence of the gravimeters in the order of a few µGal. For applications in geosciences where e.g. gravity changes over time need to be analyzed, the temporal stability of an absolute gravimeter is most important. Therefore, the proposition is made to replace the IGSN 71 by an up-to-date gravity reference system which is based upon repeated absolute gravimeter comparisons and a global network of well controlled gravity reference stations.

  13. Method to obtain absolute impurity density profiles combining charge exchange and beam emission spectroscopy without absolute intensity calibrationa)

    NASA Astrophysics Data System (ADS)

    Kappatou, A.; Jaspers, R. J. E.; Delabie, E.; Marchuk, O.; Biel, W.; Jakobs, M. A.

    2012-10-01

    Investigation of impurity transport properties in tokamak plasmas is essential and a diagnostic that can provide information on the impurity content is required. Combining charge exchange recombination spectroscopy (CXRS) and beam emission spectroscopy (BES), absolute radial profiles of impurity densities can be obtained from the CXRS and BES intensities, electron density and CXRS and BES emission rates, without requiring any absolute calibration of the spectra. The technique is demonstrated here with absolute impurity density radial profiles obtained in TEXTOR plasmas, using a high efficiency charge exchange spectrometer with high etendue, that measures the CXRS and BES spectra along the same lines-of-sight, offering an additional advantage for the determination of absolute impurity densities.

  14. Physical localization of molecular markers and assignment of the 15th linkage group to chromosome 11 of the karyotype in cassava (Manihot esculenta Crantz) by primed in situ labeling.

    PubMed

    Wang, Y; Wang, J F; Yin, H; Gao, H Q; Zhuang, N S; Liu, J P

    2015-07-28

    Physical localization of molecular markers and assignment of the 15th linkage group to chromosome 11 of the karyotype in cassava (Manihot esculenta Crantz) were achieved using primed in situ labeling. Amplified signals for both the EST507-1 and SSRY13-5 markers were consistently observed in different stages of cell division. A comparison of the length, arm ratio, and other morphological characteristics of somatic metaphase chromosomes in karyotype analysis indicated that the EST507-1 and SSRY13-5 markers were localized on the short and long arm of cassava chromosome 11 with the relative map positions of 41.67 and 23.07, respectively. The physical localization of the 2 markers on chromosome 11 of the karyotype corresponds to their positions on the 15th linkage group in cassava.

  15. Absolute irradiance of the Moon for on-orbit calibration

    USGS Publications Warehouse

    Stone, T.C.; Kieffer, H.H.; ,

    2002-01-01

    The recognized need for on-orbit calibration of remote sensing imaging instruments drives the ROLO project effort to characterize the Moon for use as an absolute radiance source. For over 5 years the ground-based ROLO telescopes have acquired spatially-resolved lunar images in 23 VNIR (Moon diameter ???500 pixels) and 9 SWIR (???250 pixels) passbands at phase angles within ??90 degrees. A numerical model for lunar irradiance has been developed which fits hundreds of ROLO images in each band, corrected for atmospheric extinction and calibrated to absolute radiance, then integrated to irradiance. The band-coupled extinction algorithm uses absorption spectra of several gases and aerosols derived from MODTRAN to fit time-dependent component abundances to nightly observations of standard stars. The absolute radiance scale is based upon independent telescopic measurements of the star Vega. The fitting process yields uncertainties in lunar relative irradiance over small ranges of phase angle and the full range of lunar libration well under 0.5%. A larger source of uncertainty enters in the absolute solar spectral irradiance, especially in the SWIR, where solar models disagree by up to 6%. Results of ROLO model direct comparisons to spacecraft observations demonstrate the ability of the technique to track sensor responsivity drifts to sub-percent precision. Intercomparisons among instruments provide key insights into both calibration issues and the absolute scale for lunar irradiance.

  16. Absolute neutrophil values in malignant patients on cytotoxic chemotherapy.

    PubMed

    Madu, A J; Ibegbulam, O G; Ocheni, S; Madu, K A; Aguwa, E N

    2011-01-01

    A total of eighty patients with various malignancies seen between September 2008 and April 2009 at the University of Nigeria Teaching Hospital (UNTH) Ituku Ozalla, Enugu, Nigeria, had their absolute neutrophil counts, done at Days 0 and 12 of the first cycle of their various chemotherapeutic regimens. They were adult patients who had been diagnosed of various malignancies, consisting of Breast cancer 36 (45%), Non-Hodgkin's lymphoma 8 (10%), Hodgkin's lymphoma 13 (16.25%), Colorectal carcinoma 6 (7.5%), Multiple myeloma 7 (8.75%), Cervical carcinoma 1 (1.25%) and other malignancies 9 (11.25%), Manual counting of absolute neutrophil count was done using Turks solution and improved Neubauer counting chamber and Galen 2000 Olympus microscope. The socio demographic data of the patients were assessed from a questionnaire. There were 27 males (33.75%) and 53 females (66.25%). Their ages ranged from 18 - 80 years with a median of 45 years. The mean absolute neutrophil count of the respondents pre-and post chemotherapy was 3.7 +/- 2.1 x 10(9)/L and 2.5 +/- 1.6 x 10(9)/L respectively. There were significant differences in both the absolute neutrophil count (p=0.00) compared to the pre-chemotherapy values. Chemotherapeutic combinations containing cyclophosphamide and Adriamycin were observed to cause significant reduction in absolute neutrophil.

  17. The Application of Optimisation Methods to Constrain Absolute Plate Motions

    NASA Astrophysics Data System (ADS)

    Tetley, M. G.; Williams, S.; Hardy, S.; Müller, D.

    2015-12-01

    Plate tectonic reconstructions are an excellent tool for understanding the configuration and behaviour of continents through time on both global and regional scales, and are relatively well understood back to ~200 Ma. However, many of these models represent only relative motions between continents, providing little information of absolute tectonic motions and their relationship with the deep Earth. Significant issues exist in solving this problem, including how to combine constraints from multiple, diverse data into a unified model of absolute plate motions; and how to address uncertainties both in the available data, and in the assumptions involved in this process (e.g. hotspot motion, true polar wander). In deep time (pre-Pangea breakup), plate reconstructions rely more heavily on paleomagnetism, but these data often imply plate velocities much larger than those observed since the breakup of the supercontinent Pangea where plate velocities are constrained by the seafloor spreading record. Here we present two complementary techniques to address these issues, applying parallelized numerical methods to quantitatively investigate absolute plate motions through time. Firstly, we develop a data-fit optimized global absolute reference frame constrained by kinematic reconstruction data, hotspot-trail observations, and trench migration statistics. Secondly we calculate optimized paleomagnetic data-derived apparent polar wander paths (APWPs) for both the Phanerozoic and Precambrian. Paths are generated from raw pole data with optimal spatial and temporal pole configurations calculated using all known uncertainties and quality criteria to produce velocity-optimized absolute motion paths through deep time.

  18. The Interplay Between Conformation and Absolute Configuration in Chiral Electron Dynamics of Small Diols.

    PubMed

    Daly, Steven; Tia, Maurice; Garcia, Gustavo A; Nahon, Laurent; Powis, Ivan

    2016-09-01

    A competition between chiral characteristics alternatively attributable to either conformation or to absolute configuration is identified. Circular dichroism associated with photoexcitation of the outer orbital of configurational enantiomers of 1,3- and 2,3-butanediols has been examined with a focus on the large changes in electron chiral asymmetry produced by different molecular conformations. Experimental gas-phase measurements offer support for the theoretical modeling of this chiroptical effect. A surprising prediction is that a conformationally produced pseudo-enantiomerism in 1,3-butanediol generates a chiral response in the frontier electron dynamics that outweighs the influence of the permanent configurational handedness established at the asymmetrically substituted carbon. Induced conformation, and specifically induced conformational chirality, may thus be a dominating factor in chiral molecular recognition in such systems. PMID:27445202

  19. Principle of relative locality

    SciTech Connect

    Amelino-Camelia, Giovanni; Freidel, Laurent; Smolin, Lee; Kowalski-Glikman, Jerzy

    2011-10-15

    We propose a deepening of the relativity principle according to which the invariant arena for nonquantum physics is a phase space rather than spacetime. Descriptions of particles propagating and interacting in spacetimes are constructed by observers, but different observers, separated from each other by translations, construct different spacetime projections from the invariant phase space. Nonetheless, all observers agree that interactions are local in the spacetime coordinates constructed by observers local to them. This framework, in which absolute locality is replaced by relative locality, results from deforming energy-momentum space, just as the passage from absolute to relative simultaneity results from deforming the linear addition of velocities. Different aspects of energy-momentum space geometry, such as its curvature, torsion and nonmetricity, are reflected in different kinds of deformations of the energy-momentum conservation laws. These are in principle all measurable by appropriate experiments. We also discuss a natural set of physical hypotheses which singles out the cases of energy-momentum space with a metric compatible connection and constant curvature.

  20. Absolute configuration and crystal packing for three chiral drugs prone to spontaneous resolution: Guaifenesin, methocarbamol and mephenesin

    NASA Astrophysics Data System (ADS)

    Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Krivolapov, Dmitry B.; Pashagin, Alexander V.; Litvinov, Igor A.

    2009-02-01

    Popular chiral drugs, guaifenesin, methocarbamol, and mephenesin were investigated by single-crystal X-ray analysis both for enantiopure and racemic samples. The absolute configurations for all substances were established through Flack parameter method. The conglomerate-forming nature for the compounds was confirmed by equivalence of crystal characteristics of enantiopure and racemic samples. The molecular structures and crystal packing details were evaluated and compared with one another for all three investigated substances.

  1. Method for estimating absolute lung volumes at constant inflation pressure.

    PubMed

    Hills, B A; Barrow, R E

    1979-10-01

    A method has been devised for measuring functional residual capacity in the intact killed animal or absolute lung volumes in any excised lung preparation without changing the inflation pressure. This is achieved by titrating the absolute pressure of a chamber in which the preparation is compressed until a known volume of air has entered the lungs. This technique was used to estimate the volumes of five intact rabbit lungs and five rigid containers of known dimensions by means of Boyle's law. Results were found to agree to within +/- 1% with values determined by alternative methods. In the discussion the advantage of determining absolute lung volumes at almost any stage in a study of lung mechanics without the determination itself changing inflation pressure and, hence, lung volume is emphasized. PMID:511699

  2. System and method for calibrating a rotary absolute position sensor

    NASA Technical Reports Server (NTRS)

    Davis, Donald R. (Inventor); Permenter, Frank Noble (Inventor); Radford, Nicolaus A (Inventor)

    2012-01-01

    A system includes a rotary device, a rotary absolute position (RAP) sensor generating encoded pairs of voltage signals describing positional data of the rotary device, a host machine, and an algorithm. The algorithm calculates calibration parameters usable to determine an absolute position of the rotary device using the encoded pairs, and is adapted for linearly-mapping an ellipse defined by the encoded pairs to thereby calculate the calibration parameters. A method of calibrating the RAP sensor includes measuring the rotary position as encoded pairs of voltage signals, linearly-mapping an ellipse defined by the encoded pairs to thereby calculate the calibration parameters, and calculating an absolute position of the rotary device using the calibration parameters. The calibration parameters include a positive definite matrix (A) and a center point (q) of the ellipse. The voltage signals may include an encoded sine and cosine of a rotary angle of the rotary device.

  3. Method and apparatus for two-dimensional absolute optical encoding

    NASA Technical Reports Server (NTRS)

    Leviton, Douglas B. (Inventor)

    2004-01-01

    This invention presents a two-dimensional absolute optical encoder and a method for determining position of an object in accordance with information from the encoder. The encoder of the present invention comprises a scale having a pattern being predetermined to indicate an absolute location on the scale, means for illuminating the scale, means for forming an image of the pattern; and detector means for outputting signals derived from the portion of the image of the pattern which lies within a field of view of the detector means, the field of view defining an image reference coordinate system, and analyzing means, receiving the signals from the detector means, for determining the absolute location of the object. There are two types of scale patterns presented in this invention: grid type and starfield type.

  4. PHASES: A Project to Perform Absolute Spectrophotometry from Space

    NASA Astrophysics Data System (ADS)

    del Burgo, C.; Vather, D.; Allende Prieto, C.; Murphy, N.

    2013-04-01

    This paper presents the current status of the opto-mechanical design of PHASES (Planet Hunting and AsteroSeismology Explorer Spectrophotometer), which is a project to develop a space-borne telescope to obtain absolute flux calibrated spectra of bright stars. The science payload is intended to be housed in a micro-satellite launched into a low-earth Sun-synchronous orbit with an inclination to the equator of 98.7° and a local time ascending node LTAN of 6:00 AM. PHASES will be able to measure micromagnitude photometric variations due to stellar oscillations/activity and planet/moon transits. It consists of a 20 cm aperture modified Baker telescope feeding two detectors: the tracking detector provides the fine telescope guidance system with a required pointing stability of 0.2″, and the science detector performs spectrophotometry in the wavelength range 370-960 nm with a resolving power between 200 and 900. The spectrograph is designed to provide 1% RMS flux calibrated spectra with signal-to-noise ratios > 100 for stars with V < 10 in short integration times. Our strategy to calibrate the system using A type stars is explained. From comparison with model atmospheres it would be possible to determine the stellar angular diameters with an uncertainty of approximately 0.5%. In the case of a star hosting a transiting planet it would be possible to derive its light curve, and then the planet to stellar radius ratio. Bright stars have high precision Hipparcos parallaxes and the expected level of accuracy for their fluxes will be propagated to the stellar radii, and more significantly to the planetary radii. The scientific drivers for PHASES give rise to some design challenges, which are particularly related to the opto-mechanics for extreme environmental conditions. The optical design has been developed with the primary goal of avoiding stray light reaching the science detector. Three different proposals for the opto-mechanical design are under investigation.

  5. Neural Sensitivity to Absolute and Relative Anticipated Reward in Adolescents

    PubMed Central

    Vaidya, Jatin G.; Knutson, Brian; O'Leary, Daniel S.; Block, Robert I.; Magnotta, Vincent

    2013-01-01

    Adolescence is associated with a dramatic increase in risky and impulsive behaviors that have been attributed to developmental differences in neural processing of rewards. In the present study, we sought to identify age differences in anticipation of absolute and relative rewards. To do so, we modified a commonly used monetary incentive delay (MID) task in order to examine brain activity to relative anticipated reward value (neural sensitivity to the value of a reward as a function of other available rewards). This design also made it possible to examine developmental differences in brain activation to absolute anticipated reward magnitude (the degree to which neural activity increases with increasing reward magnitude). While undergoing fMRI, 18 adolescents and 18 adult participants were presented with cues associated with different reward magnitudes. After the cue, participants responded to a target to win money on that trial. Presentation of cues was blocked such that two reward cues associated with $.20, $1.00, or $5.00 were in play on a given block. Thus, the relative value of the $1.00 reward varied depending on whether it was paired with a smaller or larger reward. Reflecting age differences in neural responses to relative anticipated reward (i.e., reference dependent processing), adults, but not adolescents, demonstrated greater activity to a $1 reward when it was the larger of the two available rewards. Adults also demonstrated a more linear increase in ventral striatal activity as a function of increasing absolute reward magnitude compared to adolescents. Additionally, reduced ventral striatal sensitivity to absolute anticipated reward (i.e., the difference in activity to medium versus small rewards) correlated with higher levels of trait Impulsivity. Thus, ventral striatal activity in anticipation of absolute and relative rewards develops with age. Absolute reward processing is also linked to individual differences in Impulsivity. PMID:23544046

  6. Neural sensitivity to absolute and relative anticipated reward in adolescents.

    PubMed

    Vaidya, Jatin G; Knutson, Brian; O'Leary, Daniel S; Block, Robert I; Magnotta, Vincent

    2013-01-01

    Adolescence is associated with a dramatic increase in risky and impulsive behaviors that have been attributed to developmental differences in neural processing of rewards. In the present study, we sought to identify age differences in anticipation of absolute and relative rewards. To do so, we modified a commonly used monetary incentive delay (MID) task in order to examine brain activity to relative anticipated reward value (neural sensitivity to the value of a reward as a function of other available rewards). This design also made it possible to examine developmental differences in brain activation to absolute anticipated reward magnitude (the degree to which neural activity increases with increasing reward magnitude). While undergoing fMRI, 18 adolescents and 18 adult participants were presented with cues associated with different reward magnitudes. After the cue, participants responded to a target to win money on that trial. Presentation of cues was blocked such that two reward cues associated with $.20, $1.00, or $5.00 were in play on a given block. Thus, the relative value of the $1.00 reward varied depending on whether it was paired with a smaller or larger reward. Reflecting age differences in neural responses to relative anticipated reward (i.e., reference dependent processing), adults, but not adolescents, demonstrated greater activity to a $1 reward when it was the larger of the two available rewards. Adults also demonstrated a more linear increase in ventral striatal activity as a function of increasing absolute reward magnitude compared to adolescents. Additionally, reduced ventral striatal sensitivity to absolute anticipated reward (i.e., the difference in activity to medium versus small rewards) correlated with higher levels of trait Impulsivity. Thus, ventral striatal activity in anticipation of absolute and relative rewards develops with age. Absolute reward processing is also linked to individual differences in Impulsivity. PMID:23544046

  7. Non-Invasive Method of Determining Absolute Intracranial Pressure

    NASA Technical Reports Server (NTRS)

    Yost, William T. (Inventor); Cantrell, John H., Jr. (Inventor); Hargens, Alan E. (Inventor)

    2004-01-01

    A method is presented for determining absolute intracranial pressure (ICP) in a patient. Skull expansion is monitored while changes in ICP are induced. The patient's blood pressure is measured when skull expansion is approximately zero. The measured blood pressure is indicative of a reference ICP value. Subsequently, the method causes a known change in ICP and measured the change in skull expansion associated therewith. The absolute ICP is a function of the reference ICP value, the known change in ICP and its associated change in skull expansion; and a measured change in skull expansion.

  8. Absolutely maximally entangled states, combinatorial designs, and multiunitary matrices

    NASA Astrophysics Data System (ADS)

    Goyeneche, Dardo; Alsina, Daniel; Latorre, José I.; Riera, Arnau; Życzkowski, Karol

    2015-09-01

    Absolutely maximally entangled (AME) states are those multipartite quantum states that carry absolute maximum entanglement in all possible bipartitions. AME states are known to play a relevant role in multipartite teleportation, in quantum secret sharing, and they provide the basis novel tensor networks related to holography. We present alternative constructions of AME states and show their link with combinatorial designs. We also analyze a key property of AME states, namely, their relation to tensors, which can be understood as unitary transformations in all of their bipartitions. We call this property multiunitarity.

  9. In-flight absolute radiometric calibration of the thematic mapper

    NASA Technical Reports Server (NTRS)

    Castle, K. R.; Holm, R. G.; Kastner, C. J.; Palmer, J. M.; Slater, P. N.; Dinguirard, M.; Ezra, C. E.; Jackson, R. D.; Savage, R. K.

    1983-01-01

    The TM multispectral scanner system was calibrated in an absolute manner before launch. To determine the temporal changes of the absolute radiometric calibration of the entire system, spectroradiometric measurements of the ground and the atmosphere were made simultaneously with TM collections over White Sands, New Mexico. By entering the measured values in an atmospheric radiative transfer program, the radiance levels of the in four of the spectral bands of the TM were determined. Tables show values for the reflectance of snow at White Sands measured by a modular 8 channel radiometer, and values for exoatmospheric irradiance within the TM passbands, calculated for the Earth-Sun distance using a solar radiometer.

  10. Absolute photon-flux measurements in the vacuum ultraviolet

    NASA Technical Reports Server (NTRS)

    Samson, J. A. R.; Haddad, G. N.

    1974-01-01

    Absolute photon-flux measurements in the vacuum ultraviolet have extended to short wavelengths by use of rare-gas ionization chambers. The technique involves the measurement of the ion current as a function of the gas pressure in the ion chamber. The true value of the ion current, and hence the absolute photon flux, is obtained by extrapolating the ion current to zero gas pressure. Examples are given at 162 and 266 A. The short-wavelength limit is determined only by the sensitivity of the current-measuring apparatus and by present knowledge of the photoionization processes that occur in the rate gases.

  11. Measurements of the reactor neutron power in absolute units

    SciTech Connect

    Lebedev, G. V.

    2015-12-15

    The neutron power of the reactor of the Yenisei space nuclear power plant is measured in absolute units using the modernized method of correlation analysis during the ground-based tests of the Yenisei prototypes. Results of the experiments are given. The desired result is obtained in a series of experiments carried out at the stage of the plant preparation for tests. The acceptability of experimental data is confirmed by the results of measuring the reactor neutron power in absolute units at the nominal level by the thermal balance during the life cycle tests of the ground prototypes.

  12. Absolute Stability Analysis of a Phase Plane Controlled Spacecraft

    NASA Technical Reports Server (NTRS)

    Jang, Jiann-Woei; Plummer, Michael; Bedrossian, Nazareth; Hall, Charles; Jackson, Mark; Spanos, Pol

    2010-01-01

    Many aerospace attitude control systems utilize phase plane control schemes that include nonlinear elements such as dead zone and ideal relay. To evaluate phase plane control robustness, stability margin prediction methods must be developed. Absolute stability is extended to predict stability margins and to define an abort condition. A constrained optimization approach is also used to design flex filters for roll control. The design goal is to optimize vehicle tracking performance while maintaining adequate stability margins. Absolute stability is shown to provide satisfactory stability constraints for the optimization.

  13. From Hubble's Next Generation Spectral Library (NGSL) to Absolute Fluxes

    NASA Astrophysics Data System (ADS)

    Heap, S. R.; Lindler, D.

    2016-05-01

    Hubble's Next Generation Spectral Library (NGSL) consists of R˜1000 spectra of 374 stars of assorted temperature, gravity, and metallicity. Each spectrum covers the wavelength range, 0.18-1.03 μ. The library can be viewed and/or downloaded from the website, http://archive.stsci.edu/prepds/stisngsl/. Stars in the NGSL are now being used as absolute flux standards at ground-based observatories. However, the uncertainty in the absolute flux is about 2%, which does not meet the requirements of dark-energy surveys. We have therefore developed an observing procedure, data-reduction procedure, and correction algorithms that should yield fluxes with uncertainties less than 1%.

  14. STS-9 Shuttle grow - Ram angle effect and absolute intensities

    NASA Technical Reports Server (NTRS)

    Swenson, G. R.; Mende, S. B.; Clifton, K. S.

    1986-01-01

    Visible imagery from Space Shuttle mission STS-9 (Spacelab 1) has been analyzed for the ram angle effect and the absolute intensity of glow. The data are compared with earlier measurements and the anomalous high intensities at large ram angles are confirmed. Absolute intensities of the ram glow on the shuttle tile, at 6563 A, are observed to be about 20 times more intense than those measured on the AE-E spacecraft. Implications of these observations for an existing theory of glow involving NO2 are presented.

  15. Bone mineralization is regulated by signaling cross talk between molecular factors of local and systemic origin: the role of fibroblast growth factor 23.

    PubMed

    Sapir-Koren, Rony; Livshits, Gregory

    2014-01-01

    Body phosphate homeostasis is regulated by a hormonal counter-balanced intestine-bone-kidney axis. The major systemic hormones involved in this axis are parathyroid hormone (PTH), 1,25-dihydroxyvitamin-D, and fibroblast growth factor-23 (FGF23). FGF23, produced almost exclusively by the osteocytes, is a phosphaturic hormone that plays a major role in regulation of the bone remodeling process. Remodeling composite components, bone mineralization and resorption cycles create a continuous influx-efflux loop of the inorganic phosphate (Pi) through the skeleton. This "bone Pi loop," which is formed, is controlled by local and systemic factors according to phosphate homeostasis demands. Although FGF23 systemic actions in the kidney, and for the production of PTH and 1,25-dihydroxyvitamin-D are well established, its direct involvement in bone metabolism is currently poorly understood. This review presents the latest available evidence suggesting two aspects of FGF23 bone local activity: (a) Regulation of FGF23 production by both local and systemic factors. The suggested local factors include extracellular levels of Pi and pyrophosphate (PPi), (the Pi/PPi ratio), and another osteocyte-derived protein, sclerostin. In addition, 1,25-dihydroxyvitamin-D, synthesized locally by bone cells, may contribute to regulation of FGF23 production. The systemic control is achieved via PTH and 1,25-dihydroxyvitamin-D endocrine functions. (b) FGF23 acts as a local agent, directly affecting bone mineralization. We support the assumption that under balanced physiological conditions, sclerostin, by para- autocrine signaling, upregulates FGF23 production by the osteocyte. FGF23, in turn, acts as a mineralization inhibitor, by stimulating the generation of the major mineralization antagonist-PPi.

  16. Two-dimensional weak anti-localization in Bi{sub 2}Te{sub 3} thin film grown on Si(111)-(7 Multiplication-Sign 7) surface by molecular beam epitaxy

    SciTech Connect

    Roy, Anupam; Guchhait, Samaresh; Sonde, Sushant; Dey, Rik; Pramanik, Tanmoy; Rai, Amritesh; Movva, Hema C. P.; Banerjee, Sanjay K.; Colombo, Luigi

    2013-04-22

    We report on low temperature transport studies of Bi{sub 2}Te{sub 3} topological insulator thin films grown on Si(111)-(7 Multiplication-Sign 7) surface by molecular beam epitaxy. A sharp increase in the magnetoresistance with magnetic field at low temperature indicates the existence of weak anti-localization. The measured weak anti-localization effect agrees well with the Hikami-Larkin-Nagaoka model, and the extracted phase coherence length shows a power-law dependence with temperature indicating the existence of a two-dimensional system. An insulating ground state has also been observed at low temperature showing a logarithmic divergence of the resistance that appears to be the influence of electron-electron interaction in a two-dimensional system.

  17. Molecular thermometry.

    PubMed

    McCabe, Kevin M; Hernandez, Mark

    2010-05-01

    Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients' temperatures could be measured, recorded, and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review, the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nanoscale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even subcellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic, this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia-based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry rapidly moved into the clinic, so too will these molecular thermometers.

  18. Molecular Thermometry

    PubMed Central

    McCabe, Kevin M.; Hernandez, Mark

    2010-01-01

    Conventional temperature measurements rely on material responses to heat, which can be detected visually. When Galileo developed an air expansion based device to detect temperature changes, Santorio, a contemporary physician, added a scale to create the first thermometer. With this instrument, patients’ temperatures could be measured, recorded and related to changing health conditions. Today, advances in materials science and bioengineering provide new ways to report temperature at the molecular level in real time. In this review the scientific foundations and history of thermometry underpin a discussion of the discoveries emerging from the field of molecular thermometry. Intracellular nanogels and heat sensing biomolecules have been shown to accurately report temperature changes at the nano-scale. Various systems will soon provide the ability to accurately measure temperature changes at the tissue, cellular, and even sub-cellular level, allowing for detection and monitoring of very small changes in local temperature. In the clinic this will lead to enhanced detection of tumors and localized infection, and accurate and precise monitoring of hyperthermia based therapies. Some nanomaterial systems have even demonstrated a theranostic capacity for heat-sensitive, local delivery of chemotherapeutics. Just as early thermometry moved into the clinic, so too will these molecular thermometers. PMID:20139796

  19. Mathematical Model for Absolute Magnetic Measuring Systems in Industrial Applications

    NASA Astrophysics Data System (ADS)

    Fügenschuh, Armin; Fügenschuh, Marzena; Ludszuweit, Marina; Mojsic, Aleksandar; Sokół, Joanna

    2015-09-01

    Scales for measuring systems are either based on incremental or absolute measuring methods. Incremental scales need to initialize a measurement cycle at a reference point. From there, the position is computed by counting increments of a periodic graduation. Absolute methods do not need reference points, since the position can be read directly from the scale. The positions on the complete scales are encoded using two incremental tracks with different graduation. We present a new method for absolute measuring using only one track for position encoding up to micrometre range. Instead of the common perpendicular magnetic areas, we use a pattern of trapezoidal magnetic areas, to store more complex information. For positioning, we use the magnetic field where every position is characterized by a set of values measured by a hall sensor array. We implement a method for reconstruction of absolute positions from the set of unique measured values. We compare two patterns with respect to uniqueness, accuracy, stability and robustness of positioning. We discuss how stability and robustness are influenced by different errors during the measurement in real applications and how those errors can be compensated.

  20. Absolute Value Inequalities: High School Students' Solutions and Misconceptions

    ERIC Educational Resources Information Center

    Almog, Nava; Ilany, Bat-Sheva

    2012-01-01

    Inequalities are one of the foundational subjects in high school math curricula, but there is a lack of academic research into how students learn certain types of inequalities. This article fills part of the research gap by presenting the findings of a study that examined high school students' methods of approaching absolute value inequalities,…

  1. Individual Differences in Absolute and Relative Metacomprehension Accuracy

    ERIC Educational Resources Information Center

    Maki, Ruth H.; Shields, Micheal; Wheeler, Amanda Easton; Zacchilli, Tammy Lowery

    2005-01-01

    The authors investigated absolute and relative metacomprehension accuracy as a function of verbal ability in college students. Students read hard texts, revised texts, or a mixed set of texts. They then predicted their performance, took a multiple-choice test on the texts, and made posttest judgments about their performance. With hard texts,…

  2. Ion chambers simplify absolute intensity measurements in the vacuum ultraviolet

    NASA Technical Reports Server (NTRS)

    Sampson, J. A. R.

    1966-01-01

    Single or double ion chamber technique measures absolute radiation intensities in the extreme vacuum ultraviolet region of the spectrum. The ion chambers use rare gases as the ion carrier. Photon absorbed by the gas creates one ion pair so a measure of these is a measure of the number of incident photons.

  3. Lyman alpha SMM/UVSP absolute calibration and geocoronal correction

    NASA Technical Reports Server (NTRS)

    Fontenla, Juan M.; Reichmann, Edwin J.

    1987-01-01

    Lyman alpha observations from the Ultraviolet Spectrometer Polarimeter (UVSP) instrument of the Solar Maximum Mission (SMM) spacecraft were analyzed and provide instrumental calibration details. Specific values of the instrument quantum efficiency, Lyman alpha absolute intensity, and correction for geocoronal absorption are presented.

  4. Absolute configurations of zingiberenols isolated from ginger (Zingiber officinale) rhizomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The sesquiterpene alcohol zingiberenol, or 1,10-bisaboladien-3-ol, was isolated some time ago from ginger, Zingiber officinale, rhizomes, but its absolute configuration had not been determined. With three chiral centers present in the molecule, zingiberenol can exist in eight stereoisomeric forms. ...

  5. Series that Converge Absolutely but Don't Converge

    ERIC Educational Resources Information Center

    Kantrowitz, Robert; Schramm, Michael

    2012-01-01

    If a series of real numbers converges absolutely, then it converges. The usual proof requires completeness in the form of the Cauchy criterion. Failing completeness, the result is false. We provide examples of rational series that illustrate this point. The Cantor set appears in connection with one of the examples.

  6. Europe's Other Poverty Measures: Absolute Thresholds Underlying Social Assistance

    ERIC Educational Resources Information Center

    Bavier, Richard

    2009-01-01

    The first thing many learn about international poverty measurement is that European nations apply a "relative" poverty threshold and that they also do a better job of reducing poverty. Unlike the European model, the "absolute" U.S. poverty threshold does not increase in real value when the nation's standard of living rises, even though it is…

  7. Analysis of standard reference materials by absolute INAA

    SciTech Connect

    Heft, R.E.; Koszykowski, R.F.

    1981-07-01

    Three standard reference materials, flyash, soil, and ASI 4340 steel, were analyzed by a method of absolute instrumental neutron activation analysis (INAA). Two different light water pool-type reactors were used to produce equivalent analytical results even though the epithermal to thermal flux ratio in one reactor was higher than that in the other by a factor of two.

  8. Absolute calibration of Landsat instruments using the moon.

    USGS Publications Warehouse

    Kieffer, H.H.; Wildey, R.L.

    1985-01-01

    A lunar observation by Landsat could provide improved radiometric and geometric calibration of both the Thematic Mapper and the Multispectral Scanner in terms of absolute radiometry, determination of the modulation transfer function, and sensitivity to scattered light. A pitch of the spacecraft would be required. -Authors

  9. Urey: to measure the absolute age of Mars

    NASA Technical Reports Server (NTRS)

    Randolph, J. E.; Plescia, J.; Bar-Cohen, Y.; Bartlett, P.; Bickler, D.; Carlson, R.; Carr, G.; Fong, M.; Gronroos, H.; Guske, P. J.; Herring, M.; Javadi, H.; Johnson, D. W.; Larson, T.; Malaviarachchi, K.; Sherrit, S.; Stride, S.; Trebi-Ollennu, A.; Warwick, R.

    2003-01-01

    UREY, a proposed NASA Mars Scout mission will, for the first time, measure the absolute age of an identified igneous rock formation on Mars. By extension to relatively older and younger rock formations dated by remote sensing, these results will enable a new and better understanding of Martian geologic history.

  10. Is There a Rule of Absolute Neutralization in Nupe?

    ERIC Educational Resources Information Center

    Krohn, Robert

    1975-01-01

    A previously prosed rule of absolute neutralization (merging underlying low vowels) is eliminated in an alternative analysis including instead a rule that "breaks" the feature matrix of certain low vowels and redistributes the features of each vowel as a sequence of vowel-like transition plus (a). (Author/RM)

  11. Absolute Radiometer for Reproducing the Solar Irradiance Unit

    NASA Astrophysics Data System (ADS)

    Sapritskii, V. I.; Pavlovich, M. N.

    1989-01-01

    A high-precision absolute radiometer with a thermally stabilized cavity as receiving element has been designed for use in solar irradiance measurements. The State Special Standard of the Solar Irradiance Unit has been built on the basis of the developed absolute radiometer. The Standard also includes the sun tracking system and the system for automatic thermal stabilization and information processing, comprising a built-in microcalculator which calculates the irradiance according to the input program. During metrological certification of the Standard, main error sources have been analysed and the non-excluded systematic and accidental errors of the irradiance-unit realization have been determined. The total error of the Standard does not exceed 0.3%. Beginning in 1984 the Standard has been taking part in a comparison with the Å 212 pyrheliometer and other Soviet and foreign standards. In 1986 it took part in the international comparison of absolute radiometers and standard pyrheliometers of socialist countries. The results of the comparisons proved the high metrological quality of this Standard based on an absolute radiometer.

  12. Relative versus Absolute Stimulus Control in the Temporal Bisection Task

    ERIC Educational Resources Information Center

    de Carvalho, Marilia Pinhiero; Machado, Armando

    2012-01-01

    When subjects learn to associate two sample durations with two comparison keys, do they learn to associate the keys with the short and long samples (relational hypothesis), or with the specific sample durations (absolute hypothesis)? We exposed 16 pigeons to an ABA design in which phases A and B corresponded to tasks using samples of 1 s and 4 s,…

  13. Multifrequency continuous wave terahertz spectroscopy for absolute thickness determination

    SciTech Connect

    Scheller, Maik; Baaske, Kai; Koch, Martin

    2010-04-12

    We present a tunable multifrequency continuous wave terahertz spectrometer based on two laser diodes, photoconductive antennas, and a coherent detection scheme. The system is employed to determine the absolute thickness of samples utilizing a proposed synthetic difference frequency method to circumvent the 2pi uncertainty known from conventional photomixing systems while preserving a high spatial resolution.

  14. Absolute Interrogative Intonation Patterns in Buenos Aires Spanish

    ERIC Educational Resources Information Center

    Lee, Su Ar

    2010-01-01

    In Spanish, each uttered phrase, depending on its use, has one of a variety of intonation patterns. For example, a phrase such as "Maria viene manana" "Mary is coming tomorrow" can be used as a declarative or as an absolute interrogative (a yes/no question) depending on the intonation pattern that a speaker produces. Patterns of usage also…

  15. Local spin density in the Cr7Ni antiferromagnetic molecular ring and 53Cr-NMR

    SciTech Connect

    Casadei, Cecilia M; Bordonali, L; Furukawa, Yuji; Borsa, Ferdinando; Garlatti, E; Lascialfari, A; Carretta, S; Sanna, S; Timco, G; Winpenny, R

    2012-09-13

    We present 53Cr-NMR spectra collected at low temperature in a single crystal of the heterometallic antiferromagnetic (AF) ring Cr7Ni in the S = 1/2 ground state with the aim of establishing the distribution of the local electronic moment in the ring. Due to the poor S/N we observed only one signal which is ascribed to three almost equivalent 53Cr nuclei in the ring. The calculated spin density in Cr7Ni in the ground state, with the applied magnetic field both parallel and perpendicular to the plane of the ring, turns out to be AF staggered with the greatest component of the local spin {s} for the Cr3+ ions next to the Ni2+ ion. The 53Cr-NMR frequency was found to be in good agreement with the local spin density calculated theoretically by assuming a core polarization field of Hcp =₋ 11 T/μB for both orientations, close to the value found previously in Cr7Cd. Lastly, the observed orientation dependence of the local spin moments is well reproduced by the theoretical calculation and evidences the importance of single-ion and dipolar anisotropies.

  16. Potential energy hypersurface and molecular flexibility

    NASA Astrophysics Data System (ADS)

    Koča, Jaroslav

    1993-02-01

    The molecular flexibility phenomenon is discussed from the conformational potential energy(hyper) surface (PES) point of view. Flexibility is considered as a product of three terms: thermodynamic, kinetic and geometrical. Several expressions characterizing absolute and relative molecular flexibility are introduced, depending on a subspace studied of the entire conformational space, energy level E of PES as well as absolute temperature. Results obtained by programs DAISY, CICADA and PANIC in conjunction with molecular mechanics program MMX for flexibility analysis of isopentane, 2,2-dimethylpentane and isohexane molecules are introduced.

  17. Absolute stability and spatiotemporal long-range order in Floquet systems

    NASA Astrophysics Data System (ADS)

    von Keyserlingk, C. W.; Khemani, Vedika; Sondhi, S. L.

    2016-08-01

    Recent work has shown that a variety of novel phases of matter arise in periodically driven Floquet systems. Among these are many-body localized phases which spontaneously break global symmetries and exhibit novel multiplets of Floquet eigenstates separated by quantized quasienergies. Here we show that these properties are stable to all weak local deformations of the underlying Floquet drives—including those that explicitly break the defining symmetries—and that the models considered until now occupy submanifolds within these larger "absolutely stable" phases. While these absolutely stable phases have no explicit global symmetries, they spontaneously break Hamiltonian-dependent emergent symmetries, and thus continue to exhibit the novel multiplet structure. The multiplet structure in turn encodes characteristic oscillations of the emergent order parameter at multiples of the fundamental period. Altogether these phases exhibit a form of simultaneous long-range order in space and time which is new to quantum systems. We describe how this spatiotemporal order can be detected in experiments involving quenches from a broad class of initial states.

  18. Absolute V-R colors of trans-Neptunian objects

    NASA Astrophysics Data System (ADS)

    Alvarez-Candal, Alvaro; Ayala-Loera, Carmen; Ortiz, Jose-Luis; Duffard, Rene; Estela, Fernandez-Valenzuela; Santos-Sanz, Pablo

    2016-10-01

    The absolute magnitude of a minor body is the apparent magnitude that the body would have if observed from the Sun at a distance of 1AU. Absolute magnitudes are measured using phase curves, showing the change of the magnitude, normalized to unit helio and geo-centric distance, vs. phase angle. The absolute magnitude is then the Y-intercept of the curve. Absolute magnitudes are related to the total reflecting surface of the body and thus bring information of its size, coupled with the reflecting properties.Since 2011 our team has been collecting data from several telescopes spread in Europe and South America. We complemented our data with those available in the literature in order to construct phase curves of trans-Neptunian objects with at least three points. In a first release (Alvarez-Candal et al. 2016, A&A, 586, A155) we showed results for 110 trans-Neptunian objects using V magnitudes only, assuming an overall linear trend and taking into consideration rotational effects, for objects with known light-curves.In this contribution we show results for more than 130 objects, about 100 of them with phase curves in two filters: V and R. We compute absolute magnitudes and phase coefficients in both filters, when available. The average values are HV = 6.39 ± 2.37, βV = (0.09 ± 0.32) mag per degree, HR = 5.38 ± 2.30, and βR = (0.08 ± 0.42) mag per degree.

  19. GNSS Absolute Antenna Calibration at the National Geodetic Survey

    NASA Astrophysics Data System (ADS)

    Mader, G. L.; Bilich, A. L.; Geoghegan, C.

    2011-12-01

    Geodetic GNSS applications routinely demand millimeter precision and extremely high levels of accuracy. To achieve these accuracies, measurement and instrument biases at the centimeter to millimeter level must be understood. One of these biases is the antenna phase center, the apparent point of signal reception for a GNSS antenna. It has been well established that phase center patterns differ between antenna models and manufacturers; additional research suggests that the addition of a radome or the choice of antenna mount can significantly alter those a priori phase center patterns. For the more demanding GNSS positioning applications and especially in cases of mixed-antenna networks, it is all the more important to know antenna phase center variations as a function of both elevation and azimuth in the antenna reference frame and incorporate these models into analysis software. To help meet the needs of the high-precision GNSS community, the National Geodetic Survey (NGS) now operates an absolute antenna calibration facility. Located in Corbin, Virginia, this facility uses field measurements and actual GNSS satellite signals to quantitatively determine the carrier phase advance/delay introduced by the antenna element. The NGS facility was built to serve traditional NGS constituents such as the surveying and geodesy communities, however calibration services are open and available to all GNSS users as the calibration schedule permits. All phase center patterns computed by this facility will be publicly available and disseminated in both the ANTEX and NGS formats. We describe the NGS calibration facility, and discuss the observation models and strategy currently used to generate NGS absolute calibrations. We demonstrate that NGS absolute phase center variation (PCV) patterns are consistent with published values determined by other absolute antenna calibration facilities, and compare absolute calibrations to the traditional NGS relative calibrations.

  20. Enhanced Cortical Connectivity in Absolute Pitch Musicians: A Model for Local Hyperconnectivity

    ERIC Educational Resources Information Center

    Loui, Psyche; Li, H. Charles; Hohmann, Anja; Schlaug, Gottfried

    2011-01-01

    Connectivity in the human brain has received increased scientific interest in recent years. Although connection disorders can affect perception, production, learning, and memory, few studies have associated brain connectivity with graded variations in human behavior, especially among normal individuals. One group of normal individuals who possess…

  1. Molecular pathobiology of human cervical high-grade lesions: paracrine STAT3 activation in tumor-instructed myeloid cells drives local MMP-9 expression.

    PubMed

    Schröer, Nadine; Pahne, Jennifer; Walch, Barbara; Wickenhauser, Claudia; Smola, Sigrun

    2011-01-01

    In many tumors, the switch from precancerous lesions to malignancy critically relies on expression of the matrix-metalloprotease MMP-9, which is predominantly provided by infiltrating inflammatory cells. Our study defines a novel molecular cascade, how human neoplastic cells instruct tumor-associated myeloid cells to produce MMP-9. In biopsies of human papillomavirus-associated precancerous cervical intraepithelial neoplasia (CIN III lesions), we show broad activation of the transcription factor STAT3 and coexpression of MMP-9 in perivascular inflammatory cells. For the first time, we establish a causative link between tumor-mediated paracrine STAT3 activation and MMP-9 production by human tumor-instructed monocytes, whereas NF-κB activation is dispensable for this response. Our data provide evidence that STAT3 does not directly induce MMP-9 but first leads to a strong production of the monocyte chemoattractant protein-1 (CCL2) in the nanogram range. In a second phase, autocrine stimulation of the CCR2 receptor in the tumor-instructed monocytes amplifies MMP-9 expression via intracellular Ca(2+) signaling. These findings elucidate a critical mechanism in the molecular pathobiology of cervical carcinogenesis at the switch to malignancy. Particularly in tumors, which are associated with infectious agents, STAT3-driven inflammation may be pivotal to promote carcinogenesis, while at the same time limit NF-κB-dependent immune responses and thus rejection of the infected preneoplastic cells. The molecular cascade defined in this study provides the basis for a rational design of future adjuvant therapies of cervical precancerous lesions.

  2. Molecular behavior adapts to context: heparanase functions as an extracellular matrix-degrading enzyme or as a T cell adhesion molecule, depending on the local pH.

    PubMed

    Gilat, D; Hershkoviz, R; Goldkorn, I; Cahalon, L; Korner, G; Vlodavsky, I; Lider, O

    1995-05-01

    Migration of lymphocytes into inflammatory sites requires their adhesion to the vascular endothelium and subendothelial extracellular matrix (ECM). The ensuing penetration of the ECM is associated with the expression of ECM-degrading enzymes, such as endo-beta-D glucuronidase (heparanase), which cleaves heparan sulfate (HS) proteoglycans. We now report that, depending on the local pH, a mammalian heparanase can function either as an enzyme or as an adhesion molecule. At relatively acidified pH conditions, heparanase performs as an enzyme, degrading HS. In contrast, at the hydrogen ion concentration of a quiescent tissue, heparanase binds specifically to HS molecules without degrading them, and thereby anchors CD4+ human T lymphocytes. Thus, the local state of a tissue can regulate the activities of heparanase and can determine whether the molecule will function as an enzyme or as a proadhesive molecule. PMID:7722469

  3. Molecular typing of the recently expanding subtype B HIV-1 epidemic in Romania: evidence for local spread among MSMs in Bucharest area.

    PubMed

    Paraschiv, Simona; Otelea, Dan; Batan, Ionelia; Baicus, Cristian; Magiorkinis, Gkikas; Paraskevis, Dimitrios

    2012-07-01

    HIV-1 subtype B is predominant in Europe except in some countries from Eastern Europe which are characterized by a high prevalence of non-B subtypes and circulating recombinant forms (CRFs). Romania is a particular case: the HIV-1 epidemic started with subtype F1 which is still the most prevalent. Previous studies have shown an increasing prevalence of subtype B which is the second most frequent one among the newly diagnosed individuals, followed by subtype C and several CRFs as well as unique recombinant forms (URFs). Our objective was to analyze in detail the characteristics (way of dispersal, association with transmission risk groups) of the subtype B infections in Romania by means of phylogenetic analysis. Among all the individuals sampled during 2003-2010, 71 out of 1127 patients (6.3%) have been identified to be infected with subtype B strains. The most frequent route of infection identified in HIV-1 subtype B patients in Romania was MSM transmission (39.6%), followed by the heterosexual route (35.2%). Many of the patients acquired the infection abroad, mainly in Western European countries. Phylogenetic analysis indicated the existence of a local transmission network (monophyletic clade) including 14 patients, mainly MSM living in the Bucharest area. We estimate the origin of the local transmission network that dates at the beginning of the 90s; the introduction of the F1 and C subtypes occurred earlier. The rest of the sequences were intermixed with reference strains sampled across Europe suggesting that single infection were not followed by subsequent dispersal within the local population. Although HIV-1 subtype B epidemic in Romania is recent, there is evidence for local spread among the MSMs, in addition to multiple introductions.

  4. Evaluation of the Linear and Second-Order NLO Properties of Molecular Crystals within the Local Field Theory: Electron Correlation Effects, Choice of XC Functional, ZPVA Contributions, and Impact of the Geometry in the Case of 2-Methyl-4-nitroaniline.

    PubMed

    Seidler, Tomasz; Stadnicka, Katarzyna; Champagne, Benoît

    2014-05-13

    The linear [χ((1))] and second-order nonlinear [χ((2))] optical susceptibilities of the 2-methyl-4-nitroaniline (MNA) crystal are calculated within the local field theory, which consists of first computing the molecular properties, accounting for the dressing effects of the surroundings, and then taking into account the local field effects. Several aspects of these calculations are tackled with the aim of monitoring the convergence of the χ((1)) and χ((2)) predictions with respect to experiment by accounting for the effects of (i) the dressing field within successive approximations, of (ii) the first-order ZPVA corrections, and of (iii) the geometry. With respect to the reference CCSD-based results, besides double hybrid functionals, the most reliable exchange-correlation functionals are LC-BLYP for the static χ((1)) and CAM-B3LYP (and M05-2X, to a lesser extent) for the dynamic χ((1)) but they strongly underestimate χ((2)). Double hybrids perform better for χ((2)) but not necessarily for χ((1)), and, moreover, their performances are much similar to MP2, which is known to slightly overestimate β, with respect to high-level coupled-clusters calculations and, therefore, χ((2)). Other XC functionals with less HF exchange perform poorly with overestimations/underestimations of χ((1))/χ((2)), whereas the HF method leads to underestimations of both. The first-order ZPVA corrections, estimated at the B3LYP level, are usually small but not negligible. Indeed, after ZPVA corrections, the molecular polarizabilities and first hyperpolarizabilities increase by 2% and 5%, respectively, whereas their impact is magnified on the macroscopic responses with enhancements of χ((1)) by up to 5% and of χ((2)) by as much as 10%-12% at λ = 1064 nm. The geometry plays also a key role in view of predicting accurate susceptibilities, particularly for push-pull π-conjugated compounds such as MNA. So, the geometry optimized using periodic boundary conditions is characterized

  5. Molecular phylogeny and population structure of the codling moth (Cydia pomonella) in Central Europe: II. AFLP analysis reflects human-aided local adaptation of a global pest species.

    PubMed

    Thaler, R; Brandstätter, A; Meraner, A; Chabicovski, M; Parson, W; Zelger, R; Dalla Via, J; Dallinger, R

    2008-09-01

    Originally resident in southeastern Europe, the codling moth (Cydia pomonella L.) (Tortricidae) has achieved a nearly global distribution, being one of the most successful pest insect species known today. As shown in our accompanying study, mitochondrial genetic markers suggest a Pleistocenic splitting of Cydia pomonella into two refugial clades which came into secondary contact after de-glaciation. The actual distribution pattern shows, however, that Central European codling moths have experienced a geographic splitting into many strains and locally adapted populations, which is not reflected by their mitochondrial haplotype distribution. We therefore have applied, in addition to mitochondrial markers, an approach with a higher resolution potential at the population level, based on the analysis of amplification fragment length polymorphisms (AFLPs). As shown in the present study, AFLP markers elucidate the genetic structure of codling moth strains and populations from different Central European apple orchard sites. While individual genetic diversity within codling moth strains and populations was small, a high degree of genetic differentiation was observed between the analyzed strains and populations, even at a small geographic scale. One of the main factors contributing to local differentiation may be limited gene flow among adjacent codling moth populations. In addition, microclimatic, ecological, and geographic constraints also may favour the splitting of Cydia pomonella into many local populations. Lastly, codling moths in Central European fruit orchards may experience considerable selective pressure due to pest control activities. As a consequence of all these selective forces, today in Central Europe we see a patchy distribution of many locally adapted codling moth populations, each of them having its own genetic fingerprint. Because of the complete absence of any correlation between insecticide resistance and geographic or genetic distances among

  6. Molecular characterization of a sarco(endo)plasmic reticulum Ca2+-ATPase gene from Paramecium tetraurelia and localization of its gene product to sub-plasmalemmal calcium stores.

    PubMed Central

    Hauser, K; Pavlovic, N; Kissmehl, R; Plattner, H

    1998-01-01

    A cDNA encoding the gene for a sarco(endo)plasmic reticulum-type Ca2+-ATPase (SERCA) was isolated from a cDNA library of Paramecium tetraurelia by using degenerated primers according to conserved domains of SERCA-type ATPases. The identified nucleotide sequence (PtSERCA) is 3114 nucleotides in length with an open reading frame of 1037 amino acids. An intron of only 22 nucleotides occurs. Homology searches for the deduced amino acid sequence revealed 38-49% similarity to SERCA-type ATPases from organisms ranging from protozoans to mammals, with no more similarity to some parasitic protozoa of the same phylum. The calculated molecular mass of the encoded protein is 114.7 kDa. It contains the typical 10 transmembrane domains of SERCA-type ATPases and other conserved domains, such as the phosphorylation site and the ATP binding site. However, there are no binding sites for phospholamban and thapsigargin present in the PtSERCA. Antibodies raised against a cytoplasmic loop peptide between the phosphorylation site and the ATP binding site recognize on Western blots a protein of 106 kDa, exclusively in the fraction of sub-plasmalemmal calcium stores ('alveolar sacs'). In immunofluorescence studies the antibodies show labelling exclusively in the cell cortex of permeabilized cells in a pattern characteristic of the arrangement of alveolar sacs. When alveolar sacs where tested for phosphoenzyme-intermediate formation a phosphoprotein of the same molecular mass (106 kDa) could be identified. PMID:9693098

  7. Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry.

    PubMed

    Ludwig, Christina; Claassen, Manfred; Schmidt, Alexander; Aebersold, Ruedi

    2012-03-01

    For many research questions in modern molecular and systems biology, information about absolute protein quantities is imperative. This information includes, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes, or quantitative comparisons of different proteins within one sample or across samples. To date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers of samples. Here we describe and demonstrate the utility of a targeting MS technique for the estimation of absolute protein abundance in unlabeled and nonfractionated cell lysates. The method is based on selected reaction monitoring (SRM) mass spectrometry and the "best flyer" hypothesis, which assumes that the specific MS signal intensity of the most intense tryptic peptides per protein is approximately constant throughout a whole proteome. SRM-targeted best flyer peptides were selected for each protein from the peptide precursor ion signal intensities from directed MS data. The most intense transitions per peptide were selected from full MS/MS scans of crude synthetic analogs. We used Monte Carlo cross-validation to systematically investigate the accuracy of the technique as a function of the number of measured best flyer peptides and the number of SRM transitions per peptide. We found that a linear model based on the two most intense transitions of the three best flying peptides per proteins (TopPep3/TopTra2) generated optimal results with a cross-correlated mean fold error of 1.8 and a squared Pearson coefficient R(2) of 0.88. Applying the optimized model to lysates of the microbe Leptospira interrogans, we detected significant protein abundance changes of 39 target proteins upon antibiotic treatment, which correlate well with literature values. The described method is generally applicable and exploits the inherent performance advantages of SRM

  8. Greater absolute risk for all subtypes of breast cancer in the US than Malaysia.

    PubMed

    Horne, Hisani N; Beena Devi, C R; Sung, Hyuna; Tang, Tieng Swee; Rosenberg, Philip S; Hewitt, Stephen M; Sherman, Mark E; Anderson, William F; Yang, Xiaohong R

    2015-01-01

    Hormone receptor (HR) negative breast cancers are relatively more common in low-risk than high-risk countries and/or populations. However, the absolute variations between these different populations are not well established given the limited number of cancer registries with incidence rate data by breast cancer subtype. We, therefore, used two unique population-based resources with molecular data to compare incidence rates for the 'intrinsic' breast cancer subtypes between a low-risk Asian population in Malaysia and high-risk non-Hispanic white population in the National Cancer Institute's surveillance, epidemiology, and end results 18 registries database (SEER 18). The intrinsic breast cancer subtypes were recapitulated with the joint expression of the HRs (estrogen receptor and progesterone receptor) and human epidermal growth factor receptor-2 (HER2). Invasive breast cancer incidence rates overall were fivefold greater in SEER 18 than in Malaysia. The majority of breast cancers were HR-positive in SEER 18 and HR-negative in Malaysia. Notwithstanding the greater relative distribution for HR-negative cancers in Malaysia, there was a greater absolute risk for all subtypes in SEER 18; incidence rates were nearly 7-fold higher for HR-positive and 2-fold higher for HR-negative cancers in SEER 18. Despite the well-established relative breast cancer differences between low-risk and high-risk countries and/or populations, there was a greater absolute risk for HR-positive and HR-negative subtypes in the US than Malaysia. Additional analytical studies are sorely needed to determine the factors responsible for the elevated risk of all subtypes of breast cancer in high-risk countries like the United States.

  9. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil.

    PubMed

    Santos, Elisa S L; Cerqueira-Silva, Carlos Bernard M; Mori, Gustavo M; Ahnert, Dário; Mello, Durval L N; Pires, José Luis; Corrêa, Ronan X; de Souza, Anete P

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called 'Bahian cacao' or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide.

  10. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil.

    PubMed

    Santos, Elisa S L; Cerqueira-Silva, Carlos Bernard M; Mori, Gustavo M; Ahnert, Dário; Mello, Durval L N; Pires, José Luis; Corrêa, Ronan X; de Souza, Anete P

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called 'Bahian cacao' or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide. PMID:26675449

  11. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil

    PubMed Central

    Santos, Elisa S. L.; Cerqueira-Silva, Carlos Bernard M.; Mori, Gustavo M.; Ahnert, Dário; Mello, Durval L. N.; Pires, José Luis; Corrêa, Ronan X.; de Souza, Anete P.

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called ‘Bahian cacao’ or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide. PMID:26675449

  12. Comparison of local features from two Spanish hospitals reveals common and specific traits at multiple levels of the molecular epidemiology of metallo-β-lactamase-producing Pseudomonas spp.

    PubMed

    Viedma, Esther; Estepa, Vanesa; Juan, Carlos; Castillo-Vera, Jane; Rojo-Bezares, Beatriz; Seral, Cristina; Castillo, Francisco Javier; Sáenz, Yolanda; Torres, Carmen; Chaves, Fernando; Oliver, Antonio

    2014-01-01

    Twenty-seven well-characterized metallo-β-lactamase (MBL)-producing Pseudomonas strains from two distantly located hospitals were analyzed. The results revealed specific features defining the multilevel epidemiology of strains from each hospital in terms of species, clonality, predominance of high-risk clones, composition/diversity of integrons, and linkages of Tn402-related structures. Therefore, despite the global trends driving the epidemiology of MBL-producing Pseudomonas spp., the presence of local features has to be considered in order to understand this threat and implement proper control strategies.

  13. Absolute and direct microRNA quantification using DNA-gold nanoparticle probes.

    PubMed

    Degliangeli, Federica; Kshirsagar, Prakash; Brunetti, Virgilio; Pompa, Pier Paolo; Fiammengo, Roberto

    2014-02-12

    DNA-gold nanoparticle probes are implemented in a simple strategy for direct microRNA (miRNA) quantification. Fluorescently labeled DNA-probe strands are immobilized on PEGylated gold nanoparticles (AuNPs). In the presence of target miRNA, DNA-RNA heteroduplexes are formed and become substrate for the endonuclease DSN (duplex-specific nuclease). Enzymatic hydrolysis of the DNA strands yields a fluorescence signal due to diffusion of the fluorophores away from the gold surface. We show that the molecular design of our DNA-AuNP probes, with the DNA strands immobilized on top of the PEG-based passivation layer, results in nearly unaltered enzymatic activity toward immobilized heteroduplexes compared to substrates free in solution. The assay, developed in a real-time format, allows absolute quantification of as little as 0.2 fmol of miR-203. We also show the application of the assay for direct quantification of cancer-related miR-203 and miR-21 in samples of extracted total RNA from cell cultures. The possibility of direct and absolute quantification may significantly advance the use of microRNAs as biomarkers in the clinical praxis.

  14. Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

    PubMed Central

    Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

    2015-01-01

    We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples. PMID:26333806

  15. Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins.

    PubMed

    Narumi, Ryohei; Shimizu, Yoshihiro; Ukai-Tadenuma, Maki; Ode, Koji L; Kanda, Genki N; Shinohara, Yuta; Sato, Aya; Matsumoto, Katsuhiko; Ueda, Hiroki R

    2016-06-14

    Absolute values of protein expression levels in cells are crucial information for understanding cellular biological systems. Precise quantification of proteins can be achieved by liquid chromatography (LC)-mass spectrometry (MS) analysis of enzymatic digests of proteins in the presence of isotope-labeled internal standards. Thus, development of a simple and easy way for the preparation of internal standards is advantageous for the analyses of multiple target proteins, which will allow systems-level studies. Here we describe a method, termed MS-based Quantification By isotope-labeled Cell-free products (MS-QBiC), which provides the simple and high-throughput preparation of internal standards by using a reconstituted cell-free protein synthesis system, and thereby facilitates both multiplexed and sensitive quantification of absolute amounts of target proteins. This method was applied to a systems-level dynamic analysis of mammalian circadian clock proteins, which consist of transcription factors and protein kinases that govern central and peripheral circadian clocks in mammals. Sixteen proteins from 20 selected circadian clock proteins were successfully quantified from mouse liver over a 24-h time series, and 14 proteins had circadian variations. Quantified values were applied to detect internal body time using a previously developed molecular timetable method. The analyses showed that single time-point data from wild-type mice can predict the endogenous state of the circadian clock, whereas data from clock mutant mice are not applicable because of the disappearance of circadian variation. PMID:27247408

  16. Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification

    NASA Astrophysics Data System (ADS)

    Guan, Weihua; Chen, Liben; Rane, Tushar D.; Wang, Tza-Huei

    2015-09-01

    We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

  17. Absolute Configurations of Zingiberenols Isolated from Ginger (Zingiber officinale) Rhizomes.

    PubMed

    Khrimian, Ashot; Shirali, Shyam; Guzman, Filadelfo

    2015-12-24

    Two stereoisomeric zingiberenols in ginger were identified as (3R,6R,7S)-1,10-bisaboladien-3-ol (2) and (3S,6R,7S)-1,10-bisaboladien-3-ol (5). Absolute configurations were assigned by utilizing 1,10-bisaboladien-3-ol stereoisomers and two gas-chromatography columns: a 25 m Hydrodex-β-6TBDM and 60 m DB-5MS. The C-6 and C-7 absolute configurations in both zingiberenols match those of zingiberene present abundantly in ginger rhizomes. Interestingly, zingiberenol 2 has recently been identified as a male-produced sex pheromone of the rice stink bug, Oebalus poecilus, thus indicating that ginger plants may be a potential source of the sex pheromone of this bug.

  18. In-flight Absolute Radiometric Calibration of the Thematic Mapper

    NASA Technical Reports Server (NTRS)

    Castle, K. R.; Holm, R. G.; Kastner, C. J.; Palmer, J. M.; Slater, P. N.; Dinguirard, M.; Ezra, C. E.; Jackson, D.; Savage, R. K.

    1984-01-01

    The Thematic Mapper (TM) multispectral scanner system was placed into Earth orbit on July 16, 1982, as part of NASA's LANDSAT 4 payload. To determine temporal changes of the absolute radiometric calibration of the entire system in flight, spectroradiometric measurements of the ground and the atmosphere are made simultaneously with TM image acquisitions over the White Sands, New Mexico area. By entering the measured values into an atmospheric radiative transfer program, the radiance levels at the entrance pupil of the TM in four of the TM spectral bands are determined. These levels are compared to the output digital counts from the detectors that sampled the radiometrically measured ground area, thus providing an absolute radiometric calibration of the entire TM system utilizing those detectors. By reference to an adjacent, larger uniform area, the calibration is extended to all 16 detectors in each of the three bands.

  19. Absolute measurement of the extreme UV solar flux

    NASA Technical Reports Server (NTRS)

    Carlson, R. W.; Ogawa, H. S.; Judge, D. L.; Phillips, E.

    1984-01-01

    A windowless rare-gas ionization chamber has been developed to measure the absolute value of the solar extreme UV flux in the 50-575-A region. Successful results were obtained on a solar-pointing sounding rocket. The ionization chamber, operated in total absorption, is an inherently stable absolute detector of ionizing UV radiation and was designed to be independent of effects from secondary ionization and gas effusion. The net error of the measurement is + or - 7.3 percent, which is primarily due to residual outgassing in the instrument, other errors such as multiple ionization, photoelectron collection, and extrapolation to the zero atmospheric optical depth being small in comparison. For the day of the flight, Aug. 10, 1982, the solar irradiance (50-575 A), normalized to unit solar distance, was found to be 5.71 + or - 0.42 x 10 to the 10th photons per sq cm sec.

  20. In-flight absolute radiometric calibration of the thematic mapper

    NASA Technical Reports Server (NTRS)

    Castle, K. R.; Holm, R. G.; Kastner, C. J.; Palmer, J. M.; Slater, P. N.; Dinguirard, M.; Ezra, C. E.; Jackson, R. D.; Savage, R. K.

    1984-01-01

    In order to determine temporal changes of the absolute radiometric calibration of the entire TM system in flight spectroradiometric measurements of the ground and the atmosphere were made simultaneously with TM image collections over the White Sands, New Mexico area. By entering the measured values in an atmospheric radiative transfer program, the radiance levels in four of the spectral bands of the TM were determined, band 1:0.45 to 0.52 micrometers, band 2:0.53 to 0.61 micrometers band 3:0.62 to 0.70 micrometers and 4:0.78 to 0.91 micrometers. These levels were compared to the output digital counts from the detectors that sampled the radiometrically measured ground area, thus providing an absolute radiometric calibration of the entire TM system utilizing those detectors.