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Sample records for method noe dobrea

  1. Identification of individual protein-ligand NOEs in the limit of intermediate exchange

    International Nuclear Information System (INIS)

    Reibarkh, Mikhail; Malia, Thomas J.; Hopkins, Brian T.; Wagner, Gerhard

    2006-01-01

    Interactions of proteins with small molecules or other macromolecules play key roles in many biological processes and in drug action, and NMR is an excellent tool for their structural characterization. Frequently, however, line broadening due to intermediate exchange completely eliminates the signals needed for measuring specific intermolecular NOEs. This limits the use of NMR for detailed structural studies in such kinetic situations. Here we show that an optimally chosen excess of ligand over protein can reduce the extent of line broadening for both the ligand and the protein. This makes observation of ligand resonances possible but reduces the size of the measurable NOEs due to the residual line broadening and the non-stoichiometric concentrations. Because the solubility of small molecule drug leads are often limited to high micromolar concentrations, protein concentrations are restricted to even lower values in the low micromolar range. At these non-stoichiometric concentrations and in the presence of significant residual line broadening, conventional NOESY experiments very often are not sensitive enough to observe intermolecular NOEs since the signals inverted by the NOESY preparation pulse sequence relax prior to significant NOE build up. Thus, we employ methods related to driven NOE spectroscopy to investigate protein-ligand interactions in the intermediate exchange regime. In this approach, individual protein resonances are selectively irradiated for up to five seconds to build up measurable NOEs at the ligand resonances. To enable saturation of individual protein resonances we prepare deuterated protein samples selectively protonated at a few sites so that the 1D 1 H spectrum of the protein is resolved well enough to permit irradiation of individual protein signals, which do not overlap with the ligand spectrum. This approach is suitable for measuring a sufficiently large number of protein-ligand NOEs that allow calculation of initial complex structures

  2. Accuracy in the quantification of chemical exchange saturation transfer (CEST) and relayed nuclear Overhauser enhancement (rNOE) saturation transfer effects.

    Science.gov (United States)

    Zhang, Xiao-Yong; Wang, Feng; Li, Hua; Xu, Junzhong; Gochberg, Daniel F; Gore, John C; Zu, Zhongliang

    2017-07-01

    Accurate quantification of chemical exchange saturation transfer (CEST) effects, including dipole-dipole mediated relayed nuclear Overhauser enhancement (rNOE) saturation transfer, is important for applications and studies of molecular concentration and transfer rate (and thereby pH or temperature). Although several quantification methods, such as Lorentzian difference (LD) analysis, multiple-pool Lorentzian fits, and the three-point method, have been extensively used in several preclinical and clinical applications, the accuracy of these methods has not been evaluated. Here we simulated multiple-pool Z spectra containing the pools that contribute to the main CEST and rNOE saturation transfer signals in the brain, numerically fit them using the different methods, and then compared their derived CEST metrics with the known solute concentrations and exchange rates. Our results show that the LD analysis overestimates contributions from amide proton transfer (APT) and intermediate exchanging amine protons; the three-point method significantly underestimates both APT and rNOE saturation transfer at -3.5 ppm (NOE(-3.5)). The multiple-pool Lorentzian fit is more accurate than the other two methods, but only at lower irradiation powers (≤1 μT at 9.4 T) within the range of our simulations. At higher irradiation powers, this method is also inaccurate because of the presence of a fast exchanging CEST signal that has a non-Lorentzian lineshape. Quantitative parameters derived from in vivo images of rodent brain tumor obtained using an irradiation power of 1 μT were also compared. Our results demonstrate that all three quantification methods show similar contrasts between tumor and contralateral normal tissue for both APT and the NOE(-3.5). However, the quantified values of the three methods are significantly different. Our work provides insight into the fitting accuracy obtainable in a complex tissue model and provides guidelines for evaluating other newly developed

  3. Conformational analysis by quantitative NOE measurements of the β-proton pairs across individual disulfide bonds in proteins

    International Nuclear Information System (INIS)

    Takeda, Mitsuhiro; Terauchi, Tsutomu; Kainosho, Masatsune

    2012-01-01

    NOEs between the β-protons of cysteine residues across disulfide bonds in proteins provide direct information on the connectivities and conformations of these important cross-links, which are otherwise difficult to investigate. With conventional [U- 13 C, 15 N]-proteins, however, fast spin diffusion processes mediated by strong dipolar interactions between geminal β-protons prohibit the quantitative measurements and thus the analyses of long-range NOEs across disulfide bonds. We describe a robust approach for alleviating such difficulties, by using proteins selectively labeled with an equimolar mixture of (2R, 3S)-[β- 13 C; α,β- 2 H 2 ] Cys and (2R, 3R)-[β- 13 C; α,β- 2 H 2 ] Cys, but otherwise fully deuterated. Since either one of the prochiral methylene protons, namely β2 (proS) or β3 (proR), is always replaced with a deuteron and no other protons remain in proteins prepared by this labeling scheme, all four of the expected NOEs for the β-protons across disulfide bonds could be measured without any spin diffusion interference, even with long mixing times. Therefore, the NOEs for the β2 and β3 pairs across each of the disulfide bonds could be observed at high sensitivity, even though they are 25% of the theoretical maximum for each pair. With the NOE information, the disulfide bond connectivities can be unambiguously established for proteins with multiple disulfide bonds. In addition, the conformations around disulfide bonds, namely χ 2 and χ 3 , can be determined based on the precise proton distances of the four β-proton pairs, by quantitative measurements of the NOEs across the disulfide bonds. The feasibility of this method is demonstrated for bovine pancreatic trypsin inhibitor, which has three disulfide bonds.

  4. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

    Science.gov (United States)

    Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

    2014-12-11

    The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

  5. Practical aspects of the 2D 15N-{1H}-NOE experiment

    International Nuclear Information System (INIS)

    Renner, Christian; Schleicher, Michael; Moroder, Luis; Holak, Tad A.

    2002-01-01

    The heteronuclear 15 N-NOE experiment was extensively tested with respect to statistical and systematic experimental error. The dependence of signal intensity in the NOE experiment and in the reference experiment on the saturation and relaxation time was experimentally investigated. The statistics of the experimental values were accessed by numerous repetitions of identical set-ups. As a model system a protein of typical size for NMR studies was chosen, i.e., a 120 amino acid residues containing fragment of the F-actin binding gelation factor (ABP-120). The fragment exhibits fast dynamics that are accessible with the 15 N-NOE experiment with various amplitudes. The results of this study show that commonly used parameters are only adequate for accurate measurement of motions with moderate amplitude. Highly flexible parts require longer delay times and thus more experimental time than commonly used. On the other hand, a qualitative or semi-quantitative assessment of a protein's mobility on fast times scales can be obtained from rapidly recorded experiments with unusual short delay times. The findings of this study are of equal importance for highly accurate measurement of the 15 N-NOE as well as for quick identification of mobile or even unstructured residues/parts of a protein

  6. Solvation study of the non-specific lipid transfer protein from wheat by intermolecular NOEs with water and small organic molecules

    International Nuclear Information System (INIS)

    Liepinsh, Edvards; Sodano, Patrick; Tassin, Severine; Marion, Didier; Vovelle, Francoise; Otting, Gottfried

    1999-01-01

    Intermolecular nuclear Overhauser effects (NOEs) were measured between the protons of various small solvent or gas molecules and the non-specific lipid transfer protein (ns-LTP) from wheat. Intermolecular NOEs were observed with the hydrophobic pocket in the interior of wheat ns-LTP, which grew in intensity in the order cyclopropane (saturated solution) < methane (140 bar) < ethane (40 bar) < acetonitrile (5% in water) < cyclohexane (saturated solution) < benzene (saturated solution). No intermolecular NOEs were observed with dioxane (5% in water). The intermolecular NOEs were negative for all of the organic molecules tested. Intermolecular NOEs between wheat ns-LTP and water were weak or could not be distinguished from exchange-relayed NOEs. As illustrated by the NOEs with cyclohexane versus dioxane, the hydrophobic pocket in wheat ns-LTP preferably binds non-polar molecules. Yet, polar molecules like acetonitrile can also be accommodated. The pressure dependence of the NOEs between methane and wheat ns-LTP indicated incomplete occupancy, even at 190 bar methane pressure. In general, NOE intensities increased with the size of the ligand molecule and its vapor pressure. NMR of the vapor phase showed excellent resolution between the signals from the gas phase and those from the liquid phase. The vapor concentration of cyclohexane was fivefold higher than that of the dioxane solution, supporting the binding of cyclohexane versus uptake of dioxane

  7. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States); Petit, Chad M. [University of Alabama at Birmingham, Department of Biochemistry and Molecular Genetics (United States); Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-06-15

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  8. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

    International Nuclear Information System (INIS)

    Lee, Woonghee; Petit, Chad M.; Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L.

    2016-01-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  9. On the transmit field inhomogeneity correction of relaxation‐compensated amide and NOE CEST effects at 7 T

    Science.gov (United States)

    Windschuh, Johannes; Siero, Jeroen C.W.; Zaiss, Moritz; Luijten, Peter R.; Klomp, Dennis W.J.; Hoogduin, Hans

    2017-01-01

    High field MRI is beneficial for chemical exchange saturation transfer (CEST) in terms of high SNR, CNR, and chemical shift dispersion. These advantages may, however, be counter‐balanced by the increased transmit field inhomogeneity normally associated with high field MRI. The relatively high sensitivity of the CEST contrast to B 1 inhomogeneity necessitates the development of correction methods, which is essential for the clinical translation of CEST. In this work, two B 1 correction algorithms for the most studied CEST effects, amide‐CEST and nuclear Overhauser enhancement (NOE), were analyzed. Both methods rely on fitting the multi‐pool Bloch‐McConnell equations to the densely sampled CEST spectra. In the first method, the correction is achieved by using a linear B 1 correction of the calculated amide and NOE CEST effects. The second method uses the Bloch‐McConnell fit parameters and the desired B 1 amplitude to recalculate the CEST spectra, followed by the calculation of B 1‐corrected amide and NOE CEST effects. Both algorithms were systematically studied in Bloch‐McConnell equations and in human data, and compared with the earlier proposed ideal interpolation‐based B 1 correction method. In the low B 1 regime of 0.15–0.50 μT (average power), a simple linear model was sufficient to mitigate B 1 inhomogeneity effects on a par with the interpolation B 1 correction, as demonstrated by a reduced correlation of the CEST contrast with B 1 in both the simulations and the experiments. PMID:28111824

  10. An Asymmetric Deuterium Labeling Strategy to Identify Interprotomer and Intraprotomer NOEs in Oligomeric Proteins

    International Nuclear Information System (INIS)

    Jasanoff, Alan

    1998-01-01

    A major difficulty in determining the structure of an oligomeric protein by NMR is the problem of distinguishing inter- from intraprotomer NOEs. In order to address this issue in studies of the 27 kD compact trimeric domain of the MHC class II-associated invariant chain, we compared the 13C NOESY-HSQC spectrum of a uniformly 13C-labeled trimer with the spectrum of the same trimer labeled with 13C in only one protomer, and with deuterium in the other two protomers. The spectrum of the unmixed trimer included both inter- and intraprotomer NOEs while the spectrum of the mixed trimer included only intraprotomer peaks. NOEs clearly absent from the spectrum of the mixed trimer could be confidently assigned to interprotomer interactions. Asymmetrically labeled trimers were isolated by refolding a 13C-labeled shorter form of the protein with a 2H-labeled longer form, chromatographically purifying trimers with only one short chain, and then processing with trypsin to yield only protomers with the desired N- and C-termini. In contrast to earlier studies, in which statistical mixtures of differently labeled protomers were analyzed, our procedure generated only a well-defined 1:2 oligomer, and no other mixed oligomers were present. This increased the maximum possible concentration of NMR-active protomers and thus the sensitivity of the experiments. Related methods should be applicable to many oligomeric proteins, particularly those with slow protomer exchange rates

  11. Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.

    Science.gov (United States)

    Khoo, Y; Singer, A; Cowburn, D

    2017-07-01

    We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints are too imprecise and sparse for accurate structure determination. Residual dipolar coupling (RDC) measurements provide additional geometric information on the angles between atom-pair directions and axes of the principal-axis-frame. The optimization problem involving RDC is highly non-convex and requires a good initialization even within the simulated annealing framework. In this paper, we model the protein backbone as an articulated structure composed of rigid units. Determining the rotation of each rigid unit gives the full protein structure. We propose solving the non-convex optimization problems using the sum-of-squares (SOS) hierarchy, a hierarchy of convex relaxations with increasing complexity and approximation power. Unlike classical global optimization approaches, SOS optimization returns a certificate of optimality if the global optimum is found. Based on the SOS method, we proposed two algorithms-RDC-SOS and RDC-NOE-SOS, that have polynomial time complexity in the number of amino-acid residues and run efficiently on a standard desktop. In many instances, the proposed methods exactly recover the solution to the original non-convex optimization problem. To the best of our knowledge this is the first time SOS relaxation is introduced to solve non-convex optimization problems in structural biology. We further introduce a statistical tool, the Cramér-Rao bound (CRB), to provide an information theoretic bound on the highest resolution one can hope to achieve when determining protein structure from noisy measurements using any unbiased estimator. Our simulation results show that when the RDC measurements are

  12. Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints

    International Nuclear Information System (INIS)

    Furuita, Kyoko; Kataoka, Saori; Sugiki, Toshihiko; Hattori, Yoshikazu; Kobayashi, Naohiro; Ikegami, Takahisa; Shiozaki, Kazuhiro; Fujiwara, Toshimichi; Kojima, Chojiro

    2015-01-01

    NMR structure determination of soluble proteins depends in large part on distance restraints derived from NOE. In this study, we examined the impact of paramagnetic relaxation enhancement (PRE)-derived distance restraints on protein structure determination. A high-resolution structure of the loop-rich soluble protein Sin1 could not be determined by conventional NOE-based procedures due to an insufficient number of NOE restraints. By using the 867 PRE-derived distance restraints obtained from the NOE-based structure determination procedure, a high-resolution structure of Sin1 could be successfully determined. The convergence and accuracy of the determined structure were improved by increasing the number of PRE-derived distance restraints. This study demonstrates that PRE-derived distance restraints are useful in the determination of a high-resolution structure of a soluble protein when the number of NOE constraints is insufficient

  13. Design and numerical evaluation of full-authority flight control systems for conventional and thruster-augmented helicopters employed in NOE operations

    Science.gov (United States)

    Perri, Todd A.; Mckillip, R. M., Jr.; Curtiss, H. C., Jr.

    1987-01-01

    The development and methodology is presented for development of full-authority implicit model-following and explicit model-following optimal controllers for use on helicopters operating in the Nap-of-the Earth (NOE) environment. Pole placement, input-output frequency response, and step input response were used to evaluate handling qualities performance. The pilot was equipped with velocity-command inputs. A mathematical/computational trajectory optimization method was employed to evaluate the ability of each controller to fly NOE maneuvers. The method determines the optimal swashplate and thruster input histories from the helicopter's dynamics and the prescribed geometry and desired flying qualities of the maneuver. Three maneuvers were investigated for both the implicit and explicit controllers with and without auxiliary propulsion installed: pop-up/dash/descent, bob-up at 40 knots, and glideslope. The explicit controller proved to be superior to the implicit controller in performance and ease of design.

  14. Assessment of protein solution versus crystal structure determination using spin- diffusion-suppressed NOE and heteronuclear relaxation data

    International Nuclear Information System (INIS)

    LeMaster, David M.

    1997-01-01

    A spin-diffusion-suppressed NOE buildup series has been measured for E. coli thioredoxin.The extensive 13C and 15N relaxation data previously reported for this protein allow for direct interpretation of dynamical contributions to the 1H-1H cross-relaxation rates for a large proportion of the NOE cross peaks. Estimates of the average accuracy for these derived NOE distances are bounded by 4% and 10%, based on a comparison to the corresponding X-ray distances. An independent fluctuation model is proposed for prediction of the dynamical corrections to 1H-1H cross-relaxation rates, based solely on experimental structural and heteronuclear relaxation data. This analysis is aided by the demonstration that heteronuclear order parameters greater than 0.6 depend only on the variance of the H-X bond orientation,independent of the motional model in either one- or two-dimensional diffusion (i.e., 1- S2 = 3/4 sin2 2 θσ). The combination of spin-diffusion-suppressed NOE data and analysis of dynamical corrections to 1H-1H cross-relaxation rates based on heteronuclear relaxation data has allowed for a detailed interpretation of various discrepancies between the reported solution and crystal structures

  15. Position of residues in transmembrane peptides with respect to the lipid bilayer: A combined lipid NOEs and water chemical exchange approach in phospholipid bicelles

    International Nuclear Information System (INIS)

    Glover, Kerney Jebrell; Whiles, Jennifer A.; Vold, Regitze R.; Melacini, Giuseppe

    2002-01-01

    The model transmembrane peptide P16 was incorporated into small unaligned phospholipid bicelles, which provide a 'native-like' lipid bilayer compatible with high-resolution solution NMR techniques. Using amide-water chemical exchange and amide-lipid cross-relaxation measurements, the interactions between P16 and bicelles were investigated. Distinctive intermolecular NOE patterns observed in band-selective 2D-NOESY spectra of bicellar solutions with several lipid deuteration schemes indicated that P16 is preferentially interacting with the 'bilayered' region of the bicelle rather than with the rim. Furthermore, when amide-lipid NOEs were combined with amide-water chemical exchange cross-peaks of selectively 15 N-labeled P16 peptides, valuable information was obtained about the position of selected residues relative to the membrane-water interface. Specifically, three main classes were identified. Class I residues lie outside the bilayer and show amide-water exchange cross-peaks but no amide-lipid NOEs. Class II residues reside in the bilayer-water interface and show both amide-water exchange cross-peaks and amide-lipid NOEs. Class III residues are embedded within the hydrophobic core of the membrane and show no amide-water exchange cross-peaks but strong amide-lipid NOEs

  16. Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA

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    Malliavin Thérèse E

    2008-06-01

    Full Text Available Abstract Background The Ambiguous Restraints for Iterative Assignment (ARIA approach is widely used for NMR structure determination. It is based on simultaneously calculating structures and assigning NOE through an iterative protocol. The final solution consists of a set of conformers and a list of most probable assignments for the input NOE peak list. Results ARIA was extended with a series of graphical tools to facilitate a detailed analysis of the intermediate and final results of the ARIA protocol. These additional features provide (i an interactive contact map, serving as a tool for the analysis of assignments, and (ii graphical representations of structure quality scores and restraint statistics. The interactive contact map between residues can be clicked to obtain information about the restraints and their contributions. Profiles of quality scores are plotted along the protein sequence, and contact maps provide information of the agreement with the data on a residue pair level. Conclusion The graphical tools and outputs described here significantly extend the validation and analysis possibilities of NOE assignments given by ARIA as well as the analysis of the quality of the final structure ensemble. These tools are included in the latest version of ARIA, which is available at http://aria.pasteur.fr. The Web site also contains an installation guide, a user manual and example calculations.

  17. A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints

    International Nuclear Information System (INIS)

    Tang, Chun; Clore, G. Marius

    2006-01-01

    A simple and reliable approach for docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints (as few as three from a single point) in combination with a novel representation for an attractive potential between mapped interaction surfaces is described. Unambiguous assignments of very sparse intermolecular NOEs are obtained using a reverse labeling strategy in which one the components is fully deuterated with the exception of selective protonation of the δ-methyl groups of isoleucine, while the other component is uniformly 13 C-labeled. This labeling strategy can be readily extended to selective protonation of Ala, Leu, Val or Met. The attractive potential is described by a 'reduced' radius of gyration potential applied specifically to a subset of interfacial residues (those with an accessible surface area ≥ 50% in the free proteins) that have been delineated by chemical shift perturbation. Docking is achieved by rigid body minimization on the basis of a target function comprising the sparse NOE distance restraints, a van der Waals repulsion potential and the 'reduced' radius of gyration potential. The method is demonstrated for two protein-protein complexes (EIN-HPr and IIA Glc -HPr) from the bacterial phosphotransferase system. In both cases, starting from 100 different random orientations of the X-ray structures of the free proteins, 100% convergence is achieved to a single cluster (with near identical atomic positions) with an overall backbone accuracy of ∼2 A. The approach described is not limited to NMR, since interfaces can also be mapped by alanine scanning mutagenesis, and sparse intermolecular distance restraints can be derived from double cycle mutagenesis, cross-linking combined with mass spectrometry, or fluorescence energy transfer

  18. Determination of protein global folds using backbone residual dipolar coupling and long-range NOE restraints

    International Nuclear Information System (INIS)

    Giesen, Alexander W.; Homans, Steve W.; Brown, Jonathan Miles

    2003-01-01

    We report the determination of the global fold of human ubiquitin using protein backbone NMR residual dipolar coupling and long-range nuclear Overhauser effect (NOE) data as conformational restraints. Specifically, by use of a maximum of three backbone residual dipolar couplings per residue (N i -H N i , N i -C' i-1 , H N i - C' i-1 ) in two tensor frames and only backbone H N -H N NOEs, a global fold of ubiquitin can be derived with a backbone root-mean-square deviation of 1.4 A with respect to the crystal structure. This degree of accuracy is more than adequate for use in databases of structural motifs, and suggests a general approach for the determination of protein global folds using conformational restraints derived only from backbone atoms

  19. A simple and reliable approach to docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chun; Clore, G. Marius [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: mariusc@intra.niddk.nih.gov

    2006-09-15

    A simple and reliable approach for docking protein-protein complexes from very sparse NOE-derived intermolecular distance restraints (as few as three from a single point) in combination with a novel representation for an attractive potential between mapped interaction surfaces is described. Unambiguous assignments of very sparse intermolecular NOEs are obtained using a reverse labeling strategy in which one the components is fully deuterated with the exception of selective protonation of the {delta}-methyl groups of isoleucine, while the other component is uniformly {sup 13}C-labeled. This labeling strategy can be readily extended to selective protonation of Ala, Leu, Val or Met. The attractive potential is described by a 'reduced' radius of gyration potential applied specifically to a subset of interfacial residues (those with an accessible surface area {>=} 50% in the free proteins) that have been delineated by chemical shift perturbation. Docking is achieved by rigid body minimization on the basis of a target function comprising the sparse NOE distance restraints, a van der Waals repulsion potential and the 'reduced' radius of gyration potential. The method is demonstrated for two protein-protein complexes (EIN-HPr and IIA{sup Glc}-HPr) from the bacterial phosphotransferase system. In both cases, starting from 100 different random orientations of the X-ray structures of the free proteins, 100% convergence is achieved to a single cluster (with near identical atomic positions) with an overall backbone accuracy of {approx}2 A. The approach described is not limited to NMR, since interfaces can also be mapped by alanine scanning mutagenesis, and sparse intermolecular distance restraints can be derived from double cycle mutagenesis, cross-linking combined with mass spectrometry, or fluorescence energy transfer.

  20. Results of the R and D activity on the NOE scintillating fiber calorimeter

    International Nuclear Information System (INIS)

    Demitri, I.

    2001-01-01

    The NOE scintillating fiber calorimeter has undergone four years of intense R and D activity. Measurements of light attenuation and time resolution have been carried out on a variety of commercially available scintillating fibers. Both these parameters are important for the optimisation of the design of the calorimeter which will be part of the ICANOE detector

  1. Results of the R and D activity on the NOE scintillating fiber calorimeter

    Energy Technology Data Exchange (ETDEWEB)

    Demitri, I. E-mail: ivan.demitri@le.infr.it

    2001-04-01

    The NOE scintillating fiber calorimeter has undergone four years of intense R and D activity. Measurements of light attenuation and time resolution have been carried out on a variety of commercially available scintillating fibers. Both these parameters are important for the optimisation of the design of the calorimeter which will be part of the ICANOE detector.

  2. Compiled data set of exact NOE distance limits, residual dipolar couplings and scalar couplings for the protein GB3

    Directory of Open Access Journals (Sweden)

    Beat Vögeli

    2015-12-01

    Full Text Available We compiled an NMR data set consisting of exact nuclear Overhauser enhancement (eNOE distance limits, residual dipolar couplings (RDCs and scalar (J couplings for GB3, which forms one of the largest and most diverse data set for structural characterization of a protein to date. All data have small experimental errors, which are carefully estimated. We use the data in the research article Vogeli et al., 2015, Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics, J. Struct. Biol., 191, 3, 306–317, doi:10.1016/j.jsb.2015.07.008 [1] for cross-validation in multiple-state structural ensemble calculation. We advocate this set to be an ideal test case for molecular dynamics simulations and structure calculations.

  3. Chemical-exchange-sensitive MRI of amide, amine and NOE at 9.4 T versus 15.2 T.

    Science.gov (United States)

    Chung, Julius Juhyun; Choi, Wonmin; Jin, Tao; Lee, Jung Hee; Kim, Seong-Gi

    2017-09-01

    Chemical exchange (CE)-sensitive MRI benefits greatly from stronger magnetic fields; however, field effects on CE-sensitive imaging have not yet been studied well in vivo. We have compared CE-sensitive Z-spectra and maps obtained at the fields of 9.4 T and 15.2 T in phantoms and rats with off-resonance chemical-exchange-sensitive spin lock (CESL), which is similar to conventional chemical exchange saturation transfer. At higher fields, the background peak at water resonance has less spread and the exchange rate relative to chemical shift decreases, thus CESL intensity is dependent on B 0 . For the in vivo amide and nuclear Overhauser enhancement (NOE) composite resonances of rat brains, intensities were similar for both magnetic fields, but effective amide proton transfer and NOE values obtained with three-point quantification or a curve fitting method were larger at 15.2 T due to the reduced spread of attenuation at the direct water resonance. When using intermediate exchange-sensitive irradiation parameters, the amine proton signal was 65% higher at 15.2 T than at 9.4 T due to a reduced ratio of exchange rate to chemical shift. In summary, increasing magnetic field provides enhancements to CE-sensitive signals in the intermediate exchange regime and reduces contamination from background signals in the slow exchange regime. Consequently, ultrahigh magnetic field is advantageous for CE-sensitive MRI, especially for amine and hydroxyl protons. Copyright © 2017 John Wiley & Sons, Ltd.

  4. U. Blossing, G. Imsen & L. Moos (eds., The Nordic Education Model: ´A School for All´ Encounters Noe-Liberal Policy (Dordrecht: Springer, 2014

    Directory of Open Access Journals (Sweden)

    Þorlákur Axel Jónsson

    2016-03-01

    Full Text Available Book review of: Blossing, G. Imsen & L. Moos (eds, The Nordic Education Model: ´A School for All´ Encounters Noe-Liberal Policy (Dordrecht: Springer, Policy Implications of Research in Education 1, 2014

  5. A transition radiation detector interleaved with low-density targets for the NOE experiment

    CERN Document Server

    Alexandrov, K V; Bernardini, P; Brigida, M; Campana, D; Candela, A M; Caruso, R; Cassese, F; Ceres, A; D'Aquino, B; De Cataldo, G; De Mitri, I; Di Credico, A; Favuzzi, C; Fusco, P; Gargano, F; Giglietto, N; Giordano, F; Grillo, A; Guarino, F; Gustavino, C; Lamanna, E; Lauro, A; Leone, A; Loparco, F; Mancarella, G; Martello, D; Mazziotta, M N; Mikheyev, S P; Mongelli, M; Osteria, G; Palladino, Vittorio; Passeggio, G; Perchiazzi, M; Pontoniere, G; Rainó, A; Rocco, R; Romanucci, E; Rubizzo, U; Sacchetti, A; Scapparone, E; Spinelli, P; Tikhomirov, V; Vaccina, A; Vanzanella, E; Weber, M

    2001-01-01

    The NOE Collaboration has proposed a transition radiation detector (TRD) interleaved with marble targets to tag the electron decay channel of tau leptons produced by nu /sub tau /, eventually originated by nu /sub mu / oscillations in a long base line experiment. A reduced scale TRD detector prototype has been built and exposed to an electron/pion beam at the CERN PS. Discrimination capabilities between electrons and both charged and neutral pions, representing the main source of background for our measurement, have been determined obtaining rejection factors of the order of the tenth of percent for charged pions, and of a few percent for the neutral pion, matching the experiment requirements. The capabilities of this detector to measure the energy released by particles that start showering inside the targets are shown. A momentum resolution sigma /sub p//P

  6. Conformational analysis of a Chlamydia-specific disaccharide α-Kdo-(2→8)-α-Kdo-(2→O)-allyl in aqueous solution and bound to a monoclonal antibody: Observation of intermolecular transfer NOEs

    International Nuclear Information System (INIS)

    Sokolowski, Tobias; Haselhorst, Thomas; Scheffler, Karoline; Weisemann, Ruediger; Kosma, Paul; Brade, Helmut; Brade, Lore; Peters, Thomas

    1998-01-01

    The disaccharide α-Kdo-(2 → 8)-α-Kdo (Kdo: 3-deoxy-d-manno-oct-2-ulosonic acid) represents a genus-specific epitope of the lipopolysaccharide of the obligate intracellular human pathogen Chlamydia. The conformation of the synthetically derived disaccharide α-Kdo-(2 → 8)-α-Kdo-(2 → O)-allyl was studied in aqueous solution, and complexed to a monoclonal antibody S25-2. Various NMR experiments based on the detection of NOEs (or transfer NOEs) and ROEs (or transfer ROEs) were performed. A major problem was the extensive overlap of almost all 1 H NMR signals of α-Kdo-(2 → 8)-α-Kdo-(2 → O)-allyl. To overcome this difficulty, HMQC-NOESY and HMQC-trNOESY experiments were employed. Spin diffusion effects were identified using trROESY experiments, QUIET-trNOESY experiments and MINSY experiments. It was found that protein protons contribute to the observed spin diffusion effects. At 800 MHz, intermolecular trNOEs were observed between ligand protons and aromatic protons in the antibody binding site. From NMR experiments and Metropolis Monte Carlo simulations, it was concluded that α-Kdo-(2 → 8)-α-Kdo-(2 → O)-allyl in aqueous solution exists as a complex conformational mixture. Upon binding to the monoclonal antibody S25-2, only a limited range of conformations is available to α-Kdo-(2 → 8)-α-Kdo-(2 → O)-allyl. These possible bound conformations were derived from a distance geometry analysis using transfer NOEs as experimental constraints. It is clear that a conformation is selected which lies within a part of the conformational space that is highly populated in solution. This conformational space also includes the conformation found in the crystal structure. Our results provide a basis for modeling studies of the antibody-disaccharide complex

  7. (¹⁵N ± ¹³C') edited (4, 3)D-H(CC)CONH TOCSY and (4, 3)D-NOESY HNCO experiments for unambiguous side chain and NOE assignments of proteins with high shift degeneracy.

    Science.gov (United States)

    Kumar, Dinesh; Arora, Ashish

    2011-11-01

    Well-resolved and unambiguous through-bond correlations and NOE data are crucial for high-quality protein structure determination by NMR. In this context, we present here (4, 3)D reduced dimensionality (RD) experiments: H(CC)CONH TOCSY and NOESY HNCO--which instead of (15)N shifts exploit the linear combination of (15)N(i) and (13)C'(i-1) shifts (where i is a residue number) to resolve the through-bond (1)H-(1)H correlations and through-space (1)H-(1)H NOEs. The strategy makes use of the fact that (15)N and (13)C' chemical shifts when combined linearly provide a dispersion which is better compared to those of the individual chemical shifts. The extended dispersion thus available in these experiments will help to obtain the unambiguous side chain and accurate NOE assignments especially for medium-sized alpha-helical or partially unstructured proteins [molecular weight (MW) between 12-15 kDa] as well as higher MW (between 15-25 kDa) folded proteins where spectral overlap renders inaccurate and ambiguous NOEs. Further, these reduced dimensionality experiments in combination with routinely used (15)N and (13)C' edited TOCSY and NOESY experiments will provide an alternative way for high-quality NMR structure determination of large unstable proteins (with very high shift degeneracy), which are not at all amenable to 4D NMR. The utility of these experiments has been demonstrated here using (13)C/(15)N labeled ubiquitin (76 aa) protein. Copyright © 2011 John Wiley & Sons, Ltd.

  8. Conformational analysis of a Chlamydia-specific disaccharide {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl in aqueous solution and bound to a monoclonal antibody: Observation of intermolecular transfer NOEs

    Energy Technology Data Exchange (ETDEWEB)

    Sokolowski, Tobias; Haselhorst, Thomas; Scheffler, Karoline [Medizinische Universitaet, Institut fuer Chemie (Germany); Weisemann, Ruediger [Bruker Analytik GmbH, Silberstreifen (Germany); Kosma, Paul [Institut fuer Chemie der Universitaet fuer Bodenkultur Wien (Austria); Brade, Helmut; Brade, Lore [Forschungszentrum Borstel, Zentrum fuer Medizin und Biowissenschaften Parkallee 22 (Germany); Peters, Thomas [Medizinische Universitaet, Institut fuer Chemie (Germany)

    1998-07-15

    The disaccharide {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo (Kdo: 3-deoxy-d-manno-oct-2-ulosonic acid) represents a genus-specific epitope of the lipopolysaccharide of the obligate intracellular human pathogen Chlamydia. The conformation of the synthetically derived disaccharide {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl was studied in aqueous solution, and complexed to a monoclonal antibody S25-2. Various NMR experiments based on the detection of NOEs (or transfer NOEs) and ROEs (or transfer ROEs) were performed. A major problem was the extensive overlap of almost all {sup 1}H NMR signals of {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl. To overcome this difficulty, HMQC-NOESY and HMQC-trNOESY experiments were employed. Spin diffusion effects were identified using trROESY experiments, QUIET-trNOESY experiments and MINSY experiments. It was found that protein protons contribute to the observed spin diffusion effects. At 800 MHz, intermolecular trNOEs were observed between ligand protons and aromatic protons in the antibody binding site. From NMR experiments and Metropolis Monte Carlo simulations, it was concluded that {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl in aqueous solution exists as a complex conformational mixture. Upon binding to the monoclonal antibody S25-2, only a limited range of conformations is available to {alpha}-Kdo-(2{sup {yields}}8)-{alpha}-Kdo-(2{sup {yields}}O)-allyl. These possible bound conformations were derived from a distance geometry analysis using transfer NOEs as experimental constraints. It is clear that a conformation is selected which lies within a part of the conformational space that is highly populated in solution. This conformational space also includes the conformation found in the crystal structure. Our results provide a basis for modeling studies of the antibody-disaccharide complex.

  9. Accurate Determination of Leucine and Valine Side-chain Conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine Cγ-Hγ/Cβ-Hβ Residual Dipolar Couplings

    International Nuclear Information System (INIS)

    Tang, Chun; Iwahara, Junji; Clore, G. Marius

    2005-01-01

    An isotope labeling scheme is described in which specific protonation of methine and methyl protons of leucine and valine is obtained on a 15 N/ 13 C labeled background with uniform deuteration of all other non-exchangeable protons. The presence of a protonated methine group has little effect on the favorable relaxation properties of the methyl protons of Leu and Val. This labeling scheme permits the rotameric state of leucine side-chains to be readily determined by simple inspection of the pattern of Hγ(i)-H N (i) and Hγ(i)-H N (i+1) NOEs in a 3D 15 N-separated NOE spectrum free of complications arising from spectral overlap and spin-diffusion. In addition, one-bond residual dipolar couplings for the methine 13 C- 1 H bond vectors of Leu and Val can be accurately determined from an intensity J-modulated constant-time HCCH-COSY experiment and used to accurately orient the side-chains of Leu and Val. Incorporation of these data into structure refinement improves the accuracy with which the conformations of Leu and Val side-chains can be established. This is important to ensure optimal packing both within the protein core and at intermolecular interfaces. The impact of the method on protein structure determination is illustrated by application to enzyme IIA Chitobiose , a 34 kDa homotrimeric phosphotransferase protein

  10. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  11. Accurate Determination of Leucine and Valine Side-chain Conformations using U-[{sup 15}N/{sup 13}C/{sup 2}H]/[{sup 1}H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine C{gamma}-H{gamma}/C{beta}-H{beta} Residual Dipolar Couplings

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chun; Iwahara, Junji; Clore, G. Marius [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)], E-mail: mariusc@intra.niddk.nih.gov

    2005-10-15

    An isotope labeling scheme is described in which specific protonation of methine and methyl protons of leucine and valine is obtained on a {sup 15}N/{sup 13}C labeled background with uniform deuteration of all other non-exchangeable protons. The presence of a protonated methine group has little effect on the favorable relaxation properties of the methyl protons of Leu and Val. This labeling scheme permits the rotameric state of leucine side-chains to be readily determined by simple inspection of the pattern of H{gamma}(i)-H{sub N}(i) and H{gamma}(i)-H{sub N}(i+1) NOEs in a 3D {sup 15}N-separated NOE spectrum free of complications arising from spectral overlap and spin-diffusion. In addition, one-bond residual dipolar couplings for the methine {sup 13}C-{sup 1}H bond vectors of Leu and Val can be accurately determined from an intensity J-modulated constant-time HCCH-COSY experiment and used to accurately orient the side-chains of Leu and Val. Incorporation of these data into structure refinement improves the accuracy with which the conformations of Leu and Val side-chains can be established. This is important to ensure optimal packing both within the protein core and at intermolecular interfaces. The impact of the method on protein structure determination is illustrated by application to enzyme IIA{sup Chitobiose}, a 34 kDa homotrimeric phosphotransferase protein.

  12. Direct methods and residue type specific isotope labeling in NMR structure determination and model-driven sequential assignment

    International Nuclear Information System (INIS)

    Schedlbauer, Andreas; Auer, Renate; Ledolter, Karin; Tollinger, Martin; Kloiber, Karin; Lichtenecker, Roman; Ruedisser, Simon; Hommel, Ulrich; Schmid, Walther; Konrat, Robert; Kontaxis, Georg

    2008-01-01

    Direct methods in NMR based structure determination start from an unassigned ensemble of unconnected gaseous hydrogen atoms. Under favorable conditions they can produce low resolution structures of proteins. Usually a prohibitively large number of NOEs is required, to solve a protein structure ab-initio, but even with a much smaller set of distance restraints low resolution models can be obtained which resemble a protein fold. One problem is that at such low resolution and in the absence of a force field it is impossible to distinguish the correct protein fold from its mirror image. In a hybrid approach these ambiguous models have the potential to aid in the process of sequential backbone chemical shift assignment when 13 C β and 13 C' shifts are not available for sensitivity reasons. Regardless of the overall fold they enhance the information content of the NOE spectra. These, combined with residue specific labeling and minimal triple-resonance data using 13 C α connectivity can provide almost complete sequential assignment. Strategies for residue type specific labeling with customized isotope labeling patterns are of great advantage in this context. Furthermore, this approach is to some extent error-tolerant with respect to data incompleteness, limited precision of the peak picking, and structural errors caused by misassignment of NOEs

  13. De novo protein structure determination using sparse NMR data

    International Nuclear Information System (INIS)

    Bowers, Peter M.; Strauss, Charlie E.M.; Baker, David

    2000-01-01

    We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models are built from these fragments by minimizing an energy function that favors hydrophobic burial, strand pairing, and satisfaction of NOE constraints. Models generated using this procedure with ∼1 NOE constraint per residue are in some cases closer to the corresponding X-ray structures than the published NMR solution structures. The method requires only the sparse constraints available during initial stages of NMR structure determination, and thus holds promise for increasing the speed with which protein solution structures can be determined

  14. Scrambling free combinatorial labeling of alanine-β, isoleucine-δ1, leucine-proS and valine-proS methyl groups for the detection of long range NOEs

    Energy Technology Data Exchange (ETDEWEB)

    Kerfah, Rime [NMR-Bio, IBS/CEA (France); Plevin, Michael J. [University of York, Department of Biology (United Kingdom); Pessey, Ombeline [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France); Hamelin, Olivier [CNRS (France); Gans, Pierre; Boisbouvier, Jerome, E-mail: jerome.boisbouvier@ibs.fr [Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS) (France)

    2015-01-15

    Specific isotopic labeling of methyl groups in proteins has greatly extended the applicability of solution NMR spectroscopy. Simultaneous labeling of the methyl groups of several different amino acid types can offer a larger number of useful probes that can be used for structural characterisations of challenging proteins. Herein, we propose an improved AILV methyl-labeling protocol in which L and V are stereo-specifically labeled. We show that 2-ketobutyrate cannot be combined with Ala and 2-acetolactate (for the stereo-specific labeling of L and V) as this results in co-incorporation incompatibility and isotopic scrambling. Thus, we developed a robust and cost-effective enzymatic synthesis of the isoleucine precursor, 2-hydroxy-2-(1′-[{sup 2}H{sub 2}], 2′-[{sup 13}C])ethyl-3-keto-4-[{sup 2}H{sub 3}]butanoic acid, as well as an incorporation protocol that eliminates metabolic leakage. We show that application of this labeling scheme to a large 82 kDa protein permits the detection of long-range {sup 1}H–{sup 1}H NOE cross-peaks between methyl probes separated by up to 10 Å.

  15. Concluding Remarks; Zaklyuchitel'noe slovo

    Energy Technology Data Exchange (ETDEWEB)

    Budker, G. I. [Institute of Nuclear Physics, Siberian Department of the USSR Academy of Sciences, Novosibirsk, Union Of Soviet Socialist Republics (Russian Federation)

    1969-01-15

    I feel that the changes which have taken place in science in the last few years open up new possibilities, about which I should like to say a few words. In 1951 we began work on thermonuclear reactions in the confident belief that we would solve the problem with a rush and immediately. I was assigned the task of ensuring that our future thermonuclear reactor would not get too much out of hand. It was like the story of the man who wished to invent a perpetual motion machine and had taken out a patent on a method for keeping it under control. This attitude stemmed from the successes in developing ''explosive thermonuclear reactors'', a task which was achieved within a very short period of time, leaving physicists with the impression that they could do everything - and do it fast. However, experience soon showed that here we had a scientific rather than a technological problem and that it would be necessary to study in detail the physics of plasmas - which we have now been doing for over ten years. [Russian] Mne kazhetsja, chto za poslednie gody- v nauke proizoshli izmenenija, otkryvshie novye vozmozhnosti, na kotoryh ja hotel by ostanovit'sja. Ja hochu napomnit', chto v 1951 godu my nachali raboty po fizike plazmy i termojadernym reakcijam. U nas byla uverennost', chto my reshim jetu problemu s hodu, srazu. Mne bylo porucheno obespechivat' regulirovanie budushhego termojadernogo reaktora, chtoby tot ne ochen' ''razognalsja'' i ne vyshel iz-pod kontrolja. Sejchas jeto poruchenie napominaet istoriju o tom, kak odin hotel izobresti vechnyj dvigatel' i vzjal patent na to, chtoby tot ne razgonjalsja do beskonechnyh skorostej. . . Bol'shie uspehi v razrabotke ''vzryvchatyh termojadernyh reaktorov'', kotorye byli sozdany za ochen' korotkoe vremja, porodili u fizikov uverennost' v to, chto oni mogut sdelat' vse i sdelat' bystro. Odnako ochen' skoro zhizn' pokazala, chto jetim delom nuzhno zanimat'sja ne kak konstruirovaniem, a kak naukoj, chto nado razvivat' plazmennuju

  16. Main-chain-directed strategy for the assignment of 1H NMR spectra of proteins

    International Nuclear Information System (INIS)

    Englander, S.W.; Wand, A.J.

    1987-01-01

    A strategy for assigning the resonances in two-dimensional (2D) NMR spectra of proteins is described. The method emphasizes the analysis of through-space relationships between protons by use of the two-dimensional nuclear Overhauser effect (NOE) experiment. NOE patterns used in the algorithm were derived from a statistical analysis of the combinations of short proton-proton distances observed in the high-resolution crystal structures of 21 proteins. One starts with a search for authentic main-chain NH-C/sub α/H-C/sub β/H J-coupled units, which can be found with high reliability. The many main-chain units of a protein are then placed in their proper juxtaposition by recognition of predefined NOE connectivity patterns. To discover these connectivities, the 2D NOE spectrum is examined, in a prescribed order, for the distinct NOE patterns characteristic of helices, sheets, turns, and extended chain. Finally, the recognition of a few amino acid side-chain types places the discovered secondary structure elements within the polypeptide sequences. Unlike the sequential assignment approach, the main-chain-directed strategy does not rely on the difficult task of recognizing many side-chain spin systems in J-correlated spectra, the assignment process is not in general sequential with the polypeptide chain, and the prescribed connectivity patterns are cyclic rather than linear. The latter characteristic avoids ambiguous branch points in the analysis and imposed an internally confirmatory property on each forward step

  17. Solid-phase synthesis and high-resolution NMR studies of two synthetic double-helical RNA dodecamers

    International Nuclear Information System (INIS)

    Chou, S.H.; Flynn, P.; Reid, B.

    1989-01-01

    Ten-micromole solid-phase RNA synthesis has been successfully performed on an automated nucleic acid synthesizer with coupling efficiencies up to 99%, using the tert-butyldimethylsilyl group to protect the 2'-hydroxyl. The tert-butyldimethylsilyl group was easily removed by tetrabutylammonium fluoride under conditions in which virtually no 2'- to 3'-isomerization was found to occur. By use of this approach, the self-complementary RNA dodecamers r(CGCGAAUUCGCG) and r(CGCGUAUACGCG) were synthesized on an automated nucleic acid synthesizer, purified by TLC, and studied by high-resolution NMR. Imino protons were assigned from one-dimensional nuclear Overhauser effects. The nonexchangeable base, H1', and H2' protons were assigned by the sequential NOESY connectivity method. The NOE data from these two oligomers were analyzed qualitatively and compared to the ideal A- and B-type helix models of Arnott et al. (1972a,b). The internucleotide H6/H8 NOEs to the preceding H1' in r(CGCGUAUACGCG) were found to be sequence-dependent and probably reflect the roll angles between adjacent bases. The internucleotide H6/H8 to H2' NOEs of these oligomers correspond very well to an A-type conformation, but the interstrand adenine H2 NOEs to the following H1' were much stronger than those predicted from the fiber model. These strong interstrand NOEs can be rationalized by base pair slide to favor more interstrand base overlap

  18. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1

    International Nuclear Information System (INIS)

    Dolenc, Jozica; Missimer, John H.; Steinmetz, Michel O.; Gunsteren, Wilfred F. van

    2010-01-01

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 φ torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular α-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured 3 J(H N -H Cα )-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and 3 J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and 3 J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  19. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

    Science.gov (United States)

    Dolenc, Jozica; Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2010-07-01

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 phi torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular alpha-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured (3)J(H(N)-H(Calpha))-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and (3)J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and (3)J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  20. Natural outdoor environments and mental health: Stress as a possible mechanism.

    Science.gov (United States)

    Triguero-Mas, Margarita; Donaire-Gonzalez, David; Seto, Edmund; Valentín, Antònia; Martínez, David; Smith, Graham; Hurst, Gemma; Carrasco-Turigas, Glòria; Masterson, Daniel; van den Berg, Magdalena; Ambròs, Albert; Martínez-Íñiguez, Tania; Dedele, Audrius; Ellis, Naomi; Grazulevicius, Tomas; Voorsmit, Martin; Cirach, Marta; Cirac-Claveras, Judith; Swart, Wim; Clasquin, Eddy; Ruijsbroek, Annemarie; Maas, Jolanda; Jerret, Michael; Gražulevičienė, Regina; Kruize, Hanneke; Gidlow, Christopher J; Nieuwenhuijsen, Mark J

    2017-11-01

    Better mental health has been associated with exposure to natural outdoor environments (NOE). However, comprehensive studies including several indicators of exposure and outcomes, potential effect modifiers and mediators are scarce. We used novel, objective measures to explore the relationships between exposure to NOE (i.e. residential availability and contact) and different indicators of mental health, and possible modifiers and mediators. A nested cross-sectional study was conducted in: Barcelona, Spain; Stoke-on-Trent, United Kingdom; Doetinchem, Netherlands; Kaunas, Lithuania. Participants' exposure to NOE (including both surrounding greenness and green and/or blue spaces) was measured in terms of (a) amount in their residential environment (using Geographical Information Systems) and (b) their contact with NOE (using smartphone data collected over seven days). Self-reported information was collected for mental health (psychological wellbeing, sleep quality, vitality, and somatisation), and potential effect modifiers (gender, age, education level, and city) and mediators (perceived stress and social contacts), with additional objective NOE physical activity (potential mediator) derived from smartphone accelerometers. Analysis of data from 406 participants showed no statistically significant associations linking mental health and residential NOE exposure. However, NOE contact, especially surrounding greenness, was statistically significantly tied to better mental health. There were indications that these relationships were stronger for males, younger people, low-medium educated, and Doetinchem residents. Perceived stress was a mediator of most associations, and physical activity and social contacts were not. Our findings indicate that contact with NOE benefits mental health. Our results also suggest that having contact with NOE that can facilitate stress reduction could be particularly beneficial. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ2 conformation by intra-residue NOEs

    International Nuclear Information System (INIS)

    Miyanoiri, Yohei; Takeda, Mitsuhiro; Jee, JunGoo; Ono, Akira M.; Okuma, Kosuke; Terauchi, Tsutomu; Kainosho, Masatsune

    2011-01-01

    Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U– 13 C, 15 N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the 13 C– 13 C and 13 C– 1 H spin coupling networks (Kainosho et al. in Nature 440:52–57, 2006). In this paper, we propose an alternative type of SAIL-Trp with the [ζ2,ζ3- 2 H 2 ; δ1,ε3,η2- 13 C 3 ; ε1- 15 N]-indole ring ([ 12 C γ, 12 C ε2 ] SAIL-Trp), which provides a more robust way to correlate the 1 H β , 1 H α , and 1 H N to the 1 H δ1 and 1 H ε3 through the intra-residue NOEs. The assignment of the 1 H δ1 / 13 C δ1 and 1 H ε3 / 13 C ε3 signals can thus be transferred to the 1 H ε1 / 15 N ε1 and 1 H η2 / 13 C η2 signals, as with the previous type of SAIL-Trp, which has an extra 13 C at the C γ of the ring. By taking advantage of the stereospecific deuteration of one of the prochiral β-methylene protons, which was 1 H β2 in this experiment, one can determine the side-chain conformation of the Trp residue including the χ 2 angle, which is especially important for Trp residues, as they can adopt three preferred conformations. We demonstrated the usefulness of [ 12 C γ , 12 C ε2 ] SAIL-Trp for the 12 kDa DNA binding domain of mouse c-Myb protein (Myb-R2R3), which contains six Trp residues.

  2. Alternative SAIL-Trp for robust aromatic signal assignment and determination of the χ(2) conformation by intra-residue NOEs.

    Science.gov (United States)

    Miyanoiri, Yohei; Takeda, Mitsuhiro; Jee, JunGoo; Ono, Akira M; Okuma, Kosuke; Terauchi, Tsutomu; Kainosho, Masatsune

    2011-12-01

    Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U-(13)C,(15)N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the (13)C-(13)C and (13)C-(1)H spin coupling networks (Kainosho et al. in Nature 440:52-57, 2006). In this paper, we propose an alternative type of SAIL-Trp with the [ζ2,ζ3-(2)H(2); δ1,ε3,η2-(13)C(3); ε1-(15)N]-indole ring ([(12)C (γ,) ( 12) C(ε2)] SAIL-Trp), which provides a more robust way to correlate the (1)H(β), (1)H(α), and (1)H(N) to the (1)H(δ1) and (1)H(ε3) through the intra-residue NOEs. The assignment of the (1)H(δ1)/(13)C(δ1) and (1)H(ε3)/(13)C(ε3) signals can thus be transferred to the (1)H(ε1)/(15)N(ε1) and (1)H(η2)/(13)C(η2) signals, as with the previous type of SAIL-Trp, which has an extra (13)C at the C(γ) of the ring. By taking advantage of the stereospecific deuteration of one of the prochiral β-methylene protons, which was (1)H(β2) in this experiment, one can determine the side-chain conformation of the Trp residue including the χ(2) angle, which is especially important for Trp residues, as they can adopt three preferred conformations. We demonstrated the usefulness of [(12)C(γ),(12)C(ε2)] SAIL-Trp for the 12 kDa DNA binding domain of mouse c-Myb protein (Myb-R2R3), which contains six Trp residues.

  3. Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: Effect of approximations on the accuracy of derived structures

    International Nuclear Information System (INIS)

    Thomas, P.D.; Basus, V.J.; James, T.L.

    1991-01-01

    Solution structures for many proteins have been determined to date utilizing interproton distance constraints estimated from two-dimensional nuclear Overhauser effect (2D NOE) spectra. Although the simple isolated spin pair approximation (ISPA) generally used can result in systematic errors in distances, the large number of constraints enables proteins structure to be defined with reasonably high resolution. Effects of these systematic errors on the resulting protein structure are examined. Iterative relaxation matrix calculations, which account for dipolar interactions between all protons in a molecule, can accurately determine internuclear distances with little or no a priori knowledge of the molecular structure. The value of this additional complexity is also addressed. To assess these distance determination methods, hypothetical experimental data, including random noise and peak overlap, are calculated for an arbitrary true protein structure. Three methods of obtaining distance constraints from 2D NOE peak intensities are examined: one entails a conservative use of ISPA, one assumes the ISPA to be fairly accurate, and on utilizes an iterative relaxation matrix method called MARDIGRAS (matrix analysis of relaxation for discerning the geometry of an aqueous structure), developed in this laboratory. An R factor for evaluating fit between experimental and calculated 2D NOE intensities is proposed

  4. Accurate Quantitation of Water-amide Proton Exchange Rates Using the Phase-Modulated CLEAN Chemical EXchange (CLEANEX-PM) Approach with a Fast-HSQC (FHSQC) Detection Scheme

    International Nuclear Information System (INIS)

    Hwang, Tsang-Lin; Zijl, Peter C.M. van; Mori, Susumu

    1998-01-01

    Measurement of exchange rates between water and NH protons by magnetization transfer methods is often complicated by artifacts, such as intramolecular NOEs, and/or TOCSY transfer from Cα protons coincident with the water frequency, or exchange-relayed NOEs from fast exchanging hydroxyl or amine protons. By applying the Phase-Modulated CLEAN chemical EXchange (CLEANEX-PM) spin-locking sequence, 135 o (x) 120 o (-x) 110 o (x) 110 o (-x) 120 o (x) 135 o (-x) during the mixing period, these artifacts can be eliminated, revealing an unambiguous water-NH exchange spectrum. In this paper, the CLEANEX-PM mixing scheme is combined with Fast-HSQC (FHSQC) detection and used to obtain accurate chemical exchange rates from the initial slope analysis for a sample of 15N labeled staphylococcal nuclease. The results are compared to rates obtained using Water EXchange filter (WEX) II-FHSQC, and spin-echo-filtered WEX II-FHSQC measurements, and clearly identify the spurious NOE contributions in the exchange system

  5. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1

    Energy Technology Data Exchange (ETDEWEB)

    Dolenc, Jozica [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland); Missimer, John H.; Steinmetz, Michel O. [Paul Scherrer Institut, Biomolecular Research (Switzerland); Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.c [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland)

    2010-07-15

    The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16-31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 {phi} torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular {alpha}-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured {sup 3}J(H{sub N}-H{sub C{alpha}})-coupling constants, indicating that different conformers of GCN4p16-31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and {sup 3}J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and {sup 3}J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16-31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16-31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

  6. NULIFE - the European NoE 'Nuclear Plant Life Prediction'

    International Nuclear Information System (INIS)

    Cojan, Mihail

    2008-01-01

    INR Pitesti become on the 29th September 2006 a partner in the European Network of Excellence Nuclear Plant Life Prediction (NULIFE) coordinated by Technical Research Centre of Finland (VTT). The EU's Network of Excellence NULIFE has been launched under the EURATOM FP6 Program with a clear focus on integrating safety-oriented research on materials, structures and systems and exploiting the results of this integration through the production of harmonized lifetime assessment methods. NULIFE will help provide a better common understanding of, and information on, the factors affecting the lifetime of nuclear power plants which, together with associated management methods, will help facilitate extensions to the safe and economic lifetime of existing nuclear power plants. (author)

  7. NMR studies of the sporulation protein SpoIIAA: Implications for the regulation of the transcription factor {sigma}F in Bacillus subtilis

    Energy Technology Data Exchange (ETDEWEB)

    Kovacs, Helena; Comfort, David; Lord, Matthew; Yudkin, Michael; Campbell, Iain D.; Nilges, Michael

    2001-04-15

    SpoIIAA participates in a four-component mechanism for phosphorylation-dependent transcription control at the outset of sporulation. We report the refinement of the solution structure of SpoIIAA by using the automated iterative NOE assignment method ARIA. To complement the structural data, the protein dynamics were determined by measuring the T{sub 1}, T{sub 2} and NOE of the backbone {sup 15}N-nuclei. The refined structure permits a discussion of the structural features that are important for the function of SpoIIAA in the regulation of the sporulation sigma factor {sigma}{sup F}, and for homologous regulatory pathways present in B. subtilis and in other bacilli.

  8. NMR studies of the sporulation protein SpoIIAA: Implications for the regulation of the transcription factor σF in Bacillus subtilis

    International Nuclear Information System (INIS)

    Kovacs, Helena; Comfort, David; Lord, Matthew; Yudkin, Michael; Campbell, Iain D.; Nilges, Michael

    2001-01-01

    SpoIIAA participates in a four-component mechanism for phosphorylation-dependent transcription control at the outset of sporulation. We report the refinement of the solution structure of SpoIIAA by using the automated iterative NOE assignment method ARIA. To complement the structural data, the protein dynamics were determined by measuring the T 1 , T 2 and NOE of the backbone 15 N-nuclei. The refined structure permits a discussion of the structural features that are important for the function of SpoIIAA in the regulation of the sporulation sigma factor σ F , and for homologous regulatory pathways present in B. subtilis and in other bacilli

  9. Nuclear overhauser enhancement mediated chemical exchange saturation transfer imaging at 7 Tesla in glioblastoma patients.

    Directory of Open Access Journals (Sweden)

    Daniel Paech

    Full Text Available BACKGROUND AND PURPOSE: Nuclear Overhauser Enhancement (NOE mediated chemical exchange saturation transfer (CEST is a novel magnetic resonance imaging (MRI technique on the basis of saturation transfer between exchanging protons of tissue proteins and bulk water. The purpose of this study was to evaluate and compare the information provided by three dimensional NOE mediated CEST at 7 Tesla (7T and standard MRI in glioblastoma patients. PATIENTS AND METHODS: Twelve patients with newly diagnosed histologically proven glioblastoma were enrolled in this prospective ethics committee-approved study. NOE mediated CEST contrast was acquired with a modified three-dimensional gradient-echo sequence and asymmetry analysis was conducted at 3.3 ppm (B1 = 0.7 µT to calculate the magnetization transfer ratio asymmetry (MTR(asym. Contrast enhanced T1 (CE-T1 and T2-weighted images were acquired at 3T and used for data co-registration and comparison. RESULTS: Mean NOE mediated CEST signal based on MTR(asym values over all patients was significantly increased (p<0.001 in CE-T1 tumor (-1.99 ± 1.22%, tumor necrosis (-1.36 ± 1.30% and peritumoral CEST hyperintensities (PTCH within T2 edema margins (-3.56 ± 1.24% compared to contralateral normal appearing white matter (-8.38 ± 1.19%. In CE-T1 tumor (p = 0.015 and tumor necrosis (p<0.001 mean MTR(asym values were significantly higher than in PTCH. Extent of the surrounding tumor hyperintensity was smaller in eight out of 12 patients on CEST than on T2-weighted images, while four displayed at equal size. In all patients, isolated high intensity regions (0.40 ± 2.21% displayed on CEST within the CE-T1 tumor that were not discernible on CE-T1 or T2-weighted images. CONCLUSION: NOE mediated CEST Imaging at 7 T provides additional information on the structure of peritumoral hyperintensities in glioblastoma and displays isolated high intensity regions within the CE-T1 tumor that cannot be acquired on CE-T1 or T2

  10. Unambiguous Determination of Intermolecular Hydrogen Bond of NMR Structure by Molecular Dynamics Refinement Using All-Atom Force Field and Implicit Solvent Model

    International Nuclear Information System (INIS)

    Jee, Jun Goo

    2010-01-01

    It has been shown that AMD refinement is very useful for defining an intermolecular hydrogen bond in NMR structure calculation. The refined structure also provides a clue for explaining the pH dependence in Ub and UIM complexes. As reported by Choi et al., serine-mediated hydrogen bonds are the third most populated hydrogen bonds found in protein-protein intermolecular interactions, after the backbone-backbone and backbone-aspartate ones. The abundance imposes the requirement of an method to determine the interface of protein-protein complexes. The precise geometry is particularly important in the complex structures between Ub and UBDs. Ub recognizes various targets with the same surface, where both hydrophobic and hydrophobic interactions are involved. Hence, the details of the hydrophilic interactions are necessary to find the common binding modes. The structure determination of a biomolecule by NMR depends heavily on the distance restraints derived by the NOE cross peaks that are observed between two protons within 6 A through space. Therefore, the existence of the NOE peaks and their correct assignments to two corresponding protons are essential for an accurate and precise structure determination. Recent developments of NOE assignment and calculation algorithms have enabled the determination of protein 3D structures without any manual interpretation, provided chemical shifts are assigned in most atoms and sufficient NOE peaks exist. Along with these advances, the necessity of determining complicated structures such as complexes is increasing

  11. Alternative SAIL-Trp for robust aromatic signal assignment and determination of the {chi}{sub 2} conformation by intra-residue NOEs

    Energy Technology Data Exchange (ETDEWEB)

    Miyanoiri, Yohei; Takeda, Mitsuhiro [Nagoya University, Graduate School of Science, Structural Biology Research Center (Japan); Jee, JunGoo; Ono, Akira M.; Okuma, Kosuke; Terauchi, Tsutomu [Tokyo Metropolitan University, Center for Priority Areas (Japan); Kainosho, Masatsune, E-mail: kainosho@nagoya-u.jp [Nagoya University, Graduate School of Science, Structural Biology Research Center (Japan)

    2011-12-15

    Tryptophan (Trp) residues are frequently found in the hydrophobic cores of proteins, and therefore, their side-chain conformations, especially the precise locations of the bulky indole rings, are critical for determining structures by NMR. However, when analyzing [U-{sup 13}C,{sup 15}N]-proteins, the observation and assignment of the ring signals are often hampered by excessive overlaps and tight spin couplings. These difficulties have been greatly alleviated by using stereo-array isotope labeled (SAIL) proteins, which are composed of isotope-labeled amino acids optimized for unambiguous side-chain NMR assignment, exclusively through the {sup 13}C-{sup 13}C and {sup 13}C-{sup 1}H spin coupling networks (Kainosho et al. in Nature 440:52-57, 2006). In this paper, we propose an alternative type of SAIL-Trp with the [{zeta}2,{zeta}3-{sup 2}H{sub 2}; {delta}1,{epsilon}3,{eta}2-{sup 13}C{sub 3}; {epsilon}1-{sup 15}N]-indole ring ([{sup 12}C{sub {gamma},}{sup 12}C{sub {epsilon}2}] SAIL-Trp), which provides a more robust way to correlate the {sup 1}H{sub {beta}}, {sup 1}H{sub {alpha}}, and {sup 1}H{sub N} to the {sup 1}H{sub {delta}1} and {sup 1}H{sub {epsilon}3} through the intra-residue NOEs. The assignment of the {sup 1}H{sub {delta}1}/{sup 13}C{sub {delta}1} and {sup 1}H{sub {epsilon}3}/{sup 13}C{sub {epsilon}3} signals can thus be transferred to the {sup 1}H{sub {epsilon}1}/{sup 15}N{sub {epsilon}1} and {sup 1}H{sub {eta}2}/{sup 13}C{sub {eta}2} signals, as with the previous type of SAIL-Trp, which has an extra {sup 13}C at the C{sub {gamma}} of the ring. By taking advantage of the stereospecific deuteration of one of the prochiral {beta}-methylene protons, which was {sup 1}H{sub {beta}2} in this experiment, one can determine the side-chain conformation of the Trp residue including the {chi}{sub 2} angle, which is especially important for Trp residues, as they can adopt three preferred conformations. We demonstrated the usefulness of [{sup 12}C{sub {gamma}},{sup 12}C

  12. User’s trust in Biometric Authentication Systems – Do not take the end-users for granted

    OpenAIRE

    Gravnås, Henning

    2005-01-01

    NORSK: I de senere årene har mediefokuset vært rettet mot sikkerhet. Et av kravene innenfor sikkerhet, er økt behov for korrekt autentisering av en person. Det er mulig å autentisere seg ved å fremlegge bevis på noe du vet (for eksempel et passord), noe du har (for eksempel et ID-kort) eller noe du er (for eksempel biometri). Denne undersøkelsen forsøker å finne ut av i hvilken grad mulige brukere av biometriske autentiseringssystemer har tillit til et slikt system. Deltakerne ...

  13. The importance of including local correlation times in the calculation of inter-proton distances from NMR measurements: ignoring local correlation times leads to significant errors in the conformational analysis of the Glc alpha1-2Glc alpha linkage by NMR spectroscopy.

    Science.gov (United States)

    Mackeen, Mukram; Almond, Andrew; Cumpstey, Ian; Enis, Seth C; Kupce, Eriks; Butters, Terry D; Fairbanks, Antony J; Dwek, Raymond A; Wormald, Mark R

    2006-06-07

    The experimental determination of oligosaccharide conformations has traditionally used cross-linkage 1H-1H NOE/ROEs. As relatively few NOEs are observed, to provide sufficient conformational constraints this method relies on: accurate quantification of NOE intensities (positive constraints); analysis of absent NOEs (negative constraints); and hence calculation of inter-proton distances using the two-spin approximation. We have compared the results obtained by using 1H 2D NOESY, ROESY and T-ROESY experiments at 500 and 700 MHz to determine the conformation of the terminal Glc alpha1-2Glc alpha linkage in a dodecasaccharide and a related tetrasaccharide. For the tetrasaccharide, the NOESY and ROESY spectra produced the same qualitative pattern of linkage cross-peaks but the quantitative pattern, the relative peak intensities, was different. For the dodecasaccharide, the NOESY and ROESY spectra at 500 MHz produced a different qualitative pattern of linkage cross-peaks, with fewer peaks in the NOESY spectrum. At 700 MHz, the NOESY and ROESY spectra of the dodecasaccharide produced the same qualitative pattern of peaks, but again the relative peak intensities were different. These differences are due to very significant differences in the local correlation times for different proton pairs across this glycosidic linkage. The local correlation time for each proton pair was measured using the ratio of the NOESY and T-ROESY cross-relaxation rates, leaving the NOESY and ROESY as independent data sets for calculating the inter-proton distances. The inter-proton distances calculated including the effects of differences in local correlation times give much more consistent results.

  14. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Richard [Huazhong University of Science and Technology, School of Software Engineering (China); Wang, Yan [Huazhong University of Science and Technology, School of Life Science and Technology (China); Xue, Zhidong, E-mail: zdxue@hust.edu.cn [Huazhong University of Science and Technology, School of Software Engineering (China); Zhang, Yang, E-mail: zhng@umich.edu [University of Michigan, Department of Computational Medicine and Bioinformatics (United States)

    2015-08-15

    NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.

  15. Antioxidant, anti-inflammatory, anti-apoptotic, and skin regenerative properties of an Aloe vera-based extract of Nerium oleander leaves (nae-8(®)).

    Science.gov (United States)

    Benson, Kathleen F; Newman, Robert A; Jensen, Gitte S

    2015-01-01

    The goal for this study was to evaluate the effects of an Aloe vera-based Nerium oleander extract (NAE-8(®)), compared to an extract of A. vera gel alone (ALOE), and to an aqueous extract of N. oleander (AQ-NOE) in bioassays pertaining to dermatologic potential with respect to antioxidant protection, anti-inflammatory effects, and cytokine profiles in vitro. Cellular antioxidant protection was evaluated in three separate bioassays: The cellular antioxidant protection of erythrocytes (CAP-e) assay, protection of cellular viability and prevention of apoptosis, and protection of intracellular reduced glutathione levels, where the last two assays were performed using human primary dermal fibroblasts. Reduction of intracellular formation of reactive oxygen species (ROS) was tested using polymorphonuclear cells in the absence and presence of oxidative stress. Changes to cytokine and chemokine profiles when whole blood cells and human primary dermal fibroblasts were exposed to test products were determined using a 40-plex Luminex array as a method for exploring the potential cross-talk between circulating and skin-resident cells. The NAE-8(®) provided significantly better antioxidant protection in the CAP-e bioassay than AQ-NOE. NAE-8(®) and AQ-NOE both protected cellular viability and intracellular reduced glutathione, and reduced the ROS formation significantly when compared to control cells, both under inflamed and neutral culture conditions. ALOE showed minimal effect in these bioassays. In contrast to the NAE-8(®), the AQ-NOE showed induction of inflammation in the whole blood cultures, as evidenced by the high induction of CD69 expression and secretion of a number of inflammatory cytokines. The treatment of dermal fibroblasts with NAE-8(®) resulted in selective secretion of cytokines involved in collagen and hyaluronan production as well as re-epithelialization during wound healing. NAE-8(®), a novel component of a commercial cosmetic product, showed

  16. Manufacturing inspection of electrical steels using Magnetic Barkhausen Noise: residual stress detection

    Energy Technology Data Exchange (ETDEWEB)

    Samimi, A.A., E-mail: 9aa8@queensu.ca [Queen' s Univ., Applied Magnetics Group, Kingston, Ontario (Canada); Krause, T.W. [Royal Military College of Canada, NDE Lab., Kingston, Ontario (Canada); Clapham, L. [Queen' s Univ., Applied Magnetics Group, Kingston, Ontario (Canada); Gallaugher, M.; Ding, Y.; Chromik, R. [McGill Univ., Dept. of Mining and Materials Engineering, Montreal, Quebec (Canada)

    2016-09-15

    Non-oriented Electrical Steel (NOES) is the magnetic core lamination material used for flux transfer in rotary machines. The presence of residual stress associated with material processing may be detrimental to magnetic domain structure refinement and as a result, magnetic performance of NOES. Therefore, manufacturing inspection of NOES that identifies the presence of residual stress could contribute to the production of more energy efficient cores. However, standard materials evaluation is limited to destructive and off-line techniques. The present work employed Magnetic Barkhausen Noise (MBN) for nondestructive identification of local residual stress associated with stages in material processing. Analysis of MBN from single strips of NOES demonstrated clear response to applied tensile stress, mechanical shearing, the presence of an insulating coating and punching. The results establish the potential of MBN as a nondestructive testing technology for quality control of electrical steels at various stages of manufacture. (author)

  17. Knee-joint proprioception during 30-day 6 degrees head-down bed rest with isotonic and isokinetic exercise training

    Science.gov (United States)

    Bernauer, E. M.; Walby, W. F.; Ertl, A. C.; Dempster, P. T.; Bond, M.; Greenleaf, J. E.

    1994-01-01

    To determine if daily isotonic exercise or isokinetic exercise training coupled with daily leg proprioceptive training, would influence leg proprioceptive tracking responses during bed rest (BR), 19 men (36 +/- SD 4 years, 178 +/- 7 cm, 76.8 +/- 7.8 kg) were allocated into a no-exercise (NOE) training control group (n = 5), and isotonic exercise (ITE, n = 7) and isokinetic exercise (IKE, n = 7) training groups. Exercise training was conducted during BR for two 30-min periods.d-1, 5 d.week-1. Only the IKE group performed proprioceptive training using a new isokinetic procedure with each lower extremity for 2.5 min before and after the daily exercise training sessions; proprioceptive testing occurred weekly for all groups. There were no significant differences in proprioceptive tracking scores, expressed as a percentage of the perfect score of 100, in the pre-BR ambulatory control period between the three groups. Knee extension and flexion tracking responses were unchanged with NOE during BR, but were significantly greater (*p < 0.05) at the end of BR in both exercise groups when compared with NOE responses (extension: NOE 80.7 +/- 0.7%, ITE 82.9* +/- 0.6%, IKE 86.5* +/- 0.7%; flexion: NOE 77.6 +/- 1.5%, ITE 80.0 +/- 0.8% (NS), IKE 83.6* +/- 0.8%). Although proprioceptive tracking was unchanged during BR with NOE, both isotonic exercise training (without additional proprioceptive training) and especially isokinetic exercise training when combined with daily proprioceptive training, significantly improved knee proprioceptive tracking responses after 30 d of BR.

  18. Knee-Joint Proprioception During 30-Day 6 deg Head-Down Bed Rest with Isotonic and Isokinetic Exercise Training

    Science.gov (United States)

    Bernauer, E. M.; Walby, W. F.; Ertl, A. C.; Dempster, P. T.; Bond, M.; Greenleaf, J. E.

    1994-01-01

    To determine if daily isotonic exercise or isokinetic exercise training coupled with daily log proprioceptive training, would influence log proprioceptive tracking responses during Bed Rest (BR), 19 men (36 +/- SD 4 years, 178 +/- 7 cm, 76.8 +/- 7.8 kg) were allocated into a NO-Exercise (NOE) training control group (n = 5), and IsoTanic Exercise (ITE, n = 7) and IsoKinetic Exercise (IKE, n = 7) training groups. Exercise training was conducted during BR for two 30-min period / d, 5 d /week. Only the IKE group performed proprioceptive training using a now isokinetic procedure with each lower extremity for 2.5 min before and after the daily exercise training sessions; proprioceptive testing occurred weekly for all groups. There were no significant differences in proprioceptive tracking scores, expressed as a percentage of the perfect score of 100, in the pro-BR ambulatory control period between the three groups. Knee extension and flexion tracking responses were unchanged with NOE during BR, but were significantly greater (*p less than 0.05) at the end of BR in both exercise groups when compared with NOE responses (extension: NOE 80.7 +/- 0.7%, ITE 82.9 +/- 0.6%, IKE 86.5* +/- 0.7%; flexion: NOE 77.6 +/- 1.50, ITE 80.0 +/- 0.8% (NS), IKE 83.6* +/- 0.8%). Although proprioceptive tracking was unchanged during BR with NOE, both lsotonic exercise training (without additional propriaceptive training) and especially isokinetic exercise training when combined with daily proprioceptive training, significantly improved knee proprioceptive tracking responses after 30 d of BR.

  19. Transfer Rate Edited experiment for the selective detection of Chemical Exchange via Saturation Transfer (TRE-CEST).

    Science.gov (United States)

    Friedman, Joshua I; Xia, Ding; Regatte, Ravinder R; Jerschow, Alexej

    2015-07-01

    Chemical Exchange Saturation Transfer (CEST) magnetic resonance experiments have become valuable tools in magnetic resonance for the detection of low concentration solutes with far greater sensitivity than direct detection methods. Accurate measures of rates of chemical exchange provided by CEST are of particular interest to biomedical imaging communities where variations in chemical exchange can be related to subtle variations in biomarker concentration, temperature and pH within tissues using MRI. Despite their name, however, traditional CEST methods are not truly selective for chemical exchange and instead detect all forms of magnetization transfer including through-space NOE. This ambiguity crowds CEST spectra and greatly complicates subsequent data analysis. We have developed a Transfer Rate Edited CEST experiment (TRE-CEST) that uses two different types of solute labeling in order to selectively amplify signals of rapidly exchanging proton species while simultaneously suppressing 'slower' NOE-dominated magnetization transfer processes. This approach is demonstrated in the context of both NMR and MRI, where it is used to detect the labile amide protons of proteins undergoing chemical exchange (at rates⩾30s(-1)) while simultaneously eliminating signals originating from slower (∼5s(-1)) NOE-mediated magnetization transfer processes. TRE-CEST greatly expands the utility of CEST experiments in complex systems, and in-vivo, in particular, where it is expected to improve the quantification of chemical exchange and magnetization transfer rates while enabling new forms of imaging contrast. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Transfer Rate Edited experiment for the selective detection of Chemical Exchange via Saturation Transfer (TRE-CEST)

    Science.gov (United States)

    Friedman, Joshua I.; Xia, Ding; Regatte, Ravinder R.; Jerschow, Alexej

    2015-07-01

    Chemical Exchange Saturation Transfer (CEST) magnetic resonance experiments have become valuable tools in magnetic resonance for the detection of low concentration solutes with far greater sensitivity than direct detection methods. Accurate measures of rates of chemical exchange provided by CEST are of particular interest to biomedical imaging communities where variations in chemical exchange can be related to subtle variations in biomarker concentration, temperature and pH within tissues using MRI. Despite their name, however, traditional CEST methods are not truly selective for chemical exchange and instead detect all forms of magnetization transfer including through-space NOE. This ambiguity crowds CEST spectra and greatly complicates subsequent data analysis. We have developed a Transfer Rate Edited CEST experiment (TRE-CEST) that uses two different types of solute labeling in order to selectively amplify signals of rapidly exchanging proton species while simultaneously suppressing 'slower' NOE-dominated magnetization transfer processes. This approach is demonstrated in the context of both NMR and MRI, where it is used to detect the labile amide protons of proteins undergoing chemical exchange (at rates ⩾ 30 s-1) while simultaneously eliminating signals originating from slower (∼5 s-1) NOE-mediated magnetization transfer processes. TRE-CEST greatly expands the utility of CEST experiments in complex systems, and in-vivo, in particular, where it is expected to improve the quantification of chemical exchange and magnetization transfer rates while enabling new forms of imaging contrast.

  1. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  2. Comparison of multiple crystal structures with NMR data for engrailed homeodomain

    Energy Technology Data Exchange (ETDEWEB)

    Religa, Tomasz L. [MRC Centre for Protein Engineering (United Kingdom)], E-mail: tlr25@mrc-lmb.cam.ac.uk

    2008-03-15

    Two methods are currently available to solve high resolution protein structures-X-ray crystallography and nuclear magnetic resonance (NMR). Both methods usually produce highly similar structures, but small differences between both solutions are always observed. Here the raw NMR data as well as the solved NMR structure were compared to the multiple crystal structures solved for the WT 60 residue three helix bundle engrailed homeodomain (EnHD) and single point mutants. There was excellent agreement between TALOS-predicted and crystal structure-observed dihedral angles and a good agreement for the {sup 3}J(H{sup N}H{sup {alpha}}) couplings for the multiple crystal structures. Around 1% of NOEs were violated for any crystal structure, but no NOE was inconsistent with all of the crystal structures. Violations usually occurred for surface residues or for residues for which multiple discreet conformations were observed between the crystal structures. Comparison of the disorder shown in the multiple crystal structures shows little correlation with dynamics under native conditions for this protein.

  3. Achievements of the EC network of excellence HySafe

    NARCIS (Netherlands)

    Jordan, T.; Adams, P.; Azkarate, I.; Baraldi, D.; Barthelemy, H.; Bauwens, L.; Bengaouer, A.; Brennan, S.; Carcassi, M.; Dahoe, A.; Eisenreich, N.; Engebo, A.; Funnemark, E.; Gallego, E.; Gavrikov, A.; Haland, E.; Hansen, A.M.; Haugom, G.P.; Hawksworth, S.; Jedicke, O.; Kessler, A.; Kotchourko, A.; Kumar, S.; Langer, G.; Ledin, S.; Makarov, D.; Marangon, A.; Markert, F.; Middha, P.; Molkov, V.; Nilsen, S.; Papanikolaou, E.; Perrette, L.; Reinecke, E.-A.; Schmidtchen, U.; Serre-Combe, P.; Stöcklin, M.; Sully, A.; Teodorczyk, A.; Tigreat, D.; Venetsanos, A.; Verfondern, K.; Versloot, N.A.H.; Vetere, A.; Wilms, M.; Zaretskiy, N.

    2009-01-01

    In many areas European research has been largely fragmented. To support the required integration and to focus and coordinate related research efforts the European Commission created a new instrument, the Networks of Excellences (NoEs). The goal of the NoE HySafe has been to provide the basis to

  4. {sup 15}N and {sup 13}C- SOFAST-HMQC editing enhances 3D-NOESY sensitivity in highly deuterated, selectively [{sup 1}H,{sup 13}C]-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Rossi, Paolo, E-mail: rossip@umn.edu; Xia, Youlin; Khanra, Nandish; Veglia, Gianluigi, E-mail: vegli001@umn.edu; Kalodimos, Charalampos G., E-mail: ckalodim@umn.edu [University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics (United States)

    2016-12-15

    The ongoing NMR method development effort strives for high quality multidimensional data with reduced collection time. Here, we apply ‘SOFAST-HMQC’ to frequency editing in 3D NOESY experiments and demonstrate the sensitivity benefits using highly deuterated and {sup 15}N, methyl labeled samples in H{sub 2}O. The experiments benefit from a combination of selective T{sub 1} relaxation (or L-optimized effect), from Ernst angle optimization and, in certain types of experiments, from using the mixing time for both NOE buildup and magnetization recovery. This effect enhances sensitivity by up to 2.4× at fast pulsing versus reference HMQC sequences of same overall length and water suppression characteristics. Representative experiments designed to address interesting protein NMR challenges are detailed. Editing capabilities are exploited with heteronuclear {sup 15}N,{sup 13}C-edited, or with diagonal-free {sup 13}C aromatic/methyl-resolved 3D-SOFAST-HMQC–NOESY–HMQC. The latter experiment is used here to elucidate the methyl-aromatic NOE network in the hydrophobic core of the 19 kDa FliT-FliJ flagellar protein complex. Incorporation of fast pulsing to reference experiments such as 3D-NOESY–HMQC boosts digital resolution, simplifies the process of NOE assignment and helps to automate protein structure determination.

  5. Analysis of the structural quality of the CASD-NMR 2013 entries

    Energy Technology Data Exchange (ETDEWEB)

    Ragan, Timothy J.; Fogh, Rasmus H. [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom); Tejero, Roberto [Universidad de Valencia, Departamento de Química Física (Spain); Vranken, Wim [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Montelione, Gaetano T. [Rutgers, The State University of New Jersey, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium (United States); Rosato, Antonio [University of Florence, Magnetic Resonance Center, Department of Chemistry (Italy); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom)

    2015-08-15

    We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and quality to those generated by a skilled researcher, at least for small, single domain proteins such as the ten targets tested. The most robust results appear to be obtained when NOESY peak lists are used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from the same data showed a surprisingly low degree of overlap. Additionally, we found that there was no significant correlation between the extent of the NOE restraint overlap and the accuracy of the structure. This result was surprising given the importance of NOE data in producing good quality structures. We suggest that this could be explained by the information redundancy present in NOEs between atoms contained within a fixed covalent network.

  6. Investigation of the spatial structure of des-Gly9-[Arg8]vasopressin by the methods of two-dimensional NMR spectroscopy and theoretical conformational analysis

    International Nuclear Information System (INIS)

    Shenderovich, M.D.; Sekatsis, I.P.; Liepin'sh, E.E.; Nikiforovich, G.V.; Papsuevich, O.S.

    1986-01-01

    An assignment of the 1 H NMR signals of des-Gly 9 -[Arg 8 ]vasopressin in dimethyl sulfoxide has been made by 2D spectroscopy. The SSCCs and temperature coefficients Δδ/Δ T have been obtained for the amide protons and the system of NOE cross-peaks in the two-dimensional NOESY spectrum has been analyzed. The most important information on the spatial structure of des-Gly 9 -[Arg 8 ]vasopressin is given by the low value of the temperature coefficient Δδ/Δ T of the Asn 5 amide proton and the NOE between the α-protons of Cys 1 and Cys 6 . It is assumed that the screening of the NH proton of the Asn 5 residue from the solvent is connected with a β-bend of the backbone in the 2-5 sequence, and the distance between the C/sup α/H atoms of the Cys 1 and Cys 6 residues does not exceed 4 A. Bearing these limitations in mind, a theoretical conformational analysis of the molecule has been made. The group of low-energy conformations of the backbone obtained has been compared with the complete set of NMR characteristics

  7. Social'noe sodejstvie: Kaliningradskaja oblast' i regiony osnovnoj chasti Rossii

    Directory of Open Access Journals (Sweden)

    Toropov P.

    2015-02-01

    Full Text Available The authors look at the concept of social facilitation as a possible component of Russian social consolidation in the course of social reforms. The article focuses on the results of an empirical study of the levels and characteristics of competence in social facilitation, which is here understood as the ability to apply certain knowledge and systems of skills and as a success rate of actions based on experience in improving the conditions of social development. The study was conducted in the Kaliningrad region in 2012—2013. The data was obtained through a survey of 400 respondents using the authors’ methodology encompassing eight basic elements of competence and a structured interview aimed at a better understanding of the subject of the study and attitudes towards it. The data is compared against the results of a similar study in two regions of central Russia with similar conditions. The results suggest a disharmonic and inconsistent structure of competence in social facilitation, low motivation for social activity in youth, and a narrow range of ideas about possible areas of personal activities in the current conditions. Gender differences are identified in the level and structure of competence. The authors believe that certain differences in competence components identified through mathematical methods are determined by the geographical characteristics of the Kaliningrad region — its exclave nature, a relatively small territory, and proximity to the EU countries. It is stressed that the regional conditions affecting motivation, forms and areas of activities, and structure of experience should be taken into account in selecting means and methods of organising youth activities. They can also serve as a basis for the regional youth policy.

  8. Multigroup transport calculations of critical and fuel assemblies with taking into account the scattering anisotropy

    International Nuclear Information System (INIS)

    Rubin, I.E.; Dneprovskaya, N.M.

    2005-01-01

    A technique for calculation of reactor lattices by means of the transmission probabilities with taking into account the scattering anisotropy is generalized for the multigroup case. The errors of the calculated multiplication coefficients and energy release distributions do noe exceed practically the errors, of these values, obtained by the Monte Carlo method. The proposed method is most effective when determining the small difference effects [ru

  9. The solvation of carbohydrates in dimethylsulfoxide and water

    International Nuclear Information System (INIS)

    Berger, S.; Diaz, M.D.; Horwat, Ch.

    1999-01-01

    The solvation of sucrose and other carbohydrates in DMSO and water is probed by intermolecular NOE measurements. The NOE effects are interpreted in terms of specific binding of the solvent to certain sites of the molecules. It is shown that DMSO attaches to specific sites of the sucrose molecule, whereas for water such a clear differentiation cannot be proven. (author)

  10. Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings - an assessment of the interrelation of NMR restraints

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Pernille Rose; Axelsen, Jacob Bock [University of Copenhagen, Institute of Molecular Biology (Denmark); Lerche, Mathilde Hauge [Amersham Health (Sweden); Poulsen, Flemming M. [University of Copenhagen, Institute of Molecular Biology (Denmark)], E-mail: fmp@apk.molbio.ku.dk

    2004-01-15

    We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on {sup 1}H{sup N}-{sup 15}N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of {sup 13}CO-{sup 13}C{sup {alpha}} and {sup 15}N-{sup 13}CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.8 A resolution X-ray structure of this protein. A systematic restraint study was performed, in which four types of restraints, residual dipolar couplings, hydrogen bonds, TALOS angles and NOEs, were allowed in two states. This study revealed the importance of using several types of residual dipolar couplings to get good hydrogen bond geometry. The study also showed that using a small set of NOEs derived only from the amide protons, together with a full set of residual dipolar couplings resulted in structures of very high quality. When reducing the NOE set, it is mainly the side-chain to side-chain NOEs that are removed. Despite of this the effect on the side-chain packing is very small when a reduced NOE set is used, which implies that the over all fold of a protein structure is mainly determined by correct folding of the backbone.

  11. Towards prognostic biomarkers from BOLD fluctuations to differentiate a first epileptic seizure from new-onset epilepsy.

    Science.gov (United States)

    Gupta, Lalit; Janssens, Rick; Vlooswijk, Mariëlle C G; Rouhl, Rob P W; de Louw, Anton; Aldenkamp, Albert P; Ulman, Shrutin; Besseling, René M H; Hofman, Paul A M; van Kranen-Mastenbroek, Vivianne H; Hilkman, Danny M; Jansen, Jacobus F A; Backes, Walter H

    2017-03-01

    The diagnosis of epilepsy cannot be reliably made prior to a patient's second seizure in most cases. Therefore, adequate diagnostic tools are needed to differentiate subjects with a first seizure from those with a seizure preceding the onset of epilepsy. The objective was to explore spontaneous blood oxygen level-dependent (BOLD) fluctuations in subjects with a first-ever seizure and patients with new-onset epilepsy (NOE), and to find characteristic biomarkers for seizure recurrence after the first seizure. We examined 17 first-seizure subjects, 19 patients with new-onset epilepsy (NOE), and 18 healthy controls. All subjects underwent clinical investigation and received electroencephalography and resting-state functional magnetic resonance imaging (MRI). The BOLD time series were analyzed in terms of regional homogeneity (ReHo) and fractional amplitude of low-frequency fluctuations (fALFFs). We found significantly stronger amplitudes (higher fALFFs) in patients with NOE relative to first-seizure subjects and healthy controls. The frequency range of 73-198 mHz (slow-3 subband) appeared most useful for discriminating patients with NOE from first-seizure subjects. The ReHo measure did not show any significant differences. The fALFF appears to be a noninvasive measure that characterizes spontaneous BOLD fluctuations and shows stronger amplitudes in the slow-3 subband of patients with NOE relative first-seizure subjects and healthy controls. A larger study population with follow-up is required to determine whether fALFF holds promise as a potential biomarker for identifying subjects at increased risk to develop epilepsy. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

  12. Clinical and computerized evaluation in study of temporo-mandibular joint intracapsular disease.

    Science.gov (United States)

    Ciavarella, D; Mastrovincenzo, M; Sabatucci, A; Parziale, V; Granatelli, F; Violante, F; Bossù, M; Lo Muzio, L; Chimenti, C

    2010-03-01

    In this work authors show a diagnostic criteria in study of TMID: neuro occlusal clinical evaluation (NOE), T-Scan 2 system and surface electromyography (sEMG). Nine patients 25-30 years old with TMID problem and 9 healthy group control have been selected and examined. On each patients it has been performed NOE, T-Scan and sEMG test. NOE has been calculated on each patient photos lateral mandibular excursion angle called: masticatory functional angle (AFM). T-Scan System is a computerized occlusal analyzer that provide in-depth understanding of the overall balance of the occlusion. At the same time of T-Scan record sEMG tests, in resting position and in maximum clench, have been performed. In healthy control there were no AFM difference. In no healthy group there were difference between the two AFM greater than 6 degrees. T-Scan COF showed how in healthy group control there was never a difference of COF greater than 5%. In no healthy group the difference were greater than 5% Pjoint sound than the balance side P<0.001. sEMG show how in TMID patients maximum masseter activation is always lower than maximum masseter activation of healthy subjects P<0.001. Neuro occlusal clinical evaluation (NOE) in TMID patients is supported by instrumental evaluation.

  13. Study on irradiated polymerization of acrylonitrile by NMR

    International Nuclear Information System (INIS)

    Zhao Xin; Lin Hao

    1999-01-01

    Sup 13 C CP/MAS spectra and nuclear Overhauser effects (NOE) at room temperature have been measured for acrylonitrile (AN) in homophase irradiated polymerization. With the increase of radiation dose the chemical shift of cracking peaks and NOE are variation. This implies that the polymerized mechanism of AN were changed with the variation of irradiated doses and dose rate. There is the stronger affinity electron group (-CN) in acrylonitrile monomer. It may be polymerized by various ways and mechanism and be gained the polymer of difference structures and molecular weight of polyacrylonitrile (PAN). Starmicarbon and Starker obtained higher molecular weight of polyacrylonitrile by peroxysulfate-pyrosulfite in oxidation-reduction system. The superhigh molecular weight of PAN was synthesized chemically according to the method of Wu et. al. by suspension polymerization. In this paper we discussed that the relative concentrations of steric dyads and triads in the chain structure in PAN and the irradiation polymerized mechanism of acrylonitrile monomer in room temperature by different dose and dose rate

  14. Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA

    Energy Technology Data Exchange (ETDEWEB)

    Mareuil, Fabien [Institut Pasteur, Cellule d' Informatique pour la Biologie (France); Malliavin, Thérèse E.; Nilges, Michael; Bardiaux, Benjamin, E-mail: bardiaux@pasteur.fr [Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528 (France)

    2015-08-15

    In biological NMR, assignment of NOE cross-peaks and calculation of atomic conformations are critical steps in the determination of reliable high-resolution structures. ARIA is an automated approach that performs NOE assignment and structure calculation in a concomitant manner in an iterative procedure. The log-harmonic shape for distance restraint potential and the Bayesian weighting of distance restraints, recently introduced in ARIA, were shown to significantly improve the quality and the accuracy of determined structures. In this paper, we propose two modifications of the ARIA protocol: (1) the softening of the force field together with adapted hydrogen radii, which is meaningful in the context of the log-harmonic potential with Bayesian weighting, (2) a procedure that automatically adjusts the violation tolerance used in the selection of active restraints, based on the fitting of the structure to the input data sets. The new ARIA protocols were fine-tuned on a set of eight protein targets from the CASD–NMR initiative. As a result, the convergence problems previously observed for some targets was resolved and the obtained structures exhibited better quality. In addition, the new ARIA protocols were applied for the structure calculation of ten new CASD–NMR targets in a blind fashion, i.e. without knowing the actual solution. Even though optimisation of parameters and pre-filtering of unrefined NOE peak lists were necessary for half of the targets, ARIA consistently and reliably determined very precise and highly accurate structures for all cases. In the context of integrative structural biology, an increasing number of experimental methods are used that produce distance data for the determination of 3D structures of macromolecules, stressing the importance of methods that successfully make use of ambiguous and noisy distance data.

  15. 1H and 15N resonance assignments of oxidized flavodoxin from Anacystis nidulans with 3D NMR

    International Nuclear Information System (INIS)

    Clubb, R.T.; Thanabal, V.; Wagner, G.; Osborne, C.

    1991-01-01

    Proton and nitrogen-15 sequence-specific nuclear magnetic resonance assignments have been determined for recombinant oxidized flavodoxin from Anacystis nidulans. Assignments were obtained by using 15 N- 1 H heteronuclear three-dimensional (3D) NMR spectroscopy on a uniformly nitrogen-15 enriched sample of the protein, pH 6.6, at 30C. For 165 residues, the backbone and a large fraction of the side-chain proton resonances have been assigned. Medium- and long-range NOE's have been used to characterize the secondary structure. In solution, flavodoxin consists of a five-stranded parallel β sheet involving residues 3-9, 31-37, 49-56, 81-89, 114-117, and 141-144. Medium-range NOE's indicate that presence of several helices. Several 15 N and 1 H resonances of the flavin mononucleotide (FMN) prosthetic group have been assigned. The FMN-binding site has been investigated by using polypeptide-FMN NOE's

  16. Field assessment of the susceptibility of onion cultivars to thrips attack – preliminary results

    Directory of Open Access Journals (Sweden)

    Pobożniak Maria

    2016-03-01

    Full Text Available Field experiments on the susceptibility of onion to thrips infestation were carried out in 2012 and 2013. The investigation used 18 cultivars and 5 breeding lines of Allium cepa, and the species A. fistulosum and A. roylei. In 2012 A. fistulosum was one of the most infested plants, whereas in 2013 infestation was no more than average. The most infested cultivars of A. cepa were ‘Efekt’, ‘Alonso F1’, ‘Alibaba’ and ‘Wama’ and the ‘NOE5’ breeding line. In 2012 the extent of damage ranged from 12 to 55%, in 2013 from 20 to 30%. The ‘NOE2’, ‘NOE3’ and ‘Wama’ cultivars were the most seriously damaged by thrips. Leaf damage to A. fistulosum was minimal. No damage was caused to the wild species A. roylei by feeding onion thrips.

  17. Stereospecific assignments of glycine in proteins by stereospecific deuteration and {sup 15}N labeling

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, A.P.; Curley, R.W. Jr.; Panigot, M.J.; Fesik, S.W. [Ohio State Univ., Columbus, OH (United States)

    1994-12-01

    Stereospecific assignments are important for accurately determining the three-dimensional structures of proteins through the use of multidimensional NMR techniques. It is especially important to stereospecifically assign the glycine {alpha}-protons in proteins because of the potential for different backbone conformations of this residue. These stereospecific assignments are critical for interpreting the {sup 3}J{sub NH,{alpha}H} coupling constants and NOEs involving the glycine {alpha}-protons that determine the conformation of this part of the protein. However, it is often difficult to unambiguously obtain the stereospecific assignments for glycine residues by using only NOE data. In this poster, we present a method for unambiguous, stereospecific assignment of the {alpha}-protons of glycine residues. This method involves synthesis of stereo-specifically deuterated and {sup 15}N-labeled Gly using a slightly modified procedure originally described by Woodard and coworkers for the stereoselective deuteration of glycine. The stereospecifically deuterated and {sup 15}N-labeled Gy has been incorporated into recombinant proteins expressed in both bacterial systems (FKBP) and mammalian cells (u-PA). Two- and three-dimensional isotope-filtered and isotope-edited NMR experiments were used to obtain the stereospecific assignments of the glycine {alpha}-protons for these proteins.

  18. Projected [1H,15N]-HMQC-[1H,1H]-NOESY for large molecular systems: application to a 121 kDa protein-DNA complex

    International Nuclear Information System (INIS)

    Galius, Veniamin; Leontiou, Chrysoula; Richmond, Timothy; Wider, Gerhard

    2008-01-01

    We present a projected [ 1 H, 15 N]-HMQC-[ 1 H, 1 H]-NOESY experiment for observation of NOE interactions between amide protons with degenerate 15 N chemical shifts in large molecular systems. The projection is achieved by simultaneous evolution of the multiple quantum coherence of the nitrogen spin and the attached proton spin. In this way NOE signals can be separated from direct-correlation peaks also in spectra with low resolution by fully exploiting both 1 H and 15 N frequency differences, such that sensitivity can be increased by using short maximum evolution times. The sensitivity of the experiment is not dependent on the projection angle for projections up to 45 deg. and no additional pulses or delays are required as compared to the conventional 2D [ 1 H, 15 N]-HMQC-NOESY. The experiment provides two distinct 2D spectra corresponding to the positive and negative angle projections, respectively. With a linear combination of 1D cross-sections from the two projections the unavoidable sensitivity loss in projection spectra can be compensated for each particular NOE interaction. We demonstrate the application of the novel projection experiment for the observation of an NOE interaction between two sequential glycines with degenerate 15 N chemical shifts in a 121.3 kDa complex of the linker H1 histone protein with a 152 bp linear DNA

  19. Discriminating binding and positioning of amphiphiles to lipid bilayers by {sup 1}H NMR

    Energy Technology Data Exchange (ETDEWEB)

    Evanics, F. [Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd. North Mississauga, Ont., L5L 1C6 (Canada); Prosser, R.S. [Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd. North Mississauga, Ont., L5L 1C6 (Canada)]. E-mail: sprosser@utm.utoronto.ca

    2005-04-04

    The binding and positioning in lipid bilayers of three well-known drugs--imipramine, nicotine, and caffeine--have been studied using {sup 1}H NMR. The membrane model system consisted of 'fast-tumbling' lipid bicelles, in which a bilayered lipid domain, composed of the unsaturated lipid, 1,2-dimyristelaidoyl-sn-glycero-3-phosphocholine (DMLPC) was surrounded by a rim of deuterated detergent-like lipids, consisting of 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC-d22). Binding and immersion depth information was obtained by three experiments. (1) {sup 1}H chemical shift perturbations, upon transfer of the amphiphiles from water to a bicelle mixture, were used to estimate regions of the amphiphiles that interact with the membrane. (2) Water contact to resolvable protons was measured through a Nuclear Overhauser Effect (NOE) between water and resolvable drug and lipid resonances. In the case of both lipids and membrane bound drugs, positive NOEs with large cross-relaxation rates were measured for most resonances originating from the membrane hydrophilic region, while negative NOEs were observed predominantly to resonances in the hydrophobic region of the membrane. (3) {sup 1}H NMR measurements of oxygen-induced (paramagnetic) spin-lattice relaxation rates, which are known to increase with membrane immersion depth, were used to corroborate conclusions based on chemical shift perturbations and water-ligand NOEs.

  20. An Annotated Bibliography of Objective Pilot Performance Measures

    Science.gov (United States)

    1982-01-01

    realism . (Author) 224 NAVTRAEQUIPCEN IH-330 t 667. PROPHET, Wallace W., and Caro, Paul W., Simulation and Aircrew Training and Performance, Human... cinematic simulation and air training appears to be the most promising cost-effective method of developing NOE visual perception skills. Of other...flight and control dynamics. Informal trials were run with research staff and carrier-qualified pilots to evaluate realism of the displays; amount of

  1. Structural and dynamical characterization of piroxicam by 1H- and 13C-NMR relaxation studies

    International Nuclear Information System (INIS)

    Rossi, C.; Casini, A.; Picchi, M.P.; Laschi, F.; Calabria, A.; Marcolongo, R.

    1987-01-01

    Carbon spin-lattice relaxation rates of anti-inflammatory drug, piroxicam, have been measured. These results have been used in determining the reorientational rates of the proton carbon vectors. An analysis of internal motions within the pyridinyl moiety of piroxicam was carried out. Selective proton-carbon nuclear Overhauser effect (NOE) measurements were made in order to determine the solution structure of piroxicam. The effect of indirect NOE arising from exchangeable protons has been analyzed and considered. 20 refs.; 4 figs.; 3 tabs

  2. Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA

    International Nuclear Information System (INIS)

    Lee, K.M.; Marshall, A.G.

    1987-01-01

    Base-pair sequences for 5S and 5.8S RNAs are not readily extracted from proton homonuclear nuclear Overhauser enhancement (NOE) connectivity experiments alone, due to extensive peak overlap in the downfield (11-15 ppm) proton NMR spectrum. In this paper, we introduce a new method for base-pair proton peak assignment for ribosomal RNAs, based upon the distance-dependent broadening of the resonances of base-pair protons spatially proximal to a paramagnetic group. Introduction of a nitroxide spin-label covalently attached to the 3'-terminal ribose provides an unequivocal starting point for base-pair hydrogen-bond proton NMR assignment. Subsequent NOE connectivities then establish the base-pair sequence for the terminal stem of a 5S RNA. Periodate oxidation of yeast 5S RNA, followed by reaction with 4-amino-2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO-NH2) and sodium borohydride reduction, produces yeast 5S RNA specifically labeled with a paramagnetic nitroxide group at the 3'-terminal ribose. Comparison of the 500-MHz 1H NMR spectra of native and 3'-terminal spin-labeled yeast 5S RNA serves to identify the terminal base pair (G1 . C120) and its adjacent base pair (G2 . U119) on the basis of their proximity to the 3'-terminal spin-label. From that starting point, we have then identified (G . C, A . U, or G . U) and sequenced eight of the nine base pairs in the terminal helix via primary and secondary NOE's

  3. Nuclear magnetic resonance spectroscopy in the structure elucidation and biosynthesis of natural products

    International Nuclear Information System (INIS)

    Meksuriyen, D.

    1988-01-01

    Examination of a chloroform extract of Dracaena loureiri Gagnep (Agavaceae), a Thia medicinal plant possessing antibacterial activity, has led to the isolation of fifteen flavenoids. The biogenic relationships among these flavenoids isolated were briefly discussed. Definition of the skeleton and the unambiguous assignment of all of the protons of the isolates was achieved through extensive 2D-homonuclear chemical shift correlation, nuclear Overhauser effect (NOE) difference spectroscopy and 2D-NOE experiments. The 1 H and 13 C NMR spectra of staurosporine, a potent biologically active agent from Streptomyces staurosporeus, were unambiguously assigned by using 2D homonuclear chemical shift correlation, NOE, 1 H-detected heteronuclear multiple-quantum coherence via direct coupling and via multiple-bond coupling for resonance assignments of protonated and nonprotonated carbons, respectively. S. Staurosporeus was found to utilize endogenous and exogenous D- and L-isomers of trytophan in the production of staurosporine. The biosynthesis of staurosporine was examined by employing carbon-14, tritium, and carbon-13 labeled precursors

  4. Xanthanolides and xanthane epoxide derivatives from Xanthium strumarium.

    Science.gov (United States)

    Mahmoud, A A

    1998-12-01

    From the aerial parts of Xanthium strumarium, three new xanthanolide and xanthane-type sesquiterpenoids, 11alpha,13-dihydroxanthatin, 4beta,5beta-epoxyxanthatin-1alpha,4alpha-endoperoxide, and 1beta,4beta,4alpha,5alpha-diepoxyxanth-11(13)-en-12-oic acid have been isolated, together with seven known compounds. The structures were determined by spectroscopic methods, particularly high resolution 1D, 2D NMR spectroscopy and NOE experiments.

  5. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Yuanpeng Janet, E-mail: yphuang@cabm.rutgers.edu; Mao, Binchen; Xu, Fei; Montelione, Gaetano T., E-mail: gtm@rutgers.edu [Rutgers, The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and Northeast Structural Genomics Consortium (United States)

    2015-08-15

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD–NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases {sup 15}N–{sup 1}H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD–NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta.

  6. Fully automatic guidance and control for rotorcraft nap-of-the-Earth flight following planned profiles. Volume 1: Real-time piloted simulation

    Science.gov (United States)

    Clement, Warren F.; Gorder, Peter J.; Jewell, Wayne F.

    1991-01-01

    Developing a single-pilot, all-weather nap-of-the-earth (NOE) capability requires fully automatic NOE (ANOE) navigation and flight control. Innovative guidance and control concepts are investigated in a four-fold research effort that: (1) organizes the on-board computer-based storage and real-time updating of NOE terrain profiles and obstacles in course-oriented coordinates indexed to the mission flight plan; (2) defines a class of automatic anticipative pursuit guidance algorithms and necessary data preview requirements to follow the vertical, lateral, and longitudinal guidance commands dictated by the updated flight profiles; (3) automates a decision-making process for unexpected obstacle avoidance; and (4) provides several rapid response maneuvers. Acquired knowledge from the sensed environment is correlated with the forehand knowledge of the recorded environment (terrain, cultural features, threats, and targets), which is then used to determine an appropriate evasive maneuver if a nonconformity of the sensed and recorded environments is observed. This four-fold research effort was evaluated in both fixed-based and moving-based real-time piloted simulations, thereby, providing a practical demonstration for evaluating pilot acceptance of the automated concepts, supervisory override, manual operation, and re-engagement of the automatic system. Volume one describes the major components of the guidance and control laws as well as the results of the piloted simulations. Volume two describes the complete mathematical model of the fully automatic guidance system for rotorcraft NOE flight following planned flight profiles.

  7. Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR

    International Nuclear Information System (INIS)

    Lane, A.N.; Jenkins, T.C.; Neidle, S.; Brown, T.

    1991-01-01

    The conformation of the EcoRI dodecamer d(CGCGAATTCGCG) 2 has been examined in solution by 1 H and 31 P NMR. Spin-spin coupling constants and nuclear Overhauser (NOE) enhancement spectroscopy show that all deoxyriboses lie in the south domain, with a small admixture of the north conformation (0-20%). The time dependence of the nuclear Overhauser enhancements also reveals a relatively uniform conformation at the glycosidic bonds. The average helical twist is 36.5. Tilt angles are small, and roll angles are poorly determined. Both the NOE intensities and 31 P relaxation data imply conformational anomalies at the C3-G4/C9-G10 and the A5-A6/T7-T8 steps. Berenil binds in 1:1 stoichiometry to the dodecamer with high affinity and causes substantial changes in chemical shifts of the sugar protons of nucleotides Ado 5-Cyt 9 and of the H2 resonances of the two Ado residues. NOEs are observed between the aromatic protons of berenil and the H1' of both Thy 7 and Thy 8, as well as to Ado 5 and Ado 6 H2. These results firmly establish that berenil binds via the minor groove and closely approaches the nucleotides Ado 6, Thy 7, and Thy 8. Using the observed NOEs between the ligand and the DNA together with the derived glycosidic torsion angles, the authors have built models that satisfy all of the available solution data

  8. Justin Bieber - en toneangivende formidler til tweens

    OpenAIRE

    Lundeby, Maria Celine Kolberg

    2014-01-01

    Ønsket mitt med oppgaven har vært å skape en bevissthet om at populærkulturen er en formidler av noe, og at dette noe bærer i seg potensialet til å ha direkte betydning for vanlige menneskers liv. Gjennom dette utblikket har målet vært å synliggjøre noen eksempler på hvordan det som formidles kan bli gode innfallsvinkler til samtaler om og forkynnelse av kristen tro til tweens. Selv om denne oppgaven har tatt utgangspunkt i et veldig konkret eksempel, Justin Bieber, er de grunnleg...

  9. Sensitivity improvement for correlations involving arginine side-chain Nε/Hε resonances in multi-dimensional NMR experiments using broadband 15N 180o pulses

    International Nuclear Information System (INIS)

    Iwahara, Junji; Clore, G. Marius

    2006-01-01

    Due to practical limitations in available 15 N rf field strength, imperfections in 15 N 180 o pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amide groups, cross-peaks arising from the Arg guanidino 15 Nε (∼85 ppm) are highly attenuated by the presence of multiple INEPT transfer steps. To improve the sensitivity for correlations involving Arg Nε-Hε groups, we have incorporated 15 N broadband 180 deg. pulses into 3D 15 N-separated NOE-HSQC and HNCACB experiments. Two 15 N-WURST pulses incorporated at the INEPT transfer steps of the 3D 15 N-separated NOE-HSQC pulse sequence resulted in a ∼1.5-fold increase in sensitivity for the Arg Nε-Hε signals at 800 MHz. For the 3D HNCACB experiment, five 15 N Abramovich-Vega pulses were incorporated for broadband inversion and refocusing, and the sensitivity of Arg 1 Hε- 15 Nε- 13 Cγ/ 13 Cδ correlation peaks was enhanced by a factor of ∼1.7 at 500 MHz. These experiments eliminate the necessity for additional experiments to assign Arg 1 Hε and 15 Nε resonances. In addition, the increased sensitivity afforded for the detection of NOE cross-peaks involving correlations with the 15 Nε/ 1 Hε of Arg in 3D 15 N-separated NOE experiments should prove to be very useful for structural analysis of interactions involving Arg side-chains

  10. Synthesis and applications of selectively {sup 13}C-labeled RNA

    Energy Technology Data Exchange (ETDEWEB)

    SantaLucia, J. Jr.; Shen, L.X.; Lewis, H.; Cai, Z.; Tinoci, I. Jr. [Univ. of California, Berkeley, CA (United States)

    1994-12-01

    Spectral overlap is a substantial problem in NMR studies of RNA molecules >30 nucleotides. To overcome this difficulty, we synthesized selectively {sup 13}C-labeled RNAs and adapted several isotope-edited two- and three-dimensional NMR experiments originally developed for protein studies. We optimized protocols for synthesis of multi-gram quantities of CTP, UTp, ATP, and GTP using a combination of synthetic organic and enzymatic methods. Uracil is prepared in 40 to 50% yield from {sup 13}C-cyanide in two steps. Using acetyl- tribenzoyl-ribose and standard chemistry uracil is then attached to the sugar (90% yield). The tribenzoyl-uridine intermediate is converted into uridine or cytidine quantitatively, depending on the deblocking protocol. Labeled purines are synthesized using simple pyrimidine precursors and reacting with {sup 13}C-formic acid (80% yield). Purine nucleosides are then synthesized using uridine phosphorylase and purine nucleoside phosphorylase. The nucleosides were converted to NMPs by treatment with POC1{sub 3} in triethylphosphate. We converted NMPs to NTPs by standard enzymatic methods. Selectively labeled RNAs were synthesized by run-off transcription using {sup 13}C-labeled NTPs. Several different strategies help solve over-lap problems in larger RNAs. Isotope-edited two-dimensional NMR experiments such as {omega}1-1/2 X-filtered NOESY simplify NMR spectra by dividing the normal NOESY spectrum into two subspectra-one involving NOEs from protons bound to {sup 12}C and one from protons bound to {sup 13}C. For example, we labeled A and U residues of a 34-nucleotide pseudoknot, and the {sup 12}C subspectrum of the 1/2 X-filtered NOESY contained NOEs only from G and C residues (along with adenine 2H); the {sup 13}C subspectrum contained NOEs only from A and U residues. Each subspectrum has less overlap than the NOESY of an unlabeled sample; the editing strategy allows each resonance to be identified by residue type (A, C, G, or U).

  11. Evaluación neuroquímica de la neuropatía óptica epidémica

    OpenAIRE

    González-Quevedo Monteagudo , Alina

    2004-01-01

    La aparición súbita en Cuba de una epidemia de neuropatía óptica en 1992,desencadenó una serie de investigaciones dirigidas a esclarecer las causas subyacentes. El presente trabajo investigó la participación del balance de aminoácidos sistémicos y en el sistema nervioso, la permeabilidad de la barrera hematoencefálica (BHE) y la neurotoxicidad del metanol en la fisiopatología de la neuropatía óptica epidémica (NOE). Se llevaron a cabo estudios en pacientes con NOE y en un modelo experimental ...

  12. Automatic guidance and control laws for helicopter obstacle avoidance

    Science.gov (United States)

    Cheng, Victor H. L.; Lam, T.

    1992-01-01

    The authors describe the implementation of a full-function guidance and control system for automatic obstacle avoidance in helicopter nap-of-the-earth (NOE) flight. The guidance function assumes that the helicopter is sufficiently responsive so that the flight path can be readily adjusted at NOE speeds. The controller, basically an autopilot for following the derived flight path, was implemented with parameter values to control a generic helicopter model used in the simulation. Evaluation of the guidance and control system with a 3-dimensional graphical helicopter simulation suggests that the guidance has the potential for providing good and meaningful flight trajectories.

  13. Dictyosphaeric acids A and B: new decalactones from an undescribed Penicillium sp. obtained from the alga Dictyosphaeria versluyii.

    Science.gov (United States)

    Bugni, Tim S; Janso, Jeffrey E; Williamson, R Thomas; Feng, Xidong; Bernan, Valerie S; Greenstein, Michael; Carter, Guy T; Maiese, William M; Ireland, Chris M

    2004-08-01

    Fungal isolate F01V25 was obtained from the alga Dictyosphaeria versluyii collected near Dravuni, Fiji, in 2001 and represented a previously undescribed Penicillium sp. Fermentation of isolate F01V25 resulted in the production of two new polyketides, dictyosphaeric acids A and B, along with the known anthraquinone carviolin. The relative stereochemistry of dictyosphaeric acids A and B was determined using the J-based configuration analysis method in conjunction with ROE and NOE correlations.

  14. Nuclear Overhauser Enhancement imaging of glioblastoma at 7 Tesla: region specific correlation with apparent diffusion coefficient and histology.

    Science.gov (United States)

    Paech, Daniel; Burth, Sina; Windschuh, Johannes; Meissner, Jan-Eric; Zaiss, Moritz; Eidel, Oliver; Kickingereder, Philipp; Nowosielski, Martha; Wiestler, Benedikt; Sahm, Felix; Floca, Ralf Omar; Neumann, Jan-Oliver; Wick, Wolfgang; Heiland, Sabine; Bendszus, Martin; Schlemmer, Heinz-Peter; Ladd, Mark Edward; Bachert, Peter; Radbruch, Alexander

    2015-01-01

    To explore the correlation between Nuclear Overhauser Enhancement (NOE)-mediated signals and tumor cellularity in glioblastoma utilizing the apparent diffusion coefficient (ADC) and cell density from histologic specimens. NOE is one type of chemical exchange saturation transfer (CEST) that originates from mobile macromolecules such as proteins and might be associated with tumor cellularity via altered protein synthesis in proliferating cells. For 15 patients with newly diagnosed glioblastoma, NOE-mediated CEST-contrast was acquired at 7 Tesla (asymmetric magnetization transfer ratio (MTRasym) at 3.3ppm, B1 = 0.7 μT). Contrast enhanced T1 (CE-T1), T2 and diffusion-weighted MRI (DWI) were acquired at 3 Tesla and coregistered. The T2 edema and the CE-T1 tumor were segmented. ADC and MTRasym values within both regions of interest were correlated voxelwise yielding the correlation coefficient rSpearman (rSp). In three patients who underwent stereotactic biopsy, cell density of 12 specimens per patient was correlated with corresponding MTRasym and ADC values of the biopsy site. Eight of 15 patients showed a weak or moderate positive correlation of MTRasym and ADC within the T2 edema (0.16≤rSp≤0.53, pcorrelations were statistically insignificant (p>0.05, n = 4) or yielded rSp≈0 (pcorrelation between MTRasym and ADC was found in CE-T1 tumor (-0.310.05, n = 6). The biopsy-analysis within CE-T1 tumor revealed a strong positive correlation between tumor cellularity and MTRasym values in two of the three patients (rSppatient3 = 0.69 and rSppatient15 = 0.87, pcorrelation of ADC and cellularity was heterogeneous (rSppatient3 = 0.545 (p = 0.067), rSppatient4 = -0.021 (p = 0.948), rSppatient15 = -0.755 (p = 0.005)). NOE-imaging is a new contrast promising insight into pathophysiologic processes in glioblastoma regarding cell density and protein content, setting itself apart from DWI. Future studies might be based on the assumption that NOE-mediated CEST visualizes

  15. Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses.

    Science.gov (United States)

    Luo, Jie; Xu, Pei; Cao, Peijian; Wan, Hongjian; Lv, Xiaonan; Xu, Shengchun; Wang, Gangjun; Cook, Melloni N; Jones, Byron C; Lu, Lu; Wang, Xusheng

    2018-01-01

    Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE) but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1), down-regulation in NOE but rescue in RSE (pattern 2), up-regulation in both restraint stress followed by a saline injection (RSS) and NOE, and further amplification in RSE (pattern 3), and up-regulation in RSS but reduction in both NOE and RSE (pattern 4). We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs) to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA) signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

  16. Integrating Genetic and Gene Co-expression Analysis Identifies Gene Networks Involved in Alcohol and Stress Responses

    Directory of Open Access Journals (Sweden)

    Jie Luo

    2018-04-01

    Full Text Available Although the link between stress and alcohol is well recognized, the underlying mechanisms of how they interplay at the molecular level remain unclear. The purpose of this study is to identify molecular networks underlying the effects of alcohol and stress responses, as well as their interaction on anxiety behaviors in the hippocampus of mice using a systems genetics approach. Here, we applied a gene co-expression network approach to transcriptomes of 41 BXD mouse strains under four conditions: stress, alcohol, stress-induced alcohol and control. The co-expression analysis identified 14 modules and characterized four expression patterns across the four conditions. The four expression patterns include up-regulation in no restraint stress and given an ethanol injection (NOE but restoration in restraint stress followed by an ethanol injection (RSE; pattern 1, down-regulation in NOE but rescue in RSE (pattern 2, up-regulation in both restraint stress followed by a saline injection (RSS and NOE, and further amplification in RSE (pattern 3, and up-regulation in RSS but reduction in both NOE and RSE (pattern 4. We further identified four functional subnetworks by superimposing protein-protein interactions (PPIs to the 14 co-expression modules, including γ-aminobutyric acid receptor (GABA signaling, glutamate signaling, neuropeptide signaling, cAMP-dependent signaling. We further performed module specificity analysis to identify modules that are specific to stress, alcohol, or stress-induced alcohol responses. Finally, we conducted causality analysis to link genetic variation to these identified modules, and anxiety behaviors after stress and alcohol treatments. This study underscores the importance of integrative analysis and offers new insights into the molecular networks underlying stress and alcohol responses.

  17. Making connections: New Orleans Evacuees' experiences in obtaining drugs.

    Science.gov (United States)

    Dunlap, Eloise; Johnson, Bruce D; Kotarba, Joseph A; Fackler, Jennifer

    2009-09-01

    Between August 29 and September 7, 2005, almost all New Orleans residents were evacuated from the area in the aftermath of Hurricane Katrina. News reports indicate that almost 130,000 New Orleans Evacuees (NOEs) were evacuated to Houston, Texas, the largest recipient of the civilian population from New Orleans. Some of these NOEs were active participants in the illicit drug market in New Orleans prior to the hurricane. The period between the flooding and the nearly complete evacuation of New Orleans as well as their subsequent displacement to Houston and other locations provided unique opportunities to study what occurs when illicit drug markets are disrupted, since populations of illicit drug users and purchasers could no longer routinely obtain their drugs in predictable ways. Utilizing qualitative data from in-depth interviews and focus groups, this article describes the ways NOEs (1) managed their drug acquisition and use following evacuation; (2) located new sources of drugs in Houston and elsewhere by tapping into shared drug culture; and (3) gained access to and learned the argot for drugs in the local drug market in new settings. This report contributes to the nascent literature on disrupted drug markets.

  18. Cowpea and peanut in southern Africa are nodulated by diverse Bradyrhizobium strains harboring nodulation genes that belong to the large pantropical clade common in Africa.

    Science.gov (United States)

    Steenkamp, Emma T; Stepkowski, Tomasz; Przymusiak, Anna; Botha, Wilhelm J; Law, Ian J

    2008-09-01

    Cowpea (Vigna unguiculata) and peanut (Arachis hypogaea) in southern Africa are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the identity of these bacteria, a collection of 22 isolates originating from the root nodules of both hosts in Botswana and South Africa was investigated using the combined sequences for the core genome genes rrs, recA, and glnII. These data separated the majority of the isolates into one of three unique lineages that most likely represent novel Bradyrhizobium species. Some isolates were also conspecific with B. yuanmingense and with B. elkanii, although none grouped with B. japonicum, B. canariense or B. liaoningense. To study the evolution of nodulation genes in these bacteria, the common nodulation gene, nodA, and host-specific nodulation genes, nodZ, noeE, and noeI, were analyzed. The nodA phylogeny showed that the cowpea and peanut Bradyrhizobium isolates represent various locally adapted groups or ecotypes that form part of Clade III of the seven known BradyrhizobiumnodA clades. This large and highly diverse clade comprises all strains from sub-Saharan Africa, as well as some originating from the Americas, Australia, Indonesia, China and Japan. Some similar groupings were supported by the other nodulation genes, although the overall phylogenies for the nodulation genes were incongruent with that inferred from the core genome genes, suggesting that horizontal gene transfer significantly influences the evolution of cowpea and peanut root-nodule bacteria. Furthermore, identification of the nodZ, noeI, and noeE genes in the isolates tested indicates that African Bradyrhizobium species may produce highly decorated nodulation factors, which potentially represent an important adaptation enabling nodulation of a great variety of legumes inhabiting the African continent.

  19. Sensitivity improvement for correlations involving arginine side-chain N{epsilon}/H{epsilon} resonances in multi-dimensional NMR experiments using broadband {sup 15}N 180{sup o} pulses

    Energy Technology Data Exchange (ETDEWEB)

    Iwahara, Junji; Clore, G. Marius [National Institutes of Health, Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease (United States)], E-mail: mariusc@intra.niddk.nih.gov

    2006-12-15

    Due to practical limitations in available {sup 15}N rf field strength, imperfections in {sup 15}N 180{sup o} pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amide groups, cross-peaks arising from the Arg guanidino {sup 15}N{epsilon} ({approx}85 ppm) are highly attenuated by the presence of multiple INEPT transfer steps. To improve the sensitivity for correlations involving Arg N{epsilon}-H{epsilon} groups, we have incorporated {sup 15}N broadband 180 deg. pulses into 3D {sup 15}N-separated NOE-HSQC and HNCACB experiments. Two {sup 15}N-WURST pulses incorporated at the INEPT transfer steps of the 3D {sup 15}N-separated NOE-HSQC pulse sequence resulted in a {approx}1.5-fold increase in sensitivity for the Arg N{epsilon}-H{epsilon} signals at 800 MHz. For the 3D HNCACB experiment, five {sup 15}N Abramovich-Vega pulses were incorporated for broadband inversion and refocusing, and the sensitivity of Arg{sup 1}H{epsilon}-{sup 15}N{epsilon}-{sup 13}C{gamma}/{sup 13}C{delta} correlation peaks was enhanced by a factor of {approx}1.7 at 500 MHz. These experiments eliminate the necessity for additional experiments to assign Arg {sup 1}H{epsilon} and {sup 15}N{epsilon} resonances. In addition, the increased sensitivity afforded for the detection of NOE cross-peaks involving correlations with the {sup 15}N{epsilon}/{sup 1}H{epsilon} of Arg in 3D {sup 15}N-separated NOE experiments should prove to be very useful for structural analysis of interactions involving Arg side-chains.

  20. Structure refinement and membrane positioning of selectively labeled OmpX in phospholipid nanodiscs

    Energy Technology Data Exchange (ETDEWEB)

    Hagn, Franz, E-mail: franz.hagn@tum.de; Wagner, Gerhard, E-mail: gerhard-wagner@hms.harvard.edu [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States)

    2015-04-15

    NMR structural studies on membrane proteins are often complicated by their large size, taking into account the contribution of the membrane mimetic. Therefore, classical resonance assignment approaches often fail. The large size of phospholipid nanodiscs, a detergent-free phospholipid bilayer mimetic, prevented their use in high-resolution solution-state NMR spectroscopy so far. We recently introduced smaller nanodiscs that are suitable for NMR structure determination. However, side-chain assignments of a membrane protein in nanodiscs still remain elusive. Here, we utilized a NOE-based approach to assign (stereo-) specifically labeled Ile, Leu, Val and Ala methyl labeled and uniformly {sup 15}N-Phe and {sup 15}N-Tyr labeled OmpX and calculated a refined high-resolution structure. In addition, we were able to obtain residual dipolar couplings (RDCs) of OmpX in nanodiscs using Pf1 phage medium for the induction of weak alignment. Back-calculated NOESY spectra of the obtained NMR structures were compared to experimental NOESYs in order to validate the quality of these structures. We further used NOE information between protonated lipid head groups and side-chain methyls to determine the position of OmpX in the phospholipid bilayer. These data were verified by paramagnetic relaxation enhancement (PRE) experiments obtained with Gd{sup 3+}-modified lipids. Taken together, this study emphasizes the need for the (stereo-) specific labeling of membrane proteins in a highly deuterated background for high-resolution structure determination, particularly in large membrane mimicking systems like phospholipid nanodiscs. Structure validation by NOESY back-calculation will be helpful for the structure determination and validation of membrane proteins where NOE assignment is often difficult. The use of protein to lipid NOEs will be beneficial for the positioning of a membrane protein in the lipid bilayer without the need for preparing multiple protein samples.

  1. Evolution of the dose values and image quality for the X-ray of thorax postero/anterior in mature patients of the service of imagenology of the Hospital Dr. Juan Noe of Arica

    International Nuclear Information System (INIS)

    Ubeda, Carlos; Galaz, Sergio; Leyton, Fernando; Delgado, Otto; Espinosa, Alfonso; Inzulza, Alonso; Ramirez, Raul; Blanco, Daniel; Oyarzun, Carlos

    2008-01-01

    Full text: International Atomic Energy Agency defined guidance level for medical exposure, for the exams of general radiology, reason why the objective of the present work was to evaluate the evolution of the doses for the radiological exam of thorax posterior/anterior among the years 2005 at 2007. The used design was of traverse, descriptive, analytic and comparative type. The study population corresponded to 2 groups of 50 patients selected at random, of both sexes that attended the imagenology service of the public hospital Dr. Juan Noe Crevanni of the city of Arica, to be carried out a X-ray of thorax posterior/anterior. The first group of patients corresponded the participants in the project ARCAL LXXV (Determination of guidance level for Conventional Radiology and Interventionist) carried out in the year 2005. The second group of patients was those incorporate ones during the year 2007 to the project RLA/9/057 (Radiological Protection of Patient in Medical Exhibitions). Both investigations were sponsored by the International Atomic Energy Agency, The Institute of Health Publishes and the Chilean Commission of Nuclear Energy. The stages of the study were divided in: characterization of the yield of the teams, taking of exams, evaluation image quality, estimate of the dose values and statistical analysis. The mean values from entrance surface air kerma for the radiological exam of thorax posterior/anterior vary of 0,14 mGy (S.D. 0.29) to 0.08 mGy (S.D. 0.31), among the years 2005 and 2007 respectively, being this significant difference (p=0.001). Both values are inferior to the value recommended in the Adenda III of the BSS. As for the proportions of execution of the approaches of image quality this it was of 0.95 for the project ARCAL LXXV and 0.92 for the project RLA/9/057, without being this significant difference. The continuous evaluation of the guidance level for medical exposure, associated to the quality of the images constitutes an estimator on the

  2. Proton NMR Studies of a Large Protein. pH, Substrate Titrations, and NOESY Experiments with Perdeuterated Yeast Phosphoglycerate Kinase Containing [ 1H]Histidine Residues

    Science.gov (United States)

    Pappu, K. M.; Serpersu, E. H.

    Fully deuterated yeast phosphoglycerate kinase ([ 2H]PGK) was prepared biosynthetically with only histidine side chains of normal ( 1H) isotopic composition. The 1H NMR spectrum of this enzyme([ 1H]His[ 2H]PGK) showed that the histidine side chains are clearly visible as sharp signals. Thus detailed structural studies by 1H NMR became feasible with isotope-hybrid phosphoglycerate kinase which is otherwise too large ( Mr ˜ 46,000) for conventional 1H NMR studies. Proton signals of bound substrates were visible in the 1H NMR spectrum even with a substrate-to-enzyme ratio of less than 1/2 (mol/mol). The 2D NOESY spectrum of enzyme-MgdATP-glycerol 3-phosphate complex showed that, although protein concentration was very high (1.5 m M), no intraprotein cross peaks were observed other than those of intraresidue histidine NOE cross peaks. In addition, intrasubstrate NOEs and intermolecular NOEs between histidine and substrate protons were visible at a 1.5/1 substrate/enzyme (mol/mol) ratio. Paramagnetic effects of a substrate analog, Cr(III)ATP, on some of the histidine side chains indicated that the formation of the ternary enzyme-substrate complex causes large conformational changes in the enzyme.

  3. KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies

    International Nuclear Information System (INIS)

    Kobayashi, Naohiro; Iwahara, Junji; Koshiba, Seizo; Tomizawa, Tadashi; Tochio, Naoya; Guentert, Peter; Kigawa, Takanori; Yokoyama, Shigeyuki

    2007-01-01

    The recent expansion of structural genomics has increased the demands for quick and accurate protein structure determination by NMR spectroscopy. The conventional strategy without an automated protocol can no longer satisfy the needs of high-throughput application to a large number of proteins, with each data set including many NMR spectra, chemical shifts, NOE assignments, and calculated structures. We have developed the new software KUJIRA, a package of integrated modules for the systematic and interactive analysis of NMR data, which is designed to reduce the tediousness of organizing and manipulating a large number of NMR data sets. In combination with CYANA, the program for automated NOE assignment and structure determination, we have established a robust and highly optimized strategy for comprehensive protein structure analysis. An application of KUJIRA in accordance with our new strategy was carried out by a non-expert in NMR structure analysis, demonstrating that the accurate assignment of the chemical shifts and a high-quality structure of a small protein can be completed in a few weeks. The high completeness of the chemical shift assignment and the NOE assignment achieved by the systematic analysis using KUJIRA and CYANA led, in practice, to increased reliability of the determined structure

  4. Integral membrane protein structure determination using pseudocontact shifts

    Energy Technology Data Exchange (ETDEWEB)

    Crick, Duncan J.; Wang, Jue X. [University of Cambridge, Department of Biochemistry (United Kingdom); Graham, Bim; Swarbrick, James D. [Monash University, Monash Institute of Pharmaceutical Sciences (Australia); Mott, Helen R.; Nietlispach, Daniel, E-mail: dn206@cam.ac.uk [University of Cambridge, Department of Biochemistry (United Kingdom)

    2015-04-15

    Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.

  5. Stereospecific assignment of the NH2 resonances from the primary amides of asparagine and glutamine side chains in isotopically labeled proteins

    International Nuclear Information System (INIS)

    McIntosh, Lawrence P.; Brun, Emmanuel; Kay, Lewis E.

    1997-01-01

    An HMQC-based pulse scheme is presented for the stereospecific assignment of asparagine and glutamine side-chain amide protons. The approach makes use of the recently developed quantitative-J correlation spectroscopy [Bax, A. et al. (1994) Methods Enzymol., 239,79-105] to distinguish the E and Z primary amide protons and, as such, eliminates the need for assignments derived from more time-consuming and potentially ambiguous NOE methods. An application of this method to a uniformly 15N,13C-labeled cellulose-binding domain is presented. When used in combination with a NOESY-HSQC experiment, the predominant χ2 dihedral angles of two asparagine side chains in this protein can also be defined

  6. A novel method for the biosynthesis of deuterated proteins with selective protonation at the aromatic rings of Phe, Tyr and Trp

    International Nuclear Information System (INIS)

    Rajesh, Sundaresan; Nietlispach, Daniel; Nakayama, Hiroshi; Takio, Koji; Laue, Ernest D.; Shibata, Takehiko; Ito, Yutaka

    2003-01-01

    A novel biosynthetic strategy is described for the preparation of deuterated proteins containing protons at the ring carbons of Phe, Tyr and Trp, using the aromatic amino acid precursor shikimic acid. Specific protonation at aromatic side chains, with complete deuteration at C α/β positions was achieved in proteins overexpressed in bacteria grown in shikimate-supplemented D 2 O medium. Co-expression of a shikimate transporter in prototrophic bacteria resulted in protonation levels of 62-79%, whereas complete labeling was accomplished using shikimate auxotrophic bacteria. Our labeling protocol permits the measurement of important aromatic side chain derived distance restraints in perdeuterated proteins that could be utilized to enhance the accuracy of NMR structures calculated using low densities of NOEs from methyl selectively protonated samples

  7. A molecular dynamics simulation investigation of the relative stability of the cyclic peptide octreotide and its deprotonated and its (CF3)-Trp substituted analogs in different solvents.

    Science.gov (United States)

    Smith, Lorna J; Rought Whitta, Georgia; Dolenc, Jožica; Wang, Dongqi; van Gunsteren, Wilfred F

    2016-10-15

    The cyclic octa-peptide octreotide and its derivatives are used as diagnostics and therapeutics in relation to particular types of cancers. This led to investigations of their conformational properties using spectroscopic, NMR and CD, methods. A CF 3 -substituted derivative, that was designed to stabilize the dominant octreotide conformer responsible for receptor binding, turned out to have a lower affinity. The obtained spectroscopic data were interpreted as to show an increased flexibility of the CF 3 derivative compared to the unsubstituted octreotide, which could then explain the lower affinity. In this article, we use MD simulation without and with time-averaged NOE distance and time-averaged local-elevation 3 J-coupling restraining representing experimental NMR data to determine the conformational properties of the different peptides in the different solvents for which experimental data are available, that are compatible with the NOE atom-atom distance bounds and the 3 J HNHα -couplings as derived from the NMR measurements. The conformational ensembles show that the CF 3 substitution in combination with the change of solvent from water to methanol leads to a decrease in flexibility and a shift in the populations of the dominant conformers that are compatible with the experimental data. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. (13)C MRS of human brain at 7 Tesla using [2-(13)C]glucose infusion and low power broadband stochastic proton decoupling.

    Science.gov (United States)

    Li, Shizhe; An, Li; Yu, Shao; Ferraris Araneta, Maria; Johnson, Christopher S; Wang, Shumin; Shen, Jun

    2016-03-01

    Carbon-13 ((13)C) MR spectroscopy (MRS) of the human brain at 7 Tesla (T) may pose patient safety issues due to high radiofrequency (RF) power deposition for proton decoupling. The purpose of present work is to study the feasibility of in vivo (13)C MRS of human brain at 7 T using broadband low RF power proton decoupling. Carboxylic/amide (13)C MRS of human brain by broadband stochastic proton decoupling was demonstrated on a 7 T scanner. RF safety was evaluated using the finite-difference time-domain method. (13)C signal enhancement by nuclear Overhauser effect (NOE) and proton decoupling was evaluated in both phantoms and in vivo. At 7 T, the peak amplitude of carboxylic/amide (13)C signals was increased by a factor of greater than 4 due to the combined effects of NOE and proton decoupling. The 7 T (13)C MRS technique used decoupling power and average transmit power of less than 35 watts (W) and 3.6 W, respectively. In vivo (13)C MRS studies of human brain can be performed at 7 T, well below the RF safety threshold, by detecting carboxylic/amide carbons with broadband stochastic proton decoupling. © 2015 Wiley Periodicals, Inc.

  9. 1H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold

    International Nuclear Information System (INIS)

    Moore, J.M.; Chazin, W.J.; Wright, P.E.; Powls, R.

    1988-01-01

    Two-dimensional 1 H NMR methods have been used to make sequence-specific resonance assignments for the 97 amino acid residues of the plastocyanin from the green alga Scenedesmus obliquus. Assignments were obtained for all backbone protons and the majority of the side-chain protons. Spin system identification relied heavily on the observation of relayed connectivities to the backbone amide proton. Sequence-specific assignments were made by using the sequential assignment procedure. During this process, an extra valine residue was identified that had not been detected in the original amino acid sequence. Elements of regular secondary structure were identified from characteristic NOE connectivities between backbone protons, coupling constant values, and the observation of slowly exchanging amide protons. The protein in solution contains eight β-strands, one short segment of helix, five reverse turns, and five loops. The β-strands may be arranged into two βsheets on the basis of extensive cross-strand NOE connectivities. The chain-folding topology determined from the NMR experiments is that of a Greek key β-barrel and is similar to that observed for French bean plastocyanin in solution and poplar plastocyanin in the crystalline state. While the overall structures are similar, several differences in local structure between the S. obliquus and higher plant plastocyanins have been identified

  10. Solution structure and dynamics of melanoma inhibitory activity protein

    International Nuclear Information System (INIS)

    Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

    2002-01-01

    Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

  11. Comparative Study of the Methods Used for the Computer Resolution of Composite Gamma-Ray Spectra; Etude Comparative des Methodes Utilisees pour la Resolution de Spectres Gamma Complexes au Moyen d'un Ordinateur; Sravnitel'noe izuchenie metodov razresheniya sostavnykh gamma-spektrov pri pomoshchi schetno-reshayushchego ustrojstva; Estudio Comparativo de los Metodos Aplicados para Resolver Espectros Gamma Complejos Mediante Calculadoras

    Energy Technology Data Exchange (ETDEWEB)

    DeHaan, A. Jr.; Leventhal, L.; Benson, P. [Tracerlab, Richmond, CA (United States)

    1965-10-15

    The resolution of complex mixtures of gamma-ray emitters has been expedited by the use of highly sophisticated gamma-ray spectrometers in association with digital computers. These instruments have now become generally available or easily accessible to technical laboratories. This paper discusses the techniques used in this laboratory to obtain the concentrations of individual gamma-emitting radionuclides in fallout samples and compares the results obtained by the various mathematical methods on composite samples. The computer derived data are compared with results obtained by radiochemical analysis of the sample. Binary mixtures were analysed by methods outlined below and then the analysis was extended to the many component system. A computer method was developed which normalizes gamma-ray spectra to minimize the effect of long-term spectrometer drift and converts the spectrum to an energy co-ordinate system. The effects of an ''unexpected photopeak, ''zero intensity component, and overlapping peaks on the solution by the various methods were investigated with special emphasis on low-level samples. The most common mathematical methods for resolving a composite gamma-ray spectrum into its components were investigated. Most of these procedures lead to estimates for the concentrations of the different gamma-ray emitters by one of the following methods: (1) The successive elimination of the radionuclides with higher energy photopeaks subtracting the pure spectrum from the composite spectrum until it has been resolved; (2) Peak resolution without stripping; (3) The establishment of a set of simultaneous linear equations of the same order as the number of radionuclides in the mixture and its solution; (4) The estimation of the unknown concentrations by the method of least-squares, either conventional or weighted; (5) A combined statistical and least-squares method employing stepwise multiple linear regression, an attempt to integrate decision-making processes into the

  12. A pilot's assessment of helicopter handling-quality factors common to both agility and instrument flying tasks

    Science.gov (United States)

    Gerdes, R. M.

    1980-01-01

    A series of simulation and flight investigations were undertaken to evaluate helicopter flying qualities and the effects of control system augmentation for nap-of-the-Earth (NOE) agility and instrument flying tasks. Handling quality factors common to both tasks were identified. Precise attitude control was determined to be a key requirement for successful accomplishment of both tasks. Factors that degraded attitude controllability were improper levels of control sensitivity and damping, and rotor system cross coupling due to helicopter angular rate and collective pitch input. Application of rate command, attitude command, and control input decouple augmentation schemes enhanced attitude control and significantly improved handling qualities for both tasks. The NOE agility and instrument flying handling quality considerations, pilot rating philosophy, and supplemental flight evaluations are also discussed.

  13. Data describing the solution structure of the WW3* domain from human Nedd4-1

    Directory of Open Access Journals (Sweden)

    Vineet Panwalkar

    2016-09-01

    Full Text Available The third WW domain (WW3* of human Nedd4-1 (Neuronal precursor cell expressed developmentally down-regulated gene 4-1 interacts with the poly-proline (PY motifs of the human epithelial Na+ channel (hENaC subunits at micromolar affinity. This data supplements the article (Panwalkar et al., 2015 [1]. We describe the NMR experiments used to solve the solution structure of the WW3* domain. We also present NOE network data for defining the rotameric state of side chains of peptide binding residues, and complement this data with χ1 dihedral angles derived from 3J couplings and molecular dynamics simulations data. Keywords: Chemical shift, Neuronal precursor cell expressed developmentally down-regulated gene 4-1, NMR, NOE distance restraints, WW domain

  14. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard; Gao, Xin; Li, Ming

    2011-01-01

    to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors

  15. Is the Neoproterozoic oxygen burst a supercontinent legacy?

    Directory of Open Access Journals (Sweden)

    Melina eMacouin

    2015-09-01

    Full Text Available The Neoproterozoic (1000–542 Myr ago witnessed the dawn of Earth as we know it with modern-style plate tectonics, high levels of O2 in atmosphere and oceans and a thriving fauna. Yet, the processes leading to the fully oxygenation of the external envelopes, its exact timing and its link with the inner workings of the planet remain poorly understood. In some ways, it is a chicken and egg question: did the Neoproterozoic Oxygenation Event (NOE cause life blooming, low-latitudes glaciations and perturbations in geochemical cycles or is it a consequence of these phenomena? Here, we suggest that the NOE may have been triggered by multi-million years oxic volcanic emissions along a protracted period at the end of the Neoproterozoic when continents were assembled in the Rodinia supercontinent. We report a very oxidized magma source at the upper mantle beneath a ring of subducting margins around Rodinia, and detail here the evidence at the margin of the Arabian shield. We investigate the 780 Ma Biotite and Pink granites and associated rocks of the Socotra Island with rock magnetic and petrographic methods. Magnetic susceptibility and isothermal remanent magnetization acquisitions show that, in these granites, both magnetite and hematite are present. Hematite subdivides magnetite grains into small grains. Magnetite and hematite are found to be primary, and formed at the early magmatic evolution of the granite at very high oxygen fugacity. Massive degassing of these oxidized magmas would reduce the sink for oxygen, and consequently contribute to its rise in the atmosphere with a net O2 flux of at least 2.25 x 107 Tmol. Our conceptual model provides a deep Earth link to the NOE and implies the oxygenation burst has occurred earlier than previously envisaged, paving the way for later changes in the outer envelopes of the planet epitomized on the extreme Neoproterozoic glaciations and the appearance of the first animals.

  16. Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements

    Science.gov (United States)

    Missimer, John H; Dolenc, Jožica; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2010-01-01

    Trigger sequences are indispensable elements for coiled-coil formation. The monomeric helical trigger sequence of the yeast transcriptional activator GCN4 has been investigated recently using several solution NMR observables including nuclear Overhauser enhancement (NOE) intensities and 3J(HN,HCα)-coupling constants, and a set of 20 model structures was proposed. Constrained to satisfy the NOE-derived distance bounds, the NMR model structures do not appear to reproduce all the measured 3J(HN-HCα)-coupling constant values, indicating that the α-helical propensity is not uniform along the GCN4 trigger sequence. A recent methodological study of unrestrained and restrained molecular dynamics (MD) simulations of the GCN4 trigger sequence in solution showed that only MD simulations incorporating time-averaged NOE distance restraints and instantaneous or local-elevation 3J-coupling restraints could satisfy the entire set of the experimental data. In this report, we assess by means of cluster analyses the model structures characteristic of the two simulations that are compatible with the measured data and compare them with the proposed 20 NMR model structures. Striking characteristics of the MD model structures are the variability of the simulated configurations and the indication of entropic stability mediated by the aromatic N-terminal residues 17Tyr and 18His, which are absent in the set of NMR model structures. PMID:20954244

  17. Three-dimensional structural analysis of the group B polysaccharide of Neisseria meningitidis 6275 by two-dimensional NMR: The polysaccharide is suggested to exist in helical conformations in solution

    Energy Technology Data Exchange (ETDEWEB)

    Yamasaki, Ryohei; Bacon, B. (Univ. of California, San Francisco (USA) Veterans Administration Medical Center, San Francisco, CA (USA))

    1991-01-22

    The solution conformations of the group B polysaccharide of Neisseria meningitidis were analyzed by DQF-COSY and pure absorption 2D NOE NMR with three mixing times. The pyranose ring of the sialic acid residue was found to be in the {sup 2}C{sub 5} conformation. The DQF-COSY analysis indicated that the orientations of H6 and H7 and of H7 and H8 are both gauche. In order to overcome the difficulties in analyzing the NOE data due to the two sets of proton overlaps, molecular modeling of {alpha}-2,8-linked sialic acid oligomers was carried out to investigate possible conformers, and theoretical NOE calculations were performed by using CORMA (complete relaxation matrix analysis). The analysis suggests that the polysaccharide adopts helical structures for which the {phi} (defined by O6-C2-O8-C8) and {psi} (C2-O8-C8-C7) angles are in the following ranges: {phi}-60 to 0{degree}, {psi} 115-175{degree} or {phi} 90-120{degree}, {psi}55-175{degree}. The weak affinity of anti-B antibodies for smaller {alpha}-2,8-linked oligosaccharides may be due to the fact that such oligomers are more flexible and may not form an ordered structure as the poly(sialic acid) does.

  18. An NMR study of the covalent and noncovalent interactions of CC-1065 and DNA

    International Nuclear Information System (INIS)

    Scahill, T.A.; Jensen, R.M.; Swenson, D.H.; Hatzenbuhler, N.T.; Petzold, G.; Wierenga, W.; Brahme, N.D.

    1990-01-01

    The binding of the antitumor drug CC-1065 has been studied with nuclear magnetic resonance (NMR) spectroscopy. This study involves two parts, the elucidation of the covalent binding site of the drug to DNA and a detailed investigation of the noncovalent interactions of CC-1065 with a DNA fragment through analysis of 2D NOE (NOESY) experiments. A CC-1065-DNA adduct was prepared, and an adenine adduct was released upon heating. NMR ( 1 H and 13 C) analysis of the adduct shows that the drug binds to N3 of adenine by reaction of its cyclopropyl group. The reaction pathway and product formed were determined by analysis of the 13 C DEPT spectra. An octamer duplex, d(CGATTAGC·GCTAATCG), was synthesized and used in the interaction study of CC-1065 and the oligomer. The duplex and the drug-octamer complex were both analyzed by 2D spectroscopy (COSY, NOESY). The relative intensity of the NOEs observed between the drug (CC-1065) and the octamer duplex shows conclusively that the drug is located in the minor groove, covalently attached to N3 of adenine 6 and positioned from the 3' → 5' end in relation to strand A [d(CGATTA 6 GC)]. A mechanism for drug binding and stabilization can be inferred from the NOE data and model-building studies

  19. Spatio-Temporal Variation in Contrasting Effects of Resident Vegetation on Establishment, Growth and Reproduction of Dry Grassland Plants: Implications for Seed Addition Experiments

    Czech Academy of Sciences Publication Activity Database

    Knappová, Jana; Knapp, J.; Münzbergová, Zuzana

    2013-01-01

    Roč. 8, č. 6 (2013), no.-e65879 E-ISSN 1932-6203 Institutional support: RVO:67985939 Keywords : germination * seed sowing * habitat suitability Subject RIV: EF - Botanics Impact factor: 3.534, year: 2013

  20. Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

    International Nuclear Information System (INIS)

    Soares, T. A.; Daura, X.; Oostenbrink, C.; Smith, L. J.; Gunsteren, W. F. van

    2004-01-01

    The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, 3 J NHα and 3 J αβ coupling constants, and 1 5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone 3 J HNα -coupling constants and 1 H- 1 5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain 3 J αβ -coupling constants and 1 H- 1 5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result

  1. Analysis of the backbone dynamics of interleukin-1β using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy

    International Nuclear Information System (INIS)

    Clore, G.M.; Driscoll, P.C.; Wingfield, P.T.; Gronenborn, A.M.

    1990-01-01

    The backbone dynamics of uniformly 15 N-labeled interleukin-1β are investigated by using two-dimensional inverse detected heteronuclear 15 N- 1 H NMR spectroscopy. 15 N T 1 , T 2 , and NOE data at a spectrometer frequency of 600 MHz are obtained for 90% of the backbone amide groups. The data provide evidence for motions on three time scales. All the residues exhibit very fast motions on a time scale of approx-lt 20-50 ps that can be characterized by a single-order parameter with an average value of 0.82 ± 0.05. Thirty-two residues also display motions on a time scale of 0.5-4 ns, slightly less than the overall rotational correlation time of the protein (8.3 ns). While the simple formulation can account for the 15 N T 1 and T 2 data, it fails to account for the 15 N- 1 H NOE data and yields calculated values for the NOEs that are either too small or negative, whereas the observed NOEs are positive. Another 42 residues are characterized by some sort of motion on the 30-ns-10-ms time scale, which results in 15 N line broadening due to chemical exchange between different conformational substates with distinct 15 N chemical shifts. In general, the motions on both the 0.5-4-ns and 30-ns-10-ms time scales are localized in surface-accessible loops and turns connecting the β-strands, as well as at the beginning and end of strands. Finally, the kinetic and equilibrium properties of a slow conformational equilibrium between a major and a minor species, involving at least 19 residues and located on one contiguous face of the molecule, are characterized by using 1 H- 15 N correlation spectroscopy, 1 H- 15 N heteronuclear multiple quantum coherence-nuclear Overhauser enhancement spectroscopy, and 1 H- 1 H nuclear Overhauser enhancement spectroscopy

  2. HySafe - The Network of Excellence for Hydrogen Safety

    International Nuclear Information System (INIS)

    Jordan, T.

    2006-01-01

    Safety always has been a critical issue for innovations as it influences the economic attractiveness and public acceptance of any new idea. Furthermore, a fair market for trading innovative products has to be based on homogenized legal regulations, which usually refer commonly accepted standards. Ideally, these standards should be the unique outcome of safety assessments, based on profound and concerted pre-normative research work. However, in Europe the research related to hydrogen safety is still fragmented. This was the reason for the European Commission to support the needed integration and focusing of the related efforts with the help of a new instrument, the so-called Networks of Excellence NoE. So, the goal of NoE HySafe is to provide the basis to facilitate the safe introduction of hydrogen as an energy carrier, by removing the described safety related obstacles. The network is constituted by 24 partners from 12 European countries and from Canada, representing private industries, especially from the automotive sector, universities and research institutions. More than 120 scientists perform integrative work in 15 work packages. A biennial report on Hydrogen Safety is going to be published, the available experimental facilities have been catalogued and qualified, educational programs are designed. After the first successful International Conference on Hydrogen Safety the second will be organized 2007 in San Sebastian, Spain. The European codes and standards activities will be supported by scientifically based information formulated in the HySafe position papers. The web-site www.hysafe.net offers a versatile platform for internal and external communication. The further work program is orientated not only at the results of a state-of-the-art report and a PIRT analysis performed within the NoE but also complies with the needs identified in the external network including other European projects related to hydrogen like StorHy, HyWays and NATURALHY. By shifting

  3. Unraveling the symmetry ambiguity in a hexamer: Calculation of the R6 human insulin structure

    International Nuclear Information System (INIS)

    O'Donoghue, Sean I.; Chang Xiaoqing; Abseher, Roger; Nilges, Michael; Led, Jens J.

    2000-01-01

    Crystallographic and NMR studies of insulin have revealed a highly flexible molecule with a range of different aggregation and structural states; the importance of these states for the function of the hormone is still unclear. To address this question, we have studied the solution structure of the insulin R 6 symmetric hexamer using NMR spectroscopy. Structure determination of symmetric oligomers by NMR is complicated due to 'symmetry ambiguity' between intra- and intermonomer NOEs, and between different classes of intermonomer NOEs. Hence, to date, only two symmetric tetramers and one symmetric pentamer (VTB, B subunit of verotoxin) have been solved by NMR; there has been no other symmetric hexamer or higher-order oligomer. Recently, we reported a solution structure for R 6 insulin hexamer. However, in that study, a crystal structure was used as a reference to resolve ambiguities caused by the threefold symmetry; the same method was used in solving VTB. Here, we have successfully recalculated R 6 insulin using the symmetry-ADR method, a computational strategy in which ambiguities are resolved using the NMR data alone. Thus the obtained structure is a refinement of the previous R 6 solution structure. Correlated motions in the final structural ensemble were analysed using a recently developed principal component method; this suggests the presence of two major conformational substates. The study demonstrates that the solution structure of higher-order symmetric oligomers can be determined unambiguously from NMR data alone, using the symmetry-ADR method. This success bodes well for future NMR studies of higher-order symmetric oligomers. The correlated motions observed in the structural ensemble suggest a new insight into the mechanism of phenol exchange and the T 6 ↔ R 6 transition of insulin in solution

  4. 78 FR 69041 - Non-Oriented Electrical Steel From the People's Republic of China, Germany, Japan, the Republic...

    Science.gov (United States)

    2013-11-18

    ... the FOPs usage for materials, labor and energy on the consumption rates of its own production of NOES... any direction of magnetization in the plane of the material. The term ``substantially equal'' in the...

  5. The effect of randomised exposure to different types of natural outdoor environments compared to exposure to an urban environment on people with indications of psychological distress in Catalonia.

    Directory of Open Access Journals (Sweden)

    Margarita Triguero-Mas

    Full Text Available Experimental studies have reported associations between short-term exposure to natural outdoor environments (NOE and health benefits. However, they lack insight into mechanisms, often have low external and ecological validity, and have rarely focused on people with some psycho-physiological affection. The aim of this study was to use a randomized, case-crossover design to investigate: (i the effects of unconstrained exposure to real natural and urban environments on psycho-physiological indicators of people with indications of psychological distress, (ii the possible differential effects of 30 and 30+180 minutes exposures, and (iii the possible mechanisms explaining these effects.People (n = 26 with indications of psychological distress were exposed to green (Collserola Natural Park, blue (Castelldefels beach and urban (Eixample neighbourhood environments in Catalonia. They were exposed to all environments in groups for a period of 30+180 minutes between October 2013 and January 2014. During the exposure period, participants were instructed to do what they would usually do in that environment. Before, during (at 30 and 30+180 minutes and after each exposure, several psycho-physiological measures were taken: mood (measured as Total Mood Disturbance, TMD, attention capacity (measured as backwards digit-span task, stress levels (measures as salivary cortisol, systolic and diastolic blood pressure, heart rate, autonomous nervous system (assessed as heart rate variability and the indicators: low frequency power (LF, high frequency power (HF, ratio between LF and HF (LF:HF, and coefficients of component variance of LF, HF, and LF:HF. We also measured several potential mediators: air pollution, noise, physical activity, social interactions, and self-perceived restoration experience.When compared with responses to urban environment, we found statistically significantly lower TMD [-4.78 (-7.77, -1.79 points difference], and salivary cortisol [-0.21 (-0

  6. Conformation of flexibly linked triterpene dimers by using RDC-enhanced NMR spectroscopy

    Science.gov (United States)

    Lakshmi, Jerripothula K.; Pattnaik, Banita; Kavitha, Rachineni; Mallavadhani, Uppuluri V.; Jagadeesh, Bharatam

    2018-06-01

    Dimers of flexibly linked pentacyclic triterpene ursolic acid (UA) and its related frameworks such as asiatic acid (AA) and oleanolic acid (OA) have recently attracted significant attention due to their enhanced anti-cancer and anti-HCV activity compared to their respective monomers. Determination of conformation/inter-monomer orientation of these molecules is very important to understand their structure-activity relationship and to develop new scaffolds, which, however, is difficult through conventional NOE based solution-state NMR spectroscopy, due to lack of long-range NOEs. In the present work, we report a precise determination of conformation of two 1,2,3-triazole-linked triterpene dimer molecules, UA-AA and UA-OA, by employing one-bond Csbnd H residual dipolar couplings (RDCs) as additional long-range orientational restraints, measured in anisotropic PDMS/CDCl3 solvent medium.

  7. Comparative Population Dynamics of Two Closely Related Species Differing in Ploidy Level

    Czech Academy of Sciences Publication Activity Database

    Černá, L.; Münzbergová, Zuzana

    2013-01-01

    Roč. 8, č. 10 (2013), no.-e75563 E-ISSN 1932-6203 Institutional support: RVO:67985939 Keywords : ploidy level * clonal growth * life-table response experiments Subject RIV: EF - Botanics Impact factor: 3.534, year: 2013

  8. EURRECA—Principles and Future for Deriving Micronutrient Recommendations

    NARCIS (Netherlands)

    Claessens, M.; Contor, L.; Dhonukshe-Rutten, R.; Groot, L.C.P.Q.M. de; Fairweather-Tait, S.J.; Gurinovic, M.; Koletzko, B.; Ommen, B. van; Raats, M.M.; Veer, P. van 't

    2013-01-01

    The EURopean micronutrient RECommendations Aligned (EURRECA) Network of Excellence (NoE) explored an approach for settingmicronutrient recommendations, which would address the variation in recommendations across Europe. Therefore, a framework for deriving and using micronutrient Dietary Reference

  9. Mixed-time parallel evolution in multiple quantum NMR experiments: sensitivity and resolution enhancement in heteronuclear NMR

    International Nuclear Information System (INIS)

    Ying Jinfa; Chill, Jordan H.; Louis, John M.; Bax, Ad

    2007-01-01

    A new strategy is demonstrated that simultaneously enhances sensitivity and resolution in three- or higher-dimensional heteronuclear multiple quantum NMR experiments. The approach, referred to as mixed-time parallel evolution (MT-PARE), utilizes evolution of chemical shifts of the spins participating in the multiple quantum coherence in parallel, thereby reducing signal losses relative to sequential evolution. The signal in a given PARE dimension, t 1 , is of a non-decaying constant-time nature for a duration that depends on the length of t 2 , and vice versa, prior to the onset of conventional exponential decay. Line shape simulations for the 1 H- 15 N PARE indicate that this strategy significantly enhances both sensitivity and resolution in the indirect 1 H dimension, and that the unusual signal decay profile results in acceptable line shapes. Incorporation of the MT-PARE approach into a 3D HMQC-NOESY experiment for measurement of H N -H N NOEs in KcsA in SDS micelles at 50 o C was found to increase the experimental sensitivity by a factor of 1.7±0.3 with a concomitant resolution increase in the indirectly detected 1 H dimension. The method is also demonstrated for a situation in which homonuclear 13 C- 13 C decoupling is required while measuring weak H3'-2'OH NOEs in an RNA oligomer

  10. Investigation of the utility of selective methyl protonation for determination of membrane protein structures

    International Nuclear Information System (INIS)

    Shih, Steve C. C.; Stoica, Ileana; Goto, Natalie K.

    2008-01-01

    Polytopic α-helical membrane proteins present one of the final frontiers for protein structural biology, with significant challenges causing severe under-representation in the protein structure databank. However, with the advent of hardware and methodology geared to the study of large molecular weight complexes, solution NMR is being increasingly considered as a tool for structural studies of these types of membrane proteins. One method that has the potential to facilitate these studies utilizes uniformly deuterated samples with protons reintroduced at one or two methyl groups of leucine, valine and isoleucine. In this work we demonstrate that in spite of the increased proportion of these amino acids in membrane proteins, the quality of structures that can be obtained from this strategy is similar to that obtained for all α-helical water soluble proteins. This is partly attributed to the observation that NOEs between residues within the transmembrane helix did not have an impact on structure quality. Instead the most important factors controlling structure accuracy were the strength of dihedral angle restraints imposed and the number of unique inter-helical pairs of residues constrained by NOEs. Overall these results suggest that the most accurate structures will arise from accurate identification of helical segments and utilization of inter-helical distance restraints from various sources to maximize the distribution of long-range restraints

  11. Resistance exercise prevents plantar flexor deconditioning during bed rest

    Science.gov (United States)

    Bamman, M. M.; Hunter, G. R.; Stevens, B. R.; Guilliams, M. E.; Greenisen, M. C.

    1997-01-01

    Because resistance exercise (REX) and unloading induce opposing neuromuscular adaptations, we tested the efficacy of REX against the effects of 14 d of bed rest unloading (BRU) on the plantar flexor muscle group. Sixteen men were randomly assigned to no exercise (NOE, N = 8) or REX (N = 8). REX performed 5 sets x 6-10 repetitions to failure of constant resistance concentric/eccentric plantar flexion every other day during BRU. One-repetition maximum (1RM) strength was tested on the training device. The angle-specific torque-velocity relationship across 5 velocities (0, 0.52, 1.05, 1.75, and 2.97 rad.s-1) and the full range-of-motion power-velocity relationship were assessed on a dynamometer. Torque-position analyses identified strength changes at shortened, neutral, and stretched muscle lengths. Concentric and eccentric contractile work were measured across ten repetitions at 1.05 rad.s-1. Maximal neural activation was measured by surface electromyography (EMG). 1RM decreased 9% in NOE and improved 11% in REX (P joint positions. Concentric (15%) and eccentric (11%) contractile work fell in NOE (P < 0.05) but not in REX. Maximal plantar flexor EMG did not change in either group. In summary, constant resistance concentric/eccentric REX completely prevented plantar flexor performance deconditioning induced by BRU. The reported benefits of REX should prove useful in prescribing exercise for astronauts in microgravity and for patients susceptible to functional decline during bed- or chair-bound hospital stays.

  12. Micromagnetic Design of Spin Dependent Tunnel Junctions for Optimized Sensing Performance

    National Research Council Canada - National Science Library

    Tondra, Mark; Daughton, James M; Nordman, Catherine; Wang, Dexin; Taylor, John

    1999-01-01

    Pinned Spin Dependent Tunneling (SDT) devices have been fabricated into high sensitivity magnetic field sensors with many favorable properties including high sensitivity (̃ 10 umOe / Hz @ 1 Hz and ̃ 100 nOe / Hz @ > 10 kHz...

  13. Differential Neutron Scattering from Hydrogenous Moderators; Diffusion Differentielle des Neutrons par des Ralentisseurs Hydrogenes; Differentsial'noe rasseyanie nejtronov iz vodorodosoderzhashchikh zamedlitelej; Dispersion Diferencial de Neutrones en Moderadores Hidrogenados

    Energy Technology Data Exchange (ETDEWEB)

    Beyster, J. R.; Young, J. C.; Neill, J. M.; Mowry, W. R. [General Atomic Division of General Dynamics Corporation, John Jay Hopkins Laboratory for Pure and Applied Science, San Diego, CA (United States)

    1965-08-15

    experiments, which are sensitive mainly to P{sub 0} scattering. In particular one may test the P{sub 1} scattering kernel appropriate to a given molecular model. Third, the transport cross-section may be calculated directly from the experiments for use in multigroup reactor analysis. (author) [French] On mesure par les methodes du temps de vol les sections efficaces differentielles de diffusion simple (d{sigma}/d {Omega}) pour les ralentisseurs usuels. On utilise des neutrons thermiques produits par une source puisee intense (accelerateur lineaire de la General Atomic) avec un parcours de vol de 12 m a l'extremite duquel est place un echantillon mince du ralentisseur a l*etude. En outre, on a egalement prevu un petit parcours de vol terminal pour les neutrons diffuses, entre l'echantillon et plusieurs detecteurs de neutrons entierement absorbants. Cette methode permet de mesurer simultanement la distribution angulaire de diffusion pour plus de 50 energies des neutrons incidents. Les intensites sont-elevees, le bruit de fond est faible et bien defini et on peut proceder a des mesures rapides pour tous les angles de diffusion compris entre 10 et 155 degres. Les auteurs presentent des mesures de la section efficace differentielle de diffusion pour le vanadium, H{sub 2}O, D{sub 2}O et ZrH. On a etudie le vanadium pour controler le dispositif experimental. On a fait des mesures avec H{sub 2}O pour diverses epaisseurs et orientations des echantillons en vue de les comparer aux calculs fondes sur divers modeles de diffusion par l'hydrogene lie et aux resultats obtenus par Springer et Reinsch. Toutes les mesures experimentales ont ete corrigees pour tenir compte des effets importants de la diffusion multiple dans les echantillons. Pour l'instant, on n'a pas observe experimentalement la variation accusee que fait prevoir le modele de diffusion de Nelkin lorsque l'energie des neutrons est d'environ 0,06 eV; ceci est du au fait que l'hypothese du rotateur unique inhibe a 0,06 eV n'a pas

  14. On-lattice agent-based simulation of populations of cells within the open-source Chaste framework

    KAUST Repository

    Figueredo, G. P.; Joshi, T. V.; Osborne, J. M.; Byrne, H. M.; Owen, M. R.

    2013-01-01

    been implemented and are available for download as part of the latest public release of Chaste (Cancer, Heart and Soft Tissue Environment; http://www.cs.ox.ac.uk/chaste/), part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment

  15. Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

    Energy Technology Data Exchange (ETDEWEB)

    Soares, T. A. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Daura, X. [Universitat Autonoma de Barcelona, InstitucioCatalana de Recerca i Estudis Avancats and Institut de Biotecnologia i Biomedicina (Spain); Oostenbrink, C. [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland); Smith, L. J. [University of Oxford, Oxford Centre for Molecular Sciences, Central Chemistry Laboratory (United Kingdom); Gunsteren, W. F. van [ETH Hoenggerberg Zuerich, Laboratory of Physical Chemistry (Switzerland)], E-mail: wfvgn@igc.phys.chem.ethz.ch

    2004-12-15

    The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom-atom distance bounds, {sup 3}J{sub NH{alpha}} and {sup 3}J{sub {alpha}}{sub {beta}} coupling constants, and {sup 1}5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom-atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0-1.5 ns while backbone {sup 3}J{sub HN{alpha}}-coupling constants and {sup 1}H- {sup 1}5N order parameters take slightly longer, 1.0-2.0 ns. As expected, side-chain {sup 3}J{sub {alpha}}{sub {beta}}-coupling constants and {sup 1}H- {sup 1}5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the

  16. Base pair mismatches and carcinogen-modified bases in DNA: an NMR study of G x T and G x O4meT pairing in dodecanucleotide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Kouchakdjian, M.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1988-01-01

    High-resolution two-dimensional NMR studies have been completed on the self-complementary d(C-G-C-G-A-G-C-T-T-G-C-G) duplex (designated G x T 12-mer) and the self-complementary d(C-G-C-G-A-G-C-T-O 4 meT-G-C-G) duplex (designated G x O 4 meT 12-mer) containing G x T and G x O 4 meT pairs at identical positions four base pairs in from either end of the duplex. The exchangeable and nonexchangeable proton resonances have been assigned from an analysis of two-dimensional nuclear Overhauser enhancement (NOESY) spectra for the G x T 12-mer and G x O 4 meT 12-mer duplexes in H 2 O and D 2 O solution. The guanosine and thymidine imino protons in the G x T mismatch resonate at 10.57 and 11.98 ppm, respectively, and exhibit a strong NOE between themselves and to imino protons of flanking base pairs in the G x T 12-mer duplex. The large upfield chemical shift of this proton relative to that of the imino proton resonance of G in the G x T mismatch or in G x C base pairs indicates that hydrogen bonding to O 4 meT is either very weak or absent. This guanosine imino proton has an NOE to the OCH 3 group of O 4 meT across the pair and NOEs to the imino protons of flanking base pairs. Taken together with data from the NMR of nonexchangeable protons, this shows that both G and O 4 meT have anti-glycosidic torsion angles and are stacked into the duplex. Comparison of the intensity of the NOEs between the guanosine imino proton and the OCH 3 of O 4 meT as well as other protons in its vicinity demonstrates that the OCH 3 group of O 4 meT adopts the syn orientation with respect to N3 of the methylated thymidine. The authors propose an alternate base pairing mode stabilized by one short hydrogen bond between the 2-amino group of guanosine and the 2-carbonyl group of O 4 met

  17. Evolution of microbial communities during electrokinetic treatment of antibiotic-polluted soil.

    Science.gov (United States)

    Li, Hongna; Li, Binxu; Zhang, Zhiguo; Zhu, Changxiong; Tian, Yunlong; Ye, Jing

    2018-02-01

    The evolution of microbial communities during the electrokinetic treatment of antibiotic-polluted soil (EKA) was investigated with chlortetracycline (CTC), oxytetracycline (OTC) and tetracycline (TC) as template antibiotics. The total population of soil microorganisms was less affected during the electrokinetic process, while living anti-CTC, anti-OTC, anti-TC and anti-MIX bacteria were inactivated by 10.48%, 31.37%, 34.76%, and 22.08%, respectively, during the 7-day treatment compared with antibiotic-polluted soil without an electric field (NOE). Accordingly, samples with NOE treatment showed a higher Shannon index than those with EKA treatment, indicating a reduction of the microbial community diversity after electrokinetic processes. The major taxonomic phyla found in the samples of EKA and NOE treatment were Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. And the distribution of Actinobacteria, Cyanobacteria, and Chloroflexi was greatly decreased compared with blank soil. In the phylum Proteobacteria, the abundance of Alphaproteobacteria was greatly reduced in the soils supplemented with antibiotics (from 13.40% in blank soil to 6.43-10.16% after treatment); while Betaproteobacteria and Deltaproteobacteria showed a different trend with their abundance increased compared to blank soil, and Gammaproteobacteria remained unchanged for all treatments (2.36-2.78%). The varied trends for different classes indicated that the major bacterial groups changed with the treatments due to their different adaptability to the antibiotics as well as to the electric field. SulI being an exception, the reduction ratio of the observed antibiotic resistance genes (ARGs) including tetC, tetG, tetW, tetM, intI1, and sulII in the 0-2cm soil sampled with EKA versus NOE treatment reached 55.17%, 3.59%, 99.26%, 89.51%, 30.40%, and 27.92%, respectively. Finally, correlation analysis was conducted between antibiotic-resistant bacteria, ARGs and taxonomic bacterial classes. It

  18. Three-dimensional solution structure of Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy.

    Science.gov (United States)

    Cai, M; Gong, Y; Kao, J L; Krishnamoorthi, R

    1995-04-18

    The solution structure of Cucurbita maxima trypsin inhibitor-V (CMTI-V), which is also a specific inhibitor of the blood coagulation protein, factor XIIa, was determined by 1H NMR spectroscopy in combination with a distance-geometry and simulated annealing algorithm. Sequence-specific resonance assignments were made for all the main-chain and most of the side-chain hydrogens. Stereospecific assignments were also made for some of the beta-, gamma-, delta-, and epsilon-hydrogens and valine methyl hydrogens. The ring conformations of all six prolines in the inhibitor were determined on the basis of 1H-1H vicinal coupling constant patterns; most of the proline ring hydrogens were stereospecifically assigned on the basis of vicinal coupling constant and intraresidue nuclear Overhauser effect (NOE) patterns. Distance constraints were determined on the basis of NOEs between pairs of hydrogens. Dihedral angle constraints were determined from estimates of scalar coupling constants and intraresidue NOEs. On the basis of 727 interproton distance and 111 torsion angle constraints, which included backbone phi angles and side-chain chi 1, chi 2, chi 3, and chi 4 angles, 22 structures were calculated by a distance geometry algorithm and refined by energy minimization and simulated annealing methods. Both main-chain and side-chain atoms are well-defined, except for a loop region, two terminal residues, and some side-chain atoms located on the molecular surface. The average root mean squared deviation in the position for equivalent atoms between the 22 individual structures and the mean structure obtained by averaging their coordinates is 0.58 +/- 0.06 A for the main-chain atoms and 1.01 +/- 0.07 A for all the non-hydrogen atoms of residues 3-40 and 49-67. These structures were compared to the X-ray crystallographic structure of another protein of the same inhibitor family-chymotrypsin inhibitor-2 from barley seeds [CI-2; McPhalen, C. A., & James, M. N. G. (1987) Biochemistry 26

  19. Continuous Morphological Variation Correlated with Genome Size Indicates Frequent Introgressive Hybridization among Diphasiastrum Species (Lycopodiaceae) in Central Europe

    Czech Academy of Sciences Publication Activity Database

    Hanušová, K.; Ekrt, L.; Vít, Petr; Kolář, Filip; Urfus, Tomáš

    2014-01-01

    Roč. 9, č. 6 (2014), no.-e99552 E-ISSN 1932-6203 R&D Projects: GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : genome size * merphometrics * Diphasiastrum Subject RIV: EF - Botanics Impact factor: 3.234, year: 2014

  20. Synthesis of some new 4-aryloxmethylcoumarins and examination ...

    Indian Academy of Sciences (India)

    Administrator

    - tone (30 ... was filtered and washed with 1 : 1 HCl (30 mL) and ...... Table 1. Results of NOE difference spectra of the compound 3b. .... vent. The ORTEP diagram is shown in figure 3. The structure unambiguously shows that the bromination.

  1. Determination of the stereochemistry of 4-chromenecarbaldehydes ...

    African Journals Online (AJOL)

    Determination of the stereochemistry of 4-chromenecarbaldehydes using Nuclear Overhauser Enhancements (NOE) ... Journal of the Ghana Science Association ... The paper reports studies on the use of 4-chromenecarbaldehydes as suitable substrates for the assessment of the accuracy of interpretations of Nuclear ...

  2. Virtual and solution conformations of oligosaccharides

    International Nuclear Information System (INIS)

    Cumming, D.A.; Carver, J.P.

    1987-01-01

    The possibility that observed nuclear Overhauser enhancements and bulk longitudinal relaxation times, parameters measured by 1 H NMR and often employed in determining the preferred solution conformation of biologically important molecules, are the result of averaging over many conformational states is quantitatively evaluated. Of particular interest was to ascertain whether certain 1 H NMR determined conformations are virtual in nature; i.e., the fraction of the population of molecules actually found at any time within the subset of conformational space defined as the solution conformation is vanishingly small. A statistical mechanics approach was utilized to calculate an ensemble average relaxation matrix from which (NOE)'s and (T 1 )'s are calculated. Model glycosidic linkages in four oligosaccharides were studied. The nature of the resultant population distributions is such that 50% of the molecular population is found within 1% of available microstates, while 99% of the molecular population occupies about 10% of the ensemble microstates, a number roughly equal to that sterically allowed. From this analysis the authors conclude that in many cases quantitative interpretation of NMR relaxation data, which attempts to define a single set of allowable torsion angle values consistent with the observed data, will lead to solution conformations that are either virtual or reflect torsion angle values possessed by a minority of the molecular population. Observed values of NMR relaxation data are the result of the complex interdependence of the population distribution and NOE (or T 1 ) surfaces in conformational space. In conformational analyses, NMR data can therefore be used to test different population distributions calculated from empirical potential energy functions

  3. Identification of localized redox states in plant-type two-iron ferrodoxins using the nuclear Overhauser effect

    International Nuclear Information System (INIS)

    Dugad, L.B.; La Mar, G.N.; Banci, L.; Bertini, I.

    1990-01-01

    The homonuclear Overhauser effect (NOE), in conjunction with nonselective spin-lattice relaxation measurements, has been employed to assign the contact-shifted resonances for the reduced form of two typical plant-type two-iron ferrodoxins from the algae Spirulina platensis and Porphyra umbilicalis. These results demonstrate that the NOE should have broad general applicability for the assignments and electronic structural elucidation of diverse subclasses of paramagnetic iron-sulfur cluster proteins. NOE connectivities were detected only among sets of resonances exhibiting characteristically different deviations from Curie behavior, providing strong support for the applicability of the spin Hamiltonian formulation for the NMR properties of the antiferromagnetically coupled iron clusters. The geminal β-methylene protons for the two cysteines bound to the iron(II) center were clearly identified, as well as the C α H and one C β H for each of the cysteines bound to the iron(III). The identification of the iron bound to cysteines 41 and 46 as the iron(II) in the reduced protein was effected on the basis of dipolar contacts between the bound cysteines. Resolved labile proton contact-shifted resonances are attributed to hydrogen bonding to the iron(III) center, and it is concluded that the contact-shifted resonances for the more numerous hydrogen bonds to the iron(II) center are not resolved from the diamagnetic envelope. The identification of the iron closer to the protein surface as the more reducible one is consistent with predictions based on a larger number of hydrogen bonds to this center

  4. An economically reliable scenario

    International Nuclear Information System (INIS)

    Anon.

    1996-01-01

    Mister Benjamin Dessus, director of the Ecotech programme at the Cnrs and author of the Noe scenario, describes his propositions for energy prospective, supported by an economic analysis. He advocates the energy diversification and the use of renewable energies. (N.C.). 1 ref., 1 tab

  5. 76 FR 1067 - Testing of Certain High Production Volume Chemicals; Second Group of Chemicals

    Science.gov (United States)

    2011-01-07

    ... Mfg & NOES (number based criteria based criteria significant chemicals (lbs) industrial of workers... 2070-AD16 Testing of Certain High Production Volume Chemicals; Second Group of Chemicals AGENCY... section 4(a)(1)(B) of the Toxic Substances Control Act (TSCA) to require manufacturers, importers, and...

  6. Hvad er forskning? Normer, videnskab og samfund.

    DEFF Research Database (Denmark)

    forskningsvurdering. Hugo F. Alrøe og Egon Noe: Et perspektivisk blik på videnskabelig uenighed og ekspertise. Cathrine Hasse: Forskerens læreproces - et kritisk, realistisk perspektiv. David Favrholdt: Om viden og videnskab. Jens Hebor: Demarkationsproblemet. Jan Faye: Hvordan adskilles astronomi fra astrologi? Finn...

  7. Variability in the Contribution of Different Life Stages to Population Growth as a Key Factor in the Invasion Success of Pinus strobus

    Czech Academy of Sciences Publication Activity Database

    Münzbergová, Zuzana; Hadincová, Věroslava; Wild, Jan; Kindlmannová, J.

    2013-01-01

    Roč. 8, č. 2 (2013), no.-e56953 E-ISSN 1932-6203 R&D Projects: GA ČR GA526/05/0430 Institutional support: RVO:67985939 Keywords : comparative demography * biological control * plant demography Subject RIV: EF - Botanics Impact factor: 3.534, year: 2013

  8. Antiprotozoal Isoflavan Quinones from Abrus precatorius ssp. africanus

    CSIR Research Space (South Africa)

    Hata, Y

    2013-04-01

    Full Text Available and semipreparative RPHPLC chromatography. Structures were established by HR-ESIMS, and 1D and 2D NMR ((sup)1H, (sup)13C, COSY, HMBC, HSQC, and NOE difference spectroscopy). Five compounds were obtained and identified as two isoflavan hydroquinones, abruquinone H (1...

  9. Using NMR Spectroscopy to Investigate the Solution Behavior of Nerve Agents and Their Binding to Acetylcholinesterase

    Science.gov (United States)

    2016-01-01

    from the NOE data and X-ray crystallography , will be used to evaluate the conformational changes associated with AChE interaction. Refined MD...P.G. Funnels, Pathways, and the Energy Landscape of Protein Folding: A Synthesis . Proteins 1995, 21, 167–195. Cavalli, A.; Bottegoni, G.; Raco

  10. Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution nuclear magnetic resonance and molecular dynamics simulations.

    Science.gov (United States)

    Pechlaner, Maria; Sigel, Roland K O; van Gunsteren, Wilfred F; Dolenc, Jožica

    2013-10-08

    Nuclear magnetic resonance (NMR) nuclear Overhauser enhancement (NOE) data obtained for a 35-nucleotide RNA segment of a bacterial group II intron indicate a helical hairpin structure in which three parts, a terminal pentaloop, a bulge, and a G-A mismatch, display no Watson-Crick base pairing. The 668 NOE upper distance bounds for atom pairs are insufficient to uniquely determine the conformation of these segments. Therefore, molecular dynamics simulations including time-averaged distance restraints have been used to obtain a conformational ensemble compatible with the observed NMR data. The ensemble shows alternating hydrogen bonding patterns for the mentioned segments. In particular, in the pentaloop and in the bulge, the hydrogen bonding networks correspond to distinct conformational clusters that could not be captured by using conventional single-structure refinement techniques. This implies that, to obtain a realistic picture of the conformational ensemble of such flexible biomolecules, it is necessary to properly account for the conformational variability in the structure refinement of RNA fragments.

  11. An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude

    Energy Technology Data Exchange (ETDEWEB)

    Orts, Julien [EMBL, Structure and Computational Biology Unit (Germany); Bartoschek, Stefan [Industriepark Hoechst, Sanofi-Aventis Deutschland GmbH, R and D LGCR/Parallel Synthesis and Natural Products (Germany); Griesinger, Christian [Max Planck Institute for Biophysical Chemistry (Germany); Monecke, Peter [Industriepark Hoechst, Sanofi-Aventis Deutschland GmbH, R and D LGCR/Structure, Design and Informatics (Germany); Carlomagno, Teresa, E-mail: teresa.carlomagno@embl.de [EMBL, Structure and Computational Biology Unit (Germany)

    2012-01-15

    Low-affinity ligands can be efficiently optimized into high-affinity drug leads by structure based drug design when atomic-resolution structural information on the protein/ligand complexes is available. In this work we show that the use of a few, easily obtainable, experimental restraints improves the accuracy of the docking experiments by two orders of magnitude. The experimental data are measured in nuclear magnetic resonance spectra and consist of protein-mediated NOEs between two competitively binding ligands. The methodology can be widely applied as the data are readily obtained for low-affinity ligands in the presence of non-labelled receptor at low concentration. The experimental inter-ligand NOEs are efficiently used to filter and rank complex model structures that have been pre-selected by docking protocols. This approach dramatically reduces the degeneracy and inaccuracy of the chosen model in docking experiments, is robust with respect to inaccuracy of the structural model used to represent the free receptor and is suitable for high-throughput docking campaigns.

  12. A vision and strategy for the virtual physiological human in 2010 and beyond.

    Science.gov (United States)

    Hunter, Peter; Coveney, Peter V; de Bono, Bernard; Diaz, Vanessa; Fenner, John; Frangi, Alejandro F; Harris, Peter; Hose, Rod; Kohl, Peter; Lawford, Pat; McCormack, Keith; Mendes, Miriam; Omholt, Stig; Quarteroni, Alfio; Skår, John; Tegner, Jesper; Randall Thomas, S; Tollis, Ioannis; Tsamardinos, Ioannis; van Beek, Johannes H G M; Viceconti, Marco

    2010-06-13

    European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also helping to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by framework 6 strategy for a European physiome (STEP) project in 2006. It is now time to assess the accomplishments of the last 2 years and update the STEP vision for the VPH. We consider the biomedical science, healthcare and information and communications technology challenges facing the project and we propose the VPH Institute as a means of sustaining the vision of VPH beyond the time frame of the NoE.

  13. Biomolecular structure refinement using the GROMOS simulation software

    International Nuclear Information System (INIS)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jožica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van

    2011-01-01

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  14. Biomolecular structure refinement using the GROMOS simulation software

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jozica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology ETH, Laboratory of Physical Chemistry (Switzerland)

    2011-11-15

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, {sup 3}J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  15. Biogeochemical Modeling of the Second Rise of Oxygen

    Science.gov (United States)

    Smith, M. L.; Catling, D.; Claire, M.; Zahnle, K.

    2014-03-01

    The rise of atmospheric oxygen set the tempo for the evolution of complex life on Earth. Oxygen levels are thought to have increased in two broad steps: one step occurred in the Archean ~ 2.45 Ga (the Great Oxidation Event or GOE), and another step occured in the Neoproterozoic ~750-580 Ma (the Neoprotoerozoic Oxygenation Event or NOE). During the NOE, oxygen levels increased from ~1-10% of the present atmospheric level (PAL) (Holland, 2006), to ~15% PAL in the late Neoproterozoic, to ~100% PAL later in the Phanerozoic. Complex life requires O2, so this transition allowed complex life to evolve. We seek to understand what caused the NOE. To explore causes for the NOE, we build upon the biogeochemical model of Claire et al. (2006), which calculates the redox evolution of the atmosphere, ocean, biosphere, and crust in the Archean through to the early Proterozoic. In this model, the balance between oxygenconsuming and oyxgen-producing fluxes evolves over time such that at ~2.4 Ga, the rapidly acting sources of oxygen outweigh the rapidly-acting sinks. Or, in other words, at ~2.4 Ga, the flux of oxygen from organic carbon burial exceeds the sinks of oxygen from reaction with reduced volcanic and metamoprphic gases. The model is able to drive oxygen levels to 1-10% PAL in the Proterozoic; however, the evolving redox fluxes in the model cannot explain how oxygen levels pushed above 1-10% in the late Proterozoic. The authors suggest that perhaps another buffer, such as sulfur, is needed to describe Proterozoic and Phanerozoic redox evolution. Geologic proxies show that in the Proterozoic, up to 10% of the deep ocean may have been sulfidic. With this ocean chemistry, the global sulfur cycle would have worked differently than it does today. Because the sulfur and oxygen cycles interact, the oxygen concentration could have permanently changed due to an evolving sulfur cycle (in combination with evolving redox fluxes associated with other parts of the oxygen cycle and carbon

  16. A vision and strategy for the virtual physiological human in 2010 and beyond

    NARCIS (Netherlands)

    Hunter, P.; Coveney, P.V.; de Bono, B.; Diaz, V.; Fenner, J.; Frangi, A.F.; Harris, P.; Hose, R.; Kohl, P.; Lawford, P.; McCormack, K.; Mendes, M.; Omholt, S.; Quarteroni, A.; Skar, J.; Tegner, J.; Thomas, S.R.; Tollis, I.; Tsamardinos, I.; van Beek, J.H.G.M.; Viceconti, M.

    2010-01-01

    European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various

  17. Phosphatidylcholine Specific PLC-Induced Dysregulation of Gap Junctions, a Robust Cellular Response to Environmental Toxicants, and Prevention by Resveratrol in a Rat Liver Cell Model

    Czech Academy of Sciences Publication Activity Database

    Sovadinová, I.; Babica, Pavel; Böke, H.; Kumar, E.; Wilke, A.; Park, J.-S.; Trosko, J. E.; Upham, B. L.

    2015-01-01

    Roč. 10, 5 no.e0124454 (2015), s. 1-16 E-ISSN 1932-6203 R&D Projects: GA MŠk LH12034 Institutional support: RVO:67985939 Keywords : gap junctional intercellular communication * resveratrol * phosphatidylcholine-specific phospholipase C Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.057, year: 2015

  18. A vision and strategy for the virtual physiological human: 2012 update

    NARCIS (Netherlands)

    Hunter, P.; Chapman, T.; Coveney, P.V.; De Bono, B.; Diaz, V.; Fenner, J.; Frangi, A.F.; Harris, P.; Hose, R.; Kohl, P.; Lawford, P.; McCormack, K.; Mendes, M.; Omholt, S.; Quarteroni, A.; Shublaq, N.; Skår, J.; Stroetmann, K.; Tegner, J.; Thomas, S.R.; Tollis, I.; Tsamardinos, I.; van Beek, J.H.G.M.; Viceconti, M.

    2013-01-01

    European funding under Framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for 5 years. The VPH Network of Excellence (NoE) has been set up to help develop common standards, open source software, freely accessible data and model repositories, and various

  19. Genetically modified cellular vaccines for therapy of human papilloma virus type 16 (HPV 16)-associated tumours

    Czech Academy of Sciences Publication Activity Database

    Bubeník, Jan

    2008-01-01

    Roč. 8, č. 3 (2008), s. 180-186 ISSN 1568-0096 Grant - others:EU-FP6-NoE Clinigene(XE) 018933 Institutional research plan: CEZ:AV0Z50520514 Keywords : HPV 16 * genetically modified vaccines Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.316, year: 2008

  20. Exact Solutions for Internuclear Vectors and Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media, and their Application in a Systematic Search Algorithm for Determining Protein Backbone Structure

    International Nuclear Information System (INIS)

    Wang Lincong; Donald, Bruce Randall

    2004-01-01

    We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (φ,ψ) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in constant time, the backbone (φ,ψ) angles for a residue from RDCs in two media on any single backbone vector type. Building upon these exact solutions we have designed a novel algorithm for determining a protein backbone substructure consisting of α-helices and β-sheets. Our algorithm employs a systematic search technique to refine the conformation of both α-helices and β-sheets and to determine their orientations using exclusively the angular restraints from RDCs. The algorithm computes the backbone substructure employing very sparse distance restraints between pairs of α-helices and β-sheets refined by the systematic search. The algorithm has been demonstrated on the protein human ubiquitin using only backbone NH RDCs, plus twelve hydrogen bonds and four NOE distance restraints. Further, our results show that both the global orientations and the conformations of α-helices and β-strands can be determined with high accuracy using only two RDCs per residue. The algorithm requires, as its input, backbone resonance assignments, the identification of α-helices and β-sheets as well as sparse NOE distance and hydrogen bond restraints.Abbreviations: NMR - nuclear magnetic resonance; RDC - residual dipolar coupling; NOE - nuclear Overhauser effect; SVD - singular value decomposition; DFS - depth-first search; RMSD - root mean square deviation; POF - principal order frame; PDB - protein data bank; SA - simulated annealing; MD - molecular dynamics

  1. Criticality safety evaluation of the fuel cycle facility electrorefiner

    International Nuclear Information System (INIS)

    Lell, R.M.; Mariani, R.D.; Fujita, E.K.; Benedict, R.W.; Turski, R.B.

    1993-01-01

    The integral Fast Reactor (IFR) being developed by Argonne National Laboratory (ANL) combines the advantages of metal-fueled, liquid-metal cooled reactors and a closed-loop fuel cycle. Some of the primary advantages are passive safety for the reactor and resistance to diversion for the heavy metal in the fuel cycle. in addition, the IFR pyroprocess recycles all the long-lived actinide activation products for casting into new fuel pins so that they may be burned in the reactor. A key component in the Fuel Cycle Facility (FCF) recycling process is the electrorefiner (ER) in which the actinides are separated from the fission products. In the process, the metal fuel is electrochemically dissolved into a high-temperature molten salt, and electrorefined uranium or uranium/plutonium products are deposited at cathodes. This report addresses the new and innovative aspects of the criticality analysis ensuing from processing metallic fuel, rather than metal oxide fuel, and from processing the spent fuel in batch operations. in particular, the criticality analysis employed a mechanistic approach as opposed to a probabilistic one. A probabilistic approach was unsuitable because of a lack of operational experience with some of the processes, rendering the estimation of accident event risk factors difficult. The criticality analysis also incorporated the uncertainties in heavy metal content attending the process items by defining normal operations envelopes (NOES) for key process parameters. The goal was to show that reasonable process uncertainties would be demonstrably safe toward criticality for continuous batch operations provided the key process parameters stayed within their NOES. Consequently the NOEs became the point of departure for accident events in the criticality analysis

  2. Criticality safety strategy for the Fuel Cycle Facility electrorefiner at Argonne National Laboratory, West

    International Nuclear Information System (INIS)

    Mariani, R.D.; Benedict, R.W.; Lell, R.M.; Turski, R.B.; Fujita, E.K.

    1993-01-01

    The Integral Fast Reactor being developed by Argonne National Laboratory (ANL) combines the advantages of metal-fueled, liquid-metal-cooled reactors and a closed fuel cycle. Presently, the Fuel Cycle Facility (FCF) at ANL-West in Idaho Falls, Idaho is being modified to recycle spent metallic fuel from Experimental Breeder Reactor II as part of a demonstration project sponsored by the Department of Energy. A key component of the FCF is the electrorefiner (ER) in which the actinides are separated from the fission products. In the electrorefining process, the metal fuel is anodically dissolved into a high-temperature molten salt and refined uranium or uranium/plutonium products are deposited at cathodes. In this report, the criticality safety strategy for the FCF ER is summarized. FCF ER operations and processes formed the basis for evaluating criticality safety and control during actinide metal fuel refining. In order to show criticality safety for the FCF ER, the reference operating conditions for the ER had to be defined. Normal operating envelopes (NOES) were then defined to bracket the important operating conditions. To keep the operating conditions within their NOES, process controls were identified that can be used to regulate the actinide forms and content within the ER. A series of operational checks were developed for each operation that wig verify the extent or success of an operation. The criticality analysis considered the ER operating conditions at their NOE values as the point of departure for credible and incredible failure modes. As a result of the analysis, FCF ER operations were found to be safe with respect to criticality

  3. Structural analysis of d(GCAATTGC)2 and its complex with berenil by nuclear magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Yoshida, Mitsuru; Banville, D.L.; Shafer, R.H.

    1990-01-01

    The structures of d(GCAATTGC) 2 and its complex with berenil in solution were analyzed by two-dimensional 1 H NMR spectroscopy. Intra- and internucleotide nuclear Overhauser effect (NOE) connectivities demonstrate that the octanucleotide duplex is primarily in the B conformation. Binding with berenil stabilizes the duplex with respect to thermal denaturation by about 10 degree C, based on the appearance of the imino proton signals. The berenil-d(GCAATTGC) 2 system is in fast exchange on the NMR time scale. The two-dimensional NMR data reveal that berenil binds in the minor groove of d(GCAATTGC) 2 . The aromatic drug protons are placed within 5 angstrom of the H2 proton of both adenines, the H1', H5', and H5 double-prime of both thymidines, and the H4', H5', and H5 double-prime of the internal guanosine. The amidine protons on berenil are also close to the H2 proton of both adenines. The duplex retains an overall B conformation in the complex with berenil. At 18 degree C, NOE contacts at longer mixing times indicate the presence of end-to-end association both in the duplex alone and also in its complex with berenil. These intermolecular contacts either vanished or diminished substantially at 45 degree C. Two molecular models are proposed for the berenil-(GCAATTGC) 2 complex; one has hydrogen bonds between the berenil amidine protons and the carbonyl oxygen, O2, of the external thymines, and the other has hydrogen bonds between the drug amidine protons and the purine nitrogen, N3, of the internal adenines. Quantitative analysis of the NOE data favors the second model

  4. An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor

    Directory of Open Access Journals (Sweden)

    Ram B. Khattri

    2016-07-01

    Full Text Available Selective hits for the glutaredoxin ortholog of Brucella melitensis are determined using STD NMR and verified by trNOE and 15N-HSQC titration. The most promising hit, RK207, was docked into the target molecule using a scoring function to compare simulated poses to experimental data. After elucidating possible poses, the hit was further optimized into the lead compound by extension with an electrophilic acrylamide warhead. We believe that focusing on selectivity in this early stage of drug discovery will limit cross-reactivity that might occur with the human ortholog as the lead compound is optimized. Kinetics studies revealed that lead compound 5 modified with an ester group results in higher reactivity than an acrylamide control; however, after modification this compound shows little selectivity for bacterial protein versus the human ortholog. In contrast, hydrolysis of compound 5 to the acid form results in a decrease in the activity of the compound. Together these results suggest that more optimization is warranted for this simple chemical scaffold, and opens the door for discovery of drugs targeted against glutaredoxin proteins—a heretofore untapped reservoir for antibiotic agents.

  5. An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor.

    Science.gov (United States)

    Khattri, Ram B; Morris, Daniel L; Davis, Caroline M; Bilinovich, Stephanie M; Caras, Andrew J; Panzner, Matthew J; Debord, Michael A; Leeper, Thomas C

    2016-07-16

    Selective hits for the glutaredoxin ortholog of Brucella melitensis are determined using STD NMR and verified by trNOE and (15)N-HSQC titration. The most promising hit, RK207, was docked into the target molecule using a scoring function to compare simulated poses to experimental data. After elucidating possible poses, the hit was further optimized into the lead compound by extension with an electrophilic acrylamide warhead. We believe that focusing on selectivity in this early stage of drug discovery will limit cross-reactivity that might occur with the human ortholog as the lead compound is optimized. Kinetics studies revealed that lead compound 5 modified with an ester group results in higher reactivity than an acrylamide control; however, after modification this compound shows little selectivity for bacterial protein versus the human ortholog. In contrast, hydrolysis of compound 5 to the acid form results in a decrease in the activity of the compound. Together these results suggest that more optimization is warranted for this simple chemical scaffold, and opens the door for discovery of drugs targeted against glutaredoxin proteins-a heretofore untapped reservoir for antibiotic agents.

  6. 78 FR 78275 - Alcohol and Drug Testing: Determination of Minimum Random Testing Rates for 2014

    Science.gov (United States)

    2013-12-26

    ...-11213, Notice No. 17] Alcohol and Drug Testing: Determination of Minimum Random Testing Rates for 2014... December 26, 2013. FOR FURTHER INFORMATION CONTACT: Jerry Powers, FRA Drug and Alcohol Program Manager, W38...-493-6313); or Sam Noe, FRA Drug and Alcohol Program Specialist, (telephone 615-719- 2951). Issued in...

  7. NMR study of 1,4-dihydropyridine derivatives endowed with long alkyl and functionalized chains

    Energy Technology Data Exchange (ETDEWEB)

    Suarez, Margarita; Salfran, Esperanza; Rodriguez, Hortensia; Coro, Julieta, E-mail: msuarez@fq.uh.c [Universidad de La Habana (Cuba). Facultad de Quimica. Lab. de Sintesis Organica; Molero, Dolores; Saez, Elena [Universidad Complutense, Madrid (Spain). CAI-RMN; Martinez-Alvarez, Roberto; Martin, Nazario [Universidad Complutense, Madrid (Spain). Facultad de Quimica. Dept. de Quimica Organica I

    2011-07-01

    The {sup 1}H , {sup 13}C and {sup 15}N NMR spectroscopic data for 1,4-dihydropyridine endowed with long alkyl and functionalized chain on C-3 and C-5, have been fully assigned by combination of one- and two dimensional experiments (DEPT, HMBC, HMQC, COSY, nOe). (author)

  8. Minutes of the Explosives Safety Seminar (20th) Held at OMNI international Hotel, Norfolk, Virginia on 24-26 August 1982. Volume II

    Science.gov (United States)

    1982-08-01

    hue an mvwe old* I noe.*iy and identify by Stoc* nowm -P) Ammunition Explosives Safety 20. AGSTRACT (Conth. an rever. sid. it noeeeary wtd identify by...explosive. All tests have been monitoreo by remote television; most also used cinematography at 500 to 1000 frames per second. Figure 2 shows an

  9. On the use of hydrogen in confined spaces: Results from the internal project InsHyde

    NARCIS (Netherlands)

    Venetsanos, A.G.; Adams, P.; Azkarate, I.; Bengaouer, A.; Brett, L.; Carcassi, M.N.; Engebø, A.; Gallego, E.; Gavrikov, A.I.; Hansen, O.R.; Hawksworth, S.; Jordan, T.; Kessler, A.; Kumar, S.; Molkov, V.; Nilsen, S.; Reinecke, E.; Stöcklin, M.; Schmidtchen, U.; Teodorczyk, A.; Tigreat, D.; Versloot, N.H.A.

    2011-01-01

    The paper presents an overview of the main achievements of the internal project InsHyde of the HySafe NoE. The scope of InsHyde was to investigate realistic small-medium indoor hydrogen leaks and provide recommendations for the safe use/storage of indoor hydrogen systems. Additionally, InsHyde

  10. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

    Science.gov (United States)

    Lee, Woonghee; Stark, Jaime L; Markley, John L

    2014-11-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

  11. Differential Experiences of Women and Minority Engineering Students in a Cooperative Education Program

    Science.gov (United States)

    Fifolt, Matthew M.; Abbott, Gypsy

    Although slight gains have been made in attracting women and minority students to the field of engineering, the differences are not great enough to meet current economic demands [National Academy of Sciences (2007). Rising above the gathering storm: Energizing and employing America for a brighter economic future, Washington, DC: National Academies Press]. Therefore, it has become imperative that colleges and universities increase efforts to both recruit and retain these students who express interest in the STEM fields [National Science Foundation (2006), Women, minorities, and persons with disabilities in science and engineering, NSF 4-311, Arlington, VA: NSF]. In engineering, one promising venue for students to gain professional experience as part of their undergraduate training is through cooperative education (co-op). However, there is a dearth of information in the research literature regarding how co-op programs can be structured to address the needs of diverse students. There is consensus, however, about one aspect of addressing the needs of diverse students, namely, mentoring and role models are key strategies for success. In this study, a mixed methods design was used to examine students' perceptions of mentoring in a cooperative education program in a southeastern university. Using Noe's [Noe, R. (1988). An investigation of the determinants of successful assigned mentoring relationships. Personnel Psychology, 1, 457-479] mentoring functions scales, which described psychosocial and career-related support, research findings indicated a statistically significant difference between gender and the psychosocial aspect of mentoring. Analysis of the qualitative data further confirmed differences in cooperative education experiences with respect to both gender and ethnicity.

  12. Et perspektivisk blik på videnskabelig uenighed og ekspertise

    DEFF Research Database (Denmark)

    Alrøe, Hugo; Noe, Egon

    2010-01-01

    Alrøe og Noes kapitel fokuserer på det forhold, at forskningen rummer meget forskellige discipliner, som har hver deres specifikke iagttagelsesapparater, teorier og lokale normer. Hvis konsensus er en norm eller bestræbelse inden for et enkelt forskersamfund, så gælder denne norm ikke nødvendigvi...

  13. Backbone dynamics of reduced plastocyanin from the cyanobacterium Anabaena variabilis: Regions involved in electron transfer have enhanced mobility

    DEFF Research Database (Denmark)

    Ma, L.X.; Hass, M.A.S.; Vierick, N.

    2003-01-01

    The dynamics of the backbone of the electron-transfer protein plastocyanin from the cyanobacterium Anabaena variabilis were determined from the N-15 and C-13(alpha) R-1 and R-2) relaxation rates and steady-state [H-1]-N-15 and [H-1]-C-13 nuclear Overhauser effects (NOEs) using the model...

  14. Recruitment and quality academic staff selection: the case study of ...

    African Journals Online (AJOL)

    The sources from which organizations decide to select personnel from are central to its ability to survive, adapt, and grow (Noe et al, 2004:171). The paper examines a case study of recruitment and selection of quality academic staff into Covenant University. The paper addresses the factors that could affect recruitment ...

  15. Classification of response-types for single-pilot NOE helicopter combat tasks

    Science.gov (United States)

    Mitchell, David G.; Hoh, Roger H.; Atencio, Adolph, Jr.

    1987-01-01

    Two piloted simulations have recently been conducted to evaluate both workload and handling qualities requirements for operation of a helicopter by a single pilot in a nap-of-the-earth combat environment. An advanced cockpit, including a moving-map display and an interactive touchpad screen, provided aircraft mission, status, and position information to the pilot. The results of the simulations are reviewed, and the impact of these results on the development of a revised helicopter handling qualities specification is discussed. Rate command is preferred over attitude command in pitch and roll, and attitude hold over groundspeed hold, for low-speed precision pointing tasks. Position hold is necessary for Level 1 handling qualities in hover when the pilot is required to perform secondary tasks. Addition of a second crew member improves pilot ratings.

  16. NMR experiments for the measurement of proton-proton and carbon-carbon residual dipolar couplings in uniformly labelled oligosaccharides

    Energy Technology Data Exchange (ETDEWEB)

    Martin-Pastor, Manuel [Universidad de Santiago de Compostela, Laboratorio Integral de Estructura de Biomoleculas Jose. R. Carracido, Unidade de Resonancia Magnetica, RIAIDT (Spain)], E-mail: mmartin@usc.es; Canales-Mayordomo, Angeles; Jimenez-Barbero, Jesus [Departamento de Estructura y funcion de proteinas, Centro de Investigaciones Biologicas, CSIC (Spain)], E-mail: jjbarbero@cib.csic.es

    2003-08-15

    A 2D-HSQC-carbon selective/proton selective-constant time COSY, 2D-HSQC-(sel C, sel H)-CT COSY experiment, which is applicable to uniformly {sup 13}C isotopically enriched samples (U-{sup 13}C) of oligosaccharides or oligonucleotides is proposed for the measurement of proton-proton RDC in crowded regions of 2D-spectra. In addition, a heteronuclear constant time-COSY experiment, {sup 13}C-{sup 13}C CT-COSY, is proposed for the measurement of one bond carbon-carbon RDC in these molecules. These two methods provide an extension, to U-{sup 13}C molecules, of the original homonuclear constant time-COSY experiment proposed by Tian et al. (1999) for saccharides. The combination of a number of these RDC with NOE data may provide the method of choice to study oligosaccharide conformation in the free and receptor-bound state.

  17. An improved algorithm for MFR fragment assembly

    International Nuclear Information System (INIS)

    Kontaxis, Georg

    2012-01-01

    A method for generating protein backbone models from backbone only NMR data is presented, which is based on molecular fragment replacement (MFR). In a first step, the PDB database is mined for homologous peptide fragments using experimental backbone-only data i.e. backbone chemical shifts (CS) and residual dipolar couplings (RDC). Second, this fragment library is refined against the experimental restraints. Finally, the fragments are assembled into a protein backbone fold using a rigid body docking algorithm using the RDCs as restraints. For improved performance, backbone nuclear Overhauser effects (NOEs) may be included at that stage. Compared to previous implementations of MFR-derived structure determination protocols this model-building algorithm offers improved stability and reliability. Furthermore, relative to CS-ROSETTA based methods, it provides faster performance and straightforward implementation with the option to easily include further types of restraints and additional energy terms.

  18. Conformation of antifreeze glycoproteins as determined from conformational energy calculations and fully assigned proton NMR spectra

    International Nuclear Information System (INIS)

    Bush, C.A.; Rao, B.N.N.

    1986-01-01

    The 1 H NMR spectra of AFGP's ranging in molecular weight from 2600 to 30,000 Daltons isolated from several different species of polar fish have been measured. The spectrum of AFGP 1-4 from Pagothenia borchgrevinki with an average of 30 repeating subunits has a single resonance for each proton of the glycotripeptide repeating unit, (ala-[gal-(β-1→3) galNAc-(α--O-]thr-ala)/sub n/. Its 1 H NMR spectrum including resonances of the amide protons has been completely assigned. Coupling constants and nuclear Overhauser enhancements (n.O.e.) between protons on distant residues imply conformational order. The 2600 dalton molecular weight glycopeptides (AFGP-8) have pro in place of ala at certain specific points in the sequence and AFGP-8R of Eleginus gracilis has arg in place of one thr. The resonances of pro and arg were assigned by decoupling. The resonances of the carboxy and amino terminals have distinct chemical shifts and were assigned in AFGP-8 of Boreogadus saida by titration. n.O.e. between α--protons and amide protons of the adjacent residue (sequential n.O.e.) were used in assignments of additional resonances and to assign the distinctive resonances of thr followed by pro. Conformational energy calculations on the repeating glycotripeptide subunit of AFGP show that the α--glucosidic linkage has a fixed conformation while the β--linkage is less rigid. A conformational model for AFGP 1-4, which is based on the calculations has the peptide in an extended left-handed helix with three residues per turn similar to polyproline II. The model is consistent with CD data, amide proton coupling constants, temperature dependence of amide proton chemical shifts

  19. Efficient Stereospecific Hβ2/3 NMR Assignment Strategy for Mid-Size Proteins

    Directory of Open Access Journals (Sweden)

    Alexandra Born

    2018-06-01

    Full Text Available We present a strategy for stereospecific NMR assignment of Hβ2 and Hβ3 protons in mid-size proteins (~150 residues. For such proteins, resonance overlap in standard experiments is severe, thereby preventing unambiguous assignment of a large fraction of β-methylenes. To alleviate this limitation, assignment experiments may be run in high static fields, where higher decoupling power is required. Three-bond Hα–Hβ J-couplings (3JHα–Hβ are critical for stereospecific assignments of β-methylene protons, and for determining rotameric χ1 states. Therefore, we modified a pulse sequence designed to measure accurate 3JHα–Hβ couplings such that probe heating was reduced, while the decoupling performance was improved. To further increase the resolution, we applied non-uniform sampling (NUS schemes in the indirect 1H and 13C dimensions. The approach was applied to two medium-sized proteins, odorant binding protein 22 (OBP22; 14.4 kDa and Pin1 (18.2 kDa, at 900 MHz polarizing fields. The coupling values obtained from NUS and linear sampling were extremely well correlated. However, NUS decreased the overlap of Hβ2/3 protons, thus supplying a higher yield of extracted 3JHα-Hβ coupling values when compared with linear sampling. A similar effect could be achieved with linear prediction applied to the linearly sampled data prior to the Fourier transformation. Finally, we used 3JHα–Hβ couplings from Pin1 in combination with either conventional or exact nuclear Overhauser enhancement (eNOE restraints to determine the stereospecific assignments of β-methylene protons. The use of eNOEs further increased the fraction of unambiguously assigned resonances when compared with procedures using conventional NOEs.

  20. Influence of bio-solution pretreatment on the structure, reactivity and torrefaction of bamboo

    International Nuclear Information System (INIS)

    Chen, Wei-Hsin; Chu, Yen-Shih; Lee, Wen-Jhy

    2017-01-01

    Highlights: • A bio-solution of natural organic enzyme-7F (NOE-7F) is used to pretreat bamboo. • The bio-solution removes hemicellulose in powdered bamboo significantly. • Bamboo powder pretreated by bio-solution may be feasible for producing bioethanol. • Penetration of bio-solution into block bamboo controls the pretreatment mechanism. • The homogeneity of bamboo is improved by the bio-solution pretreatment. - Abstract: A bio-solution of natural organic enzyme-7F (NOE-7F) is used to pretreat bamboo, with emphasis on the influence the pretreatment upon the structure, reactivity, and torrefaction of the biomass. Two different operating modes accompanied by five different soaking durations are considered. In Mode 1 the bamboo is ground followed by pretreated by the bio-solution, and an inverse procedure is used in Mode 2. The results indicate that, with the operation of Mode 1, NOE-7F removes hemicellulose in the bamboo significantly, thereby improving the homogeneity of the biomass. This pretreated bamboo may be feasible for enzymatic hydrolysis to produce bioethanol. The penetration of the bio-solution into block bamboo becomes the controlling mechanism under Mode 2 operation, and therefore relatively less hemicellulose is consumed from Mode 2. The ignition and burnout temperatures of the pretreated bamboo are higher than those of the raw bamboo, revealing the lower reactivity and higher storage safety of the former. The atomic H/C and O/C ratios as well as the calorific value of the bamboo are insensitive to the pretreatments, whereas the crystalline structure of cellulose is affected by the bio-solution to a certain extent, regardless of Mode 1 or Mode 2 operation. This suggests that torrefaction is required if the pretreated bamboo is employed as a fuel. The pretreated bamboo with Mode 2 is more suitable for torrefaction because of higher torrefaction severity.

  1. NATURAL CYCLOPENTANOID CYANOHYDRIN GLYCOSIDES .13. STRUCTURE DETERMINATION OF NATURAL EPOXYCYCLOPENTANES BY X-RAY CRYSTALLOGRAPHY AND NMR-SPECTROSCOPY

    DEFF Research Database (Denmark)

    Olafsdottir, E. S.; Sorensen, A. M.; Cornett, Claus

    1991-01-01

    nonannellated cyclopentane derivatives. The new glucosides were shown, by NMR spectroscopy (including NOE measurements), X-ray crystallography, and enzymatic hydrolysis to the corresponding cyanohydrins, to be (1R,2R,3R,4R)- and (1S,2S,3S,4S)-1-(beta-D-glucopyranosyloxy)-2,3-epoxy-4-hydroxycyclopenta ne-1...

  2. Gene therapy of cancer by vaccines carrying inserted immunostimulatory genes

    Czech Academy of Sciences Publication Activity Database

    Bubeník, Jan

    2007-01-01

    Roč. 53, č. 3 (2007), s. 71-73 ISSN 0015-5500 Grant - others:EU-FP6 NoE Clinigene(XE) 018933; Liga proti rakovině, Praha(CZ) XX Institutional research plan: CEZ:AV0Z50520514 Keywords : gene therapy * immunostimulatory genes * vaccine Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.596, year: 2007

  3. Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Kuszewski, John J.; Thottungal, Robin Augustine [National Institutes of Health, Imaging Sciences Laboratory, Center for Information Technology (United States); Clore, G. Marius [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: mariusc@mail.nih.gov; Schwieters, Charles D. [National Institutes of Health, Imaging Sciences Laboratory, Center for Information Technology (United States)], E-mail: Charles.Schwieters@nih.gov

    2008-08-15

    We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258-6273). The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined.

  4. Complete sequence-specific 1H NMR assignments for human insulin

    International Nuclear Information System (INIS)

    Kline, A.D.; Justice, R.M. Jr.

    1990-01-01

    Solvent conditions where human insulin could be studied by high-resolution NMR were determined. Both low pH and addition of acetonitrile were required to overcome the protein's self-association and to obtain useful spectra. Two hundred eighty-six 1 H resonances were located and assigned to specific sites on the protein by using two-dimensional NMR methods. The presence and position of numerous d NN sequential NOE's indicate that the insulin conformation seen in crystallographic studies is largely retained under these solution conditions. Slowly exchanging protons were observed for seven backbone amide protons and were assigned to positions A15 and A16 and to positions B15-B19. These amides all occur within helical regions of the protein

  5. Listening to the Deep-Ocean Environment (LIDO): an ESONET Initiative for the Real-Time Monitoring of Geohazards and Marine Ambient Noise

    Science.gov (United States)

    André, Michel; Favali, Paolo; Piatteli, Paolo; Miranda, Jorge; Waldmann, Christoph; Esonet Lido Demonstration Mission Team

    2010-05-01

    Understanding the link between natural and anthropogenic processes is essential for predicting the magnitude and impact of future changes of the natural balance of the oceans. Deep-sea observatories have the potential to play a key role in the assessment and monitoring of these changes. ESONET is a European Network of Excellence of deep-sea observatories that includes 55 partners belonging to 14 countries. ESONET NoE is providing data on key parameters from the subsurface down to the seafloor at representative locations that transmit them to shore. The strategies of deployment, data sampling, technological development, standardisation and data management are being integrated with projects dealing with the spatial and near surface time series. LIDO (Listening to the Deep Ocean environment) is one of these projects and proposes to establish a first nucleus of a regional network of multidisciplinary seafloor observatories contributing to the coordination of high quality research in the ESONET NoE by allowing the real-time long-term monitoring of Geohazards and Marine Ambient Noise in the Mediterranean Sea and the adjacent Atlantic waters. Specific activities address the long-term monitoring of earthquakes and tsunamis and the characterisation of ambient noise, marine mammal sounds and anthropogenic sources. The objective of this demonstration mission will be achieved through the extension of the present capabilities of the observatories working in the ESONET key-sites of Eastern Sicily (NEMO-SN1) and of the Gulf of Cadiz (GEOSTAR configured for NEAREST pilot experiment) by installing new sensor equipments related to Bioacoustics and Geohazards, as well as by implementing international standard methods in data acquisition and management.

  6. The Glaser–Hay reaction

    DEFF Research Database (Denmark)

    Vilhelmsen, Mie Højer; Jensen, Jonas; Tortzen, Christian

    2013-01-01

    The oxidative Glaser–Hay coupling of two terminal alkynes to furnish a butadiyne is a key reaction for acetylenic scaffolding. Although the reaction is performed under rather simple conditions [CuCl/TMEDA/O2 (air)], the mechanism is still under debate. Herein we present detailed studies...... on the scope of this reaction by using both 13C NMR and UV/Vis spectroscopic methods. The former method was used to study the kinetics of the coupling of aryl-substituted alkynes as the aryl carbon resonances of the reactants and products have similar NOEs and relaxation times. The reaction was found...... to be zero-order with respect to the terminal alkyne reactant under standard preparative conditions. Moreover, as the reaction proceeded, a clear change to slower reaction kinetics was observed, but it was still apparently zero-order. The onset of this change was found to depend on the catalyst loading...

  7. Invasive insects differ from non-invasive in their thermal requirements

    Czech Academy of Sciences Publication Activity Database

    Jarošík, Vojtěch; Kenis, M.; Honěk, A.; Skuhrovec, J.; Pyšek, Petr

    2015-01-01

    Roč. 10, č. 6 (2015), s. 1-11, no.e0131072 E-ISSN 1932-6203 Grant - others:European Comission(XE) FP7-212459; AV ČR(CZ) AP1002 Program:FP7; Akademická prémie - Praemium Academiae Institutional support: RVO:67985939 Keywords : insects * thermal development * invasiveness Subject RIV: EH - Ecology, Behaviour Impact factor: 3.057, year: 2015

  8. Noahs Ark of the seeds; El Arca de Noe de las semillas

    Energy Technology Data Exchange (ETDEWEB)

    Tristan, R. M.

    2015-07-01

    The so-called 'vault of the end of the world', located in the archipelago Arctic Svalbard, brings together more than 860,000 samples seeds from around the world. The purpose of your existence -like the of thousands of other banks of its kind in all the planet - is to preserve the genetic diversity of crops, most of them are now disappearing. An international treaty approved by the United Nations, and in force since 2004, allowed the construction of this 'Sanctuary' where more than one hundred countries maintain their own banks of seeds, freezing them to 18 degrees below zero to lower its biological activity. (Author)

  9. Assignment strategies in homonuclear three-dimensional 1H NMR spectra of proteins

    International Nuclear Information System (INIS)

    Vuister, G.W.; Boelens, R.; Padilla, A.; Kleywegt, G.J.; Kaptein, R.

    1990-01-01

    The increase in dimensionality of three-dimensional (3D) NMR greatly enhances the spectral resolution in comparison to 2D NMR. It alleviates the problem of resonance overlap and may extend the range of molecules amenable to structure determination by high-resolution NMR spectroscopy. Here, the authors present strategies for the assignment of protein resonances from homonuclear nonselective 3D NOE-HOHAHA spectra. A notation for connectivities between protons, corresponding to cross peaks in 3D spectra, is introduced. They show how spin systems can be identified by tracing cross-peak patterns in cross sections perpendicular to the three frequency axes. The observable 3D sequential connectivities in proteins are tabulated, and estimates for the relative intensities of the corresponding cross peaks are given for α-helical and β-sheet conformations. Intensities of the cross peaks in the 3D spectrum of pike III paravalbumin follow the predictions. The sequential-assignment procedure is illustrated for loop regions, extended and α-helical conformations for the residues Ala 54-Leu 63 of paravalbumin. NOEs that were not previously identified in 2D spectra of paravalbumin due to overlap are found

  10. Effect of metallurgical factors on the bulk magnetic properties of non-oriented electrical steels

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Pampa, E-mail: pampaghosh@gmail.com [Department of Mining and Materials Engineering, McGill University, 3610 University Street, Montreal, Que., Canada H3A 0C5 (Canada); Chromik, Richard R., E-mail: richard.chromik@mcgill.ca [Department of Mining and Materials Engineering, McGill University, 3610 University Street, Montreal, Que., Canada H3A 0C5 (Canada); Knight, Andrew M. [Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alta., Canada T6G 2V4 (Canada); Wakade, Shekhar G. [GM Powertrain, General Motors Company, 823 Joslyn Avenue, Building B, 4AJ35, Pontiac, MI 48340-2920 (United States)

    2014-04-01

    Non-oriented electrical steel (NOES) is one of the most common material used in electrical motors. Core loss and permeability are the most important properties that the motor manufacturers look for. Both these properties are structure sensitive and depend on several metallurgical factors; such as chemistry, grain size, crystallographic texture, cleanliness and stress states in non-oriented electrical steels. It has been observed in this course of the study that the grain size and Si content of NOES are the primary controlling factors to core loss, especially at higher frequencies. On the contrary, crystallographic texture plays an important role at lower frequencies. At higher frequency, core loss increases with increasing grain size and decreasing Si content of the steels. Small difference in grain size (∼50 μm) at lower frequency range has little influence on the magnetic properties but has significant adverse effect as frequency reaches high enough. - Highlights: • Magnetic properties of a set of electrical steels were measured. • Crystallographic texture, chemistry and grain size were studied for their effects on core loss and permeability. • Structure–magnetic property relationships were identified for the electrical steels.

  11. Review of Flight Training Technology

    Science.gov (United States)

    1976-07-01

    the cockpit. They might be used to train pilots in procedures to cope with NOE-altitude emergencies; howeve-r, a combination of cinematic simulation...airplanes. Although cockpit motion adds realism , thereby i-nproving pilot performanc, in the simulater Fedderqon, Vil; Guercio and Wall, i7?. Ince...operations. Light aircraft, part-task trainers, motion pictures and video tares, cinematic simulators, and digital teaching machines are among the

  12. Assessment of the Genotoxicity of olive mill waste water (OMWW) with the Vicia faba Micronucleus test

    International Nuclear Information System (INIS)

    El Hajjouji, H.; Pinelli, E.; Revel, J. C.; Hafidi, M.

    2009-01-01

    Olive mill waste water (OMW) can cause serious environmental hazards in olive producing countries, especially around the Mediterranean basin. In Morocco, olive mills are noe of the foremost polluters: the volume of OMW produced annually is estimated at 250 000 m 3 during the season of production. the present study concerns the genotoxicity of OMW generated in mills producing olive oil in Morocco. (Author)

  13. Reinvestigación de la formación de alquinilciclopropanocarbonitrilos a partir de complejos carbeno de Fischer: Diastereoselectividad y Mecanismo

    OpenAIRE

    Solis Moreno, Guillermo

    2015-01-01

    La reinvestigación de la síntesis de los alquinilciclopropanocarbonitrilos ha permitido corregir la configuración asignada al diastereoisómero mayoritario de la reacción, en la publicación original a través de experimentos de RMN de NOE y NOESY. Adicionalmente, aparece detallado el mecanismo de la reacción estudiado a través de calculos computacionales.

  14. O6-ethylguanine carcinogenic lesions in DNA: An NMR study of O6etG·C pairing in dodecanucleotide duplexes

    International Nuclear Information System (INIS)

    Kalnik, M.W.; Li, B.F.L.; Swann, P.F.; Patel, D.J.

    1989-01-01

    The pairing of O 6 etG with C located four base pairs in from either end of the self-complementary d(C1-G2-C3-O 6 etG4-A5-G6-C7-T8-C9-G10-C11-G12) duplex (designated O 6 etG·C 12-mer) has been investigated from an analysis of proton and phosphorus two-dimensional NMR experiments. The structural consequences of increasing the alkyl group size were elucidated from a comparative study of the pairing of O 6 meG4 with C9 in a related sequence (designated O 6 meG·C 12-mer). The NMR parameters for both O 6 alkG-containing dodecanucleotides are also compared with those of the control sequence containing G4·C9 base pairs (designated G·C 12-mer). The NOE cross-peaks detected in the two-dimensional NOESY spectra of the O 6 alkG·C 12-mer duplexes in H 2 O solution establish that the O 6 etG4/O 6 meG4 and C9 bases at the lesion site stack into the helix between the flanking C3·G10 and A5·T8 Watson-Crick base pairs. The observed NOEs between the amino protons of C9 and the CH 3 protons of O 6 alkG4 establish a syn orientation of the O 6 -alkyl group with respect to the N 1 of alkylated guanine. A wobble alignment of the O 6 alkG4·C9 base pair stabilized by two hydrogen bonds, one between the amino group of C9 and N 1 of O 6 alkG and the other between the amino group of O 6 alkG and N 3 of C9, is tentatively proposed on the basis of the NOEs between the amino protons of C9 at the lesion site and the imino protons of flanking Watson-Crick base pairs

  15. NMR studies of echinomycin bisintercalation complexes with d(A1-C2-G3-T4) and d(T1-C2-G3-A4) duplexes in aqueous solution: sequence-dependent formation of Hoogsteen A1 x T4 and Watson-Crick T1 x A4 base pairs flanking the bisintercalation site

    International Nuclear Information System (INIS)

    Gao, X.; Patel, D.J.

    1988-01-01

    The authors report on two-dimensional proton NMR studies of echinomycin complexes with the self-complementary d(A1-C2-G3-Tr) and d(T1-C2-G3-A4) duplexes in aqueous solution. The exchangeable and nonexchangeable antibiotic and nucleic acid protons in the 1 echinomycin per tetranucleotide duplex complexes have been assigned from analyses of scalar coupling and distance connectivities in two-dimensional data sets records in H 2 O and D 2 O solution. An analysis of the intermolecular NOE patterns for both complexes combined with large upfield imino proton and large downfield phosphorus complexation chemical shift changes demonstrates that the two quinoxaline chromophores of echinomycin bisintercalate into the minor groove surrounding the dC-dG step of each tetranucleotide duplex. Further, the quinoxaline rings selectively stack between A1 and C2 bases in the d(ACGT) complex and between T1 and C2 bases in the d(TCGA) complex. The intermolecular NOE patterns and the base and sugar proton chemical shifts for residues C2 and G3 are virtually identical for the d(ACGT) and d(TCGA) complexes. A large set of intermolecular contacts established from nuclear Overhauser effects (NOEs) between antibiotic and nucleic acid protons in the echinomycin-tetranucleotide complexes in solution are consistent with corresponding contacts reported for echinomycin-oligonucleotide complexes in the crystalline state. The authors demonstrate that the G x G base pairs adopt Watson-Crick pairing in both d(ACGT) and d(TCGA) complexes in solution. By contrast, the A1 x T4 base pairs adopt Hoogsteen pairing for the echinomycin-d(A1-C2-G3-Tr) complex while the T1 x A4 base pairs adopt Watson-Crick pairing for the echinomycin-d(T1-C2-G3-A4) complex in aqueous solution. These results emphasize the role of sequence in discriminating between Watson-Crick and Hoogsteen pairs at base pairs flanking the echinomycin bisintercalation site in solution

  16. Acid epimerization of 20-keto pregnane glycosides is determined by 2D-NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, Victor P., E-mail: vpergarw@gobiernodecanarias.org [Instituto de Productos Naturales de Canarias, Departamento de Quimica de Productos Naturales y Biotecnologia (Spain)

    2011-05-15

    Carbohydrates influence many essential biological events such as apoptosis, differentiation, tumor metastasis, cancer, neurobiology, immunology, development, host-pathogen interactions, diabetes, signal transduction, protein folding, and many other contexts. We now report on the structure determination of pregnane glycosides isolated from the aerial parts of Ceropegia fusca Bolle (Asclepiadaceae). The observation of cicatrizant, vulnerary and cytostatic activities in some humans and animals of Ceropegia fusca Bolle, a species endemic to the Canary Islands, encouraged us to begin a pharmacological study to determine their exact therapeutic properties. High resolution {sup 1}H-NMR spectra of pregnane glycosides very often display well-resolved signals that can be used as starting points in several selective NMR experiments to study scalar (J coupling), and dipolar (NOE) interactions. ROESY is especially suited for molecules such that {omega}{tau}{sub c} {approx} 1, where {tau}{sub c} are the motional correlation times and {omega} is the angular frequency. In these cases the NOE is nearly zero, while the rotating-frame Overhauser effect spectroscopy (ROESY) is always positive and increases monotonically for increasing values of {tau}{sub c}. The ROESY shows dipolar interactions cross peaks even in medium-sized molecules which are helpful in unambiguous assignment of all the interglycosidic linkages. Selective excitation was carried out using a double pulsed-field gradient spin-echo sequence (DPFGSE) in which 180 Degree-Sign Gaussian pulses are sandwiched between sine shaped z-gradients. Scalar interactions were studied by homonuclear DPFGSE-COSY and DPFGSE-TOCSY experiments, while DPFGSE-ROESY was used to monitor the spatial environment of the selectively excited proton. Dipolar interactions between nuclei close in space can be detected by the 1D GROESY experiment, which is a one-dimensional counterpart of the 2D ROESY method. The C-12 and C-17 configurations were

  17. Determination of the populations and structures of multiple conformers in an ensemble from NMR data: Multiple-copy refinement of nucleic acid structures using floating weights

    International Nuclear Information System (INIS)

    Goerler, Adrian; Ulyanov, Nikolai B.; James, Thomas L.

    2000-01-01

    A new algorithm is presented for determination of structural conformers and their populations based on NMR data. Restrained Metropolis Monte Carlo simulations or restrained energy minimizations are performed for several copies of a molecule simultaneously. The calculations are restrained with dipolar relaxation rates derived from measured NOE intensities via complete relaxation matrix analysis. The novel feature of the algorithm is that the weights of individual conformers are determined in every refinement step, by the quadratic programming algorithm, in such a way that the restraint energy is minimized. Its design ensures that the calculated populations of the individual conformers are based only on experimental restraints. Presence of internally inconsistent restraints is the driving force for determination of distinct multiple conformers. The method is applied to various simulated test systems. Conformational calculations on nucleic acids are carried out using generalized helical parameters with the program DNAminiCarlo. From different mixtures of A- and B-DNA, minor fractions as low as 10% could be determined with restrained energy minimization. For B-DNA with three local conformers (C2'-endo, O4'-exo, C3'-endo), the minor O4'-exo conformer could not be reliably determined using NOE data typically measured for DNA. The other two conformers, C2'-endo and C3'-endo, could be reproduced by Metropolis Monte Carlo simulated annealing. The behavior of the algorithm in various situations is analyzed, and a number of refinement protocols are discussed. Prior to application of this algorithm to each experimental system, it is suggested that the presence of internal inconsistencies in experimental data be ascertained. In addition, because the performance of the algorithm depends on the type of conformers involved and experimental data available, it is advisable to carry out test calculations with simulated data modeling each experimental system studied

  18. Getting the Right Traits: Reproductive and Dispersal Characteristics Predict the Invasiveness of Herbaceous Plant Species

    Czech Academy of Sciences Publication Activity Database

    Moravcová, Lenka; Pyšek, Petr; Jarošík, Vojtěch; Pergl, Jan

    2015-01-01

    Roč. 10, č. 4 (2015), s. 1-16,no.e0123634 E-ISSN 1932-6203 R&D Projects: GA ČR GB14-36079G; GA ČR GA206/05/0323 Grant - others:AV ČR(CZ) AP1002 Program:Akademická prémie - Praemium Academiae Institutional support: RVO:67985939 Keywords : species traits * prediction * invasiveness Subject RIV: EF - Botanics Impact factor: 3.057, year: 2015

  19. NK1.1+ cells are important for the development of protective immunity against MHC I-deficient, HPV16-associated tumours

    Czech Academy of Sciences Publication Activity Database

    Indrová, Marie; Šímová, Jana; Bieblová, Jana; Bubeník, Jan; Reiniš, Milan

    2011-01-01

    Roč. 25, č. 1 (2011), s. 281-288 ISSN 1021-335X R&D Projects: GA AV ČR IAA500520807 Grant - others:EU-FP6-NOE(XE) Project 018933 Institutional research plan: CEZ:AV0Z50520514 Keywords : MHC class I-deficient tumours * CD8+, CD4+, NK1.1+cell subpopulations * interferon gamma Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.835, year: 2011

  20. What is Informal Learning and What are its Antecedents? An Integrative and Meta-Analytic Review

    Science.gov (United States)

    2014-07-01

    Cerasoli, C. P., Nicklin, J. M., & Ford, M. T. (2014). Intrinsic motivation and extrinsic incentives jointly predict performance: A 40-year meta... motivation : A meta-analytic path analysis of 20 years of research. Journal of Applied Psychology , 85, 678-707. Cooper, H. (2003). Editorial...error management training: A meta-analysis. Journal of Applied Psychology , 93, 59-69. Klein, H. J., Noe, R. A., & Wang, C. W. (2006). Motivation to

  1. Genetically modified tumour vaccines producing IL-12 augment chemotherapy of HPV16-associated tumours with gemcitabine

    Czech Academy of Sciences Publication Activity Database

    Mikyšková, Romana; Indrová, Marie; Šímová, Jana; Bieblová, Jana; Bubeník, Jan; Reiniš, Milan

    2011-01-01

    Roč. 25, č. 6 (2011), s. 1683-1689 ISSN 1021-335X R&D Projects: GA ČR GA301/09/1024; GA ČR GA301/07/1410 Grant - others:EK(XE) EU-FP6-NOE018933 Institutional research plan: CEZ:AV0Z50520514 Keywords : gemcitabine * human papilloma virus * interleukin 12 * lung metastases * cellular vaccines * immunotherapy Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.835, year: 2011

  2. A Distributed User Information System

    Science.gov (United States)

    1990-03-01

    NOE08 Department of Computer Science NOVO 8 1990 University of Maryland S College Park, MD 20742 D Abstract Current user information database technology ...Transactions on Computer Systems, May 1988. [So189] K. Sollins. A plan for internet directory services. Technical report, DDN Network Information Center...2424 A Distributed User Information System DTiC Steven D. Miller, Scott Carson, and Leo Mark DELECTE Institute for Advanced Computer Studies and

  3. Isotope-edited proton NMR study on the structure of a pepsin/inhibitor complex

    International Nuclear Information System (INIS)

    Fesik, S.W.; Luly, J.R.; Erickson, J.W.; Abad-Zapatero, C.

    1988-01-01

    A general approach is illustrated for providing detailed structural information on large enzyme/inhibitor complexes using NMR spectroscopy. The method involves the use of isotopically labeled ligands to simplify two-dimensional NOE spectra of large molecular complexes by isotope-editing techniques. With this approach, the backbone and side-chain conformations (at the P 2 and P 3 sites) of a tightly bound inhibitor of porcine pepsin have bene determined. In addition, structural information on the active site of pepsin has been obtained. Due to the sequence homology between porcine pepsin and human renin, this structural information may prove useful for modeling renin/inhibitor complexes with the ultimate goal of designing more effective renin inhibitors. Moreover, this general approach can be applied to study other biological systems of interest such as other enzyme/inhibitor complexes, ligands bound to soluble receptors, and enzyme/substrate interactions

  4. Handgrip and general muscular strength and endurance during prolonged bedrest with isometric and isotonic leg exercise training

    Science.gov (United States)

    Greenleaf, J. E.; Starr, J. C.; Van Beaumont, W.; Convertino, V. A.

    1983-01-01

    Measurements of maximal grip strength and endurance at 40 percent max strength were obtained for 7 men 19-21 years of age, 1-2 days before and on the first recovery day during three 2-week bedrest (BR) periods, each separated by a 3-week ambulatory recovery period. The subjects performed isometric exercise (IME) for 1 hr/day, isotonic exercise (ITE) for 1 hr/day, and no exercise (NOE) in the three BR periods. It was found that the mean maximal grip strength was unchanged after all three BR periods. Mean grip endurance was found to be unchanged after IME and ITE training, but was significantly reduced after NOE. These results indicate that IME and ITE training during BR do not increase or decrease maximal grip strength, alghough they prevent loss of grip endurance, while the maximal strength of all other major muscle groups decreases in proportion to the length of BR to 70 days. The maximal strength reduction of the large muscle groups was found to be about twice that of the small muscle groups during BR. In addition, it is shown that changes in maximal strength after spaceflight, BR, or water immersion deconditioning cannot be predicted from changes in submaximal or maximal oxygen uptake values.

  5. Neutron flux monitoring with pre-startup channels in FBTR [Paper No.:E6

    International Nuclear Information System (INIS)

    Nagaraj, C.P.; Ramakrishnan, R.; Subha Rao, R.; Pillai, C.P.; Muralikrishan, G.; Raghavan, K.

    1993-01-01

    The pre-start up instrumentation system using boron lined proportional counters has been well designed and the counters have been rigorously tested. This system in conjunction with the regular start-up channels (with more than 3 decades overlap) covers the start up measurement range adequately and provides necessary indications, interlocks and trips on low count rate, high count rate and doubling time to ensure safety. The pre-startup channels have been operational. The reactor trip on LOG NO due to count rate on start-up channels less than 3 cps is automatically inhibited with the higher count rate obtained on the pre-startup channels. With this and log CRM readings from PSU well on scale has facilitated smooth and safe reactor start ups even with low shutdown count rates. (author). 5 figs

  6. Mastimõõtmised võimaldavad hinnata tuuleenergia ressurssi / Marko Kaasik, Steffen M. Noe

    Index Scriptorium Estoniae

    Kaasik, Marko, 1966-

    2015-01-01

    Täpseim viis tuuleenergia ressursi hindamiseks on otsemõõtmine suurte tuulikute kõrgusel. Alates 2014. a viib Eesti Maaülikool mõõtmisi läbi ultrahelianemomeetritega Järvseljal spetsiaalselt ehitatud mõõtemastis ja Tartu Ülikool Valgjärve telemastis

  7. A new Labdane Diterpene and Other Constituents from Marrubium deserti Noe ex coss.

    Directory of Open Access Journals (Sweden)

    Hocine Dendougui

    2011-01-01

    Full Text Available The phytochemical study of the chloroform soluble part of the hydroalcoholic extract of Marrubium deserti allowed us to describe a new labdane diterpene, 6-dehydroxy-19-acetyl-marrubenol (3 beside three other diterpenes : 19-acetyl-marrubenol (6 , 6-acetyl-marrubenol (7 and 16-epoxy-9-hydroxy-labda-13(16, 14- diene (1. This latter derivative is described for the first time as natural compound. Phytol (2, and three sterols: b -sitosterol (4, stigmasterol (5 and b -sitosterol 3-O-glucoside (8 were also isolated from this species. Structure elucidation of the isolated compounds was accomplished by means of spectroscopic techniques, especially NMR spectroscopy and mass spectrometry.

  8. Complete {sup 1}H and {sup 13}C NMR structural assignments for a group of four goyazensolide-type furanoheliangolides

    Energy Technology Data Exchange (ETDEWEB)

    Soares, Ana Carolina Ferreira; Silva, Aline Nazare; Matos, Priscilla Mendonca; Silva, Eder Henrique da; Heleno, Vladimir Constantino Gomes [Universidade de Franca, Franca, SP (Brazil). Nucleo de Pesquisas em Ciencias Exatas e Tecnologicas; Lopes, Norberto Peporine; Lopes, Joao Luis Callegari [Universidade de Sao Paulo (FCFRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Ciencias Farmaceuticas de Ribeirao Preto. Dept. de Quimica e Fisica; Sass, Daiane Cristina, E-mail: vheleno_05@yahoo.com.br [Universidade de Sao Paulo (FFCLRP/USP), Ribeirao Preto, SP (Brazil). Fac. de Filosofia, Ciencias e Letras de Ribeirao Preto. Dept. de Quimica

    2012-07-01

    Four goyazensolide-type sesquiterpene lactones - lychnofolide, centratherin, goyazensolide and goyazensolide acetate - were thoroughly studied by NMR experimental techniques. {sup 1}H NMR, {sup 13}C NMR {l_brace}{sup 1}H{r_brace}, COSY, HMQC, HMBC, J-res. and NOE experiments were performed to provide the needed structural information. Complete and unequivocal assignment, including the determination of all multiplicities, was obtained for each structure and the data collections are presented in tables (author)

  9. Informe científico de investigador: Agamennoni, Osvaldo Enrique (2014-2015)

    OpenAIRE

    Agamennoni, Osvaldo Enrique

    2015-01-01

    Entre los principales resultados alcanzados en el período comprendido por el siguiente informe, caben destacarse los siguientes: -Culminación de las actividades conducentes a la implementación en un ASIC(Application Specific Integrated Circuit) de una técnica de identificación no lineal medianteuna estructura de Error de Salida No lineal (NOE) que posibilita un crecimiento gradualde la cantidad de parámetros sin perder la aproximación...

  10. Reversible and formaldehyde-mediated covalent binding of a bis-amino mitoxantrone analogue to DNA.

    Science.gov (United States)

    Konda, Shyam K; Kelso, Celine; Pumuye, Paul P; Medan, Jelena; Sleebs, Brad E; Cutts, Suzanne M; Phillips, Don R; Collins, J Grant

    2016-05-18

    The ability of a bis-amino mitoxantrone anticancer drug (named WEHI-150) to form covalent adducts with DNA, after activation by formaldehyde, has been studied by electrospray ionisation mass spectrometry and HPLC. Mass spectrometry results showed that WEHI-150 could form covalent adducts with d(ACGCGCGT)2 that contained one, two or three covalent links to the octanucleotide, whereas the control drugs (daunorubicin and the anthracenediones mitoxantrone and pixantrone) only formed adducts with one covalent link to the octanucleotide. HPLC was used to examine the extent of covalent bond formation of WEHI-150 with d(CGCGCG)2 and d(CG(5Me)CGCG)2. Incubation of WEHI-150 with d(CG(5Me)CGCG)2 in the presence of formaldehyde resulted in the formation of significantly greater amounts of covalent adducts than was observed with d(CGCGCG)2. In order to understand the observed increase of covalent adducts with d(CG(5Me)CGCG)2, an NMR study of the reversible interaction of WEHI-150 at both CpG and (5Me)CpG sites was undertaken. Intermolecular NOEs were observed in the NOESY spectra of d(ACGGCCGT)2 with added WEHI-150 that indicated that the drug selectively intercalated at the CpG sites and from the major groove. In particular, NOEs were observed from the WEHI-150 H2,3 protons to the H1' protons of G3 and G7 and from the H6,7 protons to the H5 protons of C2 and C6. By contrast, intermolecular NOEs were observed between the WEHI-150 H2,3 protons to the H2'' proton of the (5Me)C3 in d(CG(5Me)CGCG)2, and between the drug aliphatic protons and the H1' proton of G4. This demonstrated that WEHI-150 preferentially intercalates at (5Me)CpG sites, compared to CpG sequences, and predominantly via the minor groove at the (5Me)CpG site. The results of this study demonstrate that WEHI-150 is likely to form interstrand DNA cross-links, upon activation by formaldehyde, and consequently exhibit greater cytotoxicity than other current anthracenedione drugs.

  11. Summaries of Research 1987

    Science.gov (United States)

    1987-01-01

    STRUCTURE OF THE GENE ENCODING THE CIRCUMSPOROZOITE PROTEIN OF PLASWODIUm YOELIJ. A RODENT MCDFL FOP EIAMINING ANTIMALARIAL SPOBOZOITE VACCINES. JOURNAL OF...BICLOGICAL CHEMISTRY 1987 MAR 5;262(7):2937-40 INFECTIOUS DISEASES 3M162770A870.AF.312-1 (DA301614) REPORT NO.E ANTIGENS, SURFACE PLAS!CDIU? AD A188...SURFACE CLONING, MOLECULAR PLASMCDIUM dERGHEI AD A185 330 NI!PI 87-C036 ROTd ?L CHUANG DM MULTIPLE EECHANIS!15 CF SEROTONERGIC SIGNAL TRANSDUCTION. LIFE

  12. Making and maintaining frames : a study of metacommunication in laiv play

    OpenAIRE

    Brenne, Geir Tore

    2005-01-01

    Dersom noen av dem som er referert eller avbildet i teksten har noe imot det av vilken som helst grunn, ta kontakt med forfatteren på og passasjen vil bli fjernet eller sladdet. ************* Summary Laiv is a leisure activity that is organised and practiced by a network of involved people in Norway. They usually have a middle class background, and are between 16-40 years of age. From time to time, groups of players organise unique plays that the...

  13. PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination

    OpenAIRE

    Lee, Woonghee; Stark, Jaime L.; Markley, John L.

    2014-01-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727–1728. doi:10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nucle...

  14. Central skull base osteomyelitis as a complication of necrotizing otitis externa: Imaging findings, complications, and challenges of diagnosis

    International Nuclear Information System (INIS)

    Adams, A.; Offiah, C.

    2012-01-01

    Central skull base osteomyelitis is a rare, life-threatening complication of necrotizing or “malignant” otitis externa (NOE), which results in destruction of the skull base. The imaging appearances can be misinterpreted as malignancy but consideration of this diagnosis, both radiologically and clinically, is imperative to avoid the need for biopsy. The aim of this review is to highlight the pertinent imaging findings on computed tomography and magnetic resonance imaging as well as the potential complications of this condition.

  15. Griffon Helicopter Neck Strain Project: Part 1: Mission Function Task Analysis and Physical Demands Analysis Report. Part 2: Physical Demands Analysis Library

    Science.gov (United States)

    2014-10-01

    characterized by the sudden onset of high acceleration forces, impact , extreme neck angles or a combination thereof. Numerous investigations on helmet and...Regular IFR 2-Full Check FE Take-off to Hover Regular Transit Contour 2-Full Check NFP Pilot Post-Take off Checks Transit NOE SAR Check Taxi to Hold...Area Transit with Slung Load Plan ISR Land at Hold Area Race Track or Circular Conduct ISR Profile Obtain IFR Clearance Loiter Figure 8 Plan

  16. CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

    International Nuclear Information System (INIS)

    Guerry, Paul; Duong, Viet Dung; Herrmann, Torsten

    2015-01-01

    UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved—including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO–ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications

  17. Advanced information processing system: The Army Fault-Tolerant Architecture detailed design overview

    Science.gov (United States)

    Harper, Richard E.; Babikyan, Carol A.; Butler, Bryan P.; Clasen, Robert J.; Harris, Chris H.; Lala, Jaynarayan H.; Masotto, Thomas K.; Nagle, Gail A.; Prizant, Mark J.; Treadwell, Steven

    1994-01-01

    The Army Avionics Research and Development Activity (AVRADA) is pursuing programs that would enable effective and efficient management of large amounts of situational data that occurs during tactical rotorcraft missions. The Computer Aided Low Altitude Night Helicopter Flight Program has identified automated Terrain Following/Terrain Avoidance, Nap of the Earth (TF/TA, NOE) operation as key enabling technology for advanced tactical rotorcraft to enhance mission survivability and mission effectiveness. The processing of critical information at low altitudes with short reaction times is life-critical and mission-critical necessitating an ultra-reliable/high throughput computing platform for dependable service for flight control, fusion of sensor data, route planning, near-field/far-field navigation, and obstacle avoidance operations. To address these needs the Army Fault Tolerant Architecture (AFTA) is being designed and developed. This computer system is based upon the Fault Tolerant Parallel Processor (FTPP) developed by Charles Stark Draper Labs (CSDL). AFTA is hard real-time, Byzantine, fault-tolerant parallel processor which is programmed in the ADA language. This document describes the results of the Detailed Design (Phase 2 and 3 of a 3-year project) of the AFTA development. This document contains detailed descriptions of the program objectives, the TF/TA NOE application requirements, architecture, hardware design, operating systems design, systems performance measurements and analytical models.

  18. Intrauterine position affects fetal weight and crown-rump length throughout gestation.

    Science.gov (United States)

    Jang, Y D; Ma, Y L; Lindemann, M D

    2014-10-01

    To investigate the effect of intrauterine positions on fetal growth throughout gestation, data from a total of 65 gilts (n = 784 fetuses) that were slaughtered at assigned days of gestation (d 43, 58, 73, 91, 101, and 108) on a project to evaluate fetal mineral deposition were used. Placenta units were removed from the uterus, and position, sex, weight, and crown-rump length (CRL) of each fetus were recorded. Fetuses were classified into 5 categories within a uterine horn for the absolute intrauterine position: the ovarian end (OE) of the uterine horn, next to the ovarian end (NOE), the middle (MD), next to the cervical end (NCE), and the cervical end (CE), and also classified for the relative fetal position with respect to the sex of adjacent fetuses. Fetuses at the OE and NOE of the uterine horn tended to be heavier (P = 0.06) and longer (P sex (fetuses surrounded by the opposite sexes) in weight or length. Male fetuses were heavier than female fetuses at d 43, 58, 73, and 108 of gestation (P position affects fetal growth more than the sex of the adjacent fetus in the uterine horn, 2) each end of the uterine horn (OE and CE) has heavier fetuses than the MD, and 3) male pigs grow faster than female pigs even before birth.

  19. Å skape et begrep om jam i utforskningen av en deleuziansk metode-ontologi

    Directory of Open Access Journals (Sweden)

    Ola Harstad

    2017-12-01

    Full Text Available Å forske med kunsten innebærer ikke bare valget av visse metoder for bruk i forskningsprosessen, men også om å ha til disposisjon spesifikke måter å tenke om metode. I denne artikkelen vil jeg synliggjøre en tenkemåte fundert i arbeidet med en skjønnlitterær lesesirkel for lærerstudenter, og min egen erfaring som improvisasjonsmusiker. Jazzens begrep om jam blir løftet frem som omdreiningspunkt for tenkemåten, som ellers har sitt teoretiske utspring i den franske filosofen Gilles Deleuze’s forestilling om bliven. Denne vitale forestillingen innebærer at verden produseres kontinuerlig, noe forskeren også bidrar til. Koblingen mellom jam, litteratur og Deleuze synliggjør dessuten en måte å tenke om metode på som understreker at det å forske med kunsten ikke bare betyr å forske på kunsten, men at kunsten på ulike måter kan virke inn på selve forskningen og slik også bidra til å affirmere verden i sin bliven. I tillegg til å tilby en måte å tenke om metode for den som skal forske med kunsten, er hensikten med artikkelen å gjøre forskeren bevisst sin egen tenkning om metode, noe som er viktig siden denne skaper mulighetsbetingelser for metodevalg og -bruk.

  20. [The and beginnings of Chilean endocrinology in the 1920s].

    Science.gov (United States)

    Sánchez Delgado, Marcelo

    2016-01-01

    Rejuvenation was a chapter of critical importance for the worldwide development of endocrinology in the 1920s. This work explores the acceptance of these techniques in Chile. Starting in the late 19th century, the Chilean Medical Journal (Revista Médica de Chile) incorporated references to experiments with endocrine gland preparations that were being conducted in Europe at the time. An appropriation of the experiments by the Austrian Eugen Steinach began in 1920, with prominent figures such as the Italian professor Juan Noe Crevani and the young Chilean student Ottmar Wilhelm. Between 1922 and 1924, Wilhelm developed a series of experiments on dogs, bulls, pigs, rats and Welfare Board patients through the so-called Steinach operation, which consisted of the sectioning of the efferent channel in one of the testicles. Professor Noe's scientific patronage policy and Wilhelm's strategy of succession in the field led the latter to hold a chair in the new School of Medicine of Universidad de Concepci6n at the age of 25. From this position, the. figure of Wilhelm was fundamental for the development of a line of endocrinological research that was able to position Universidad de Concepci6n as a scientific development centre, which was strengthened by the arrival of another disciple of Steinach in Chile, the Latvian professor Alejandro Lipschütz.

  1. European Origin of Bradyrhizobium Populations Infecting Lupins and Serradella in Soils of Western Australia and South Africa† ‡

    OpenAIRE

    Stępkowski, Tomasz; Moulin, Lionel; Krzyżańska, Agnieszka; McInnes, Alison; Law, Ian J.; Howieson, John

    2005-01-01

    We applied a multilocus phylogenetic approach to elucidate the origin of serradella and lupin Bradyrhizobium strains that persist in soils of Western Australia and South Africa. The selected strains belonged to different randomly amplified polymorphic DNA (RAPD)-PCR clusters that were distinct from RAPD clusters of applied inoculant strains. Phylogenetic analyses were performed with nodulation genes (nodA, nodZ, nolL, noeI), housekeeping genes (dnaK, recA, glnII, atpD), and 16S-23S rRNA inter...

  2. High Resolution Imaging Using Phase Retrieval. Volume 2

    Science.gov (United States)

    1991-10-01

    25. pp. 5?3-578. 195;4 tamned from random perturbations of the constraint func- 181 K. Deimling. .Vonltnear Functional Analisis , Noe% Nork Springer...to Asrh. i.e., the points tend to cluster in a region where both 6 ande (5) Stop if the stopping criterion is met; otherwise go to are large. This is...than " ... -10% and 25% are shown in Fig. 13. As the L-robustness S-. L .- .’requirement is increased, many points clustered about the 6 0

  3. An approach for high-throughput structure determination of proteins by NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Medek, Ales; Olejniczak, Edward T.; Meadows, Robert P.; Fesik, Stephen W. [Abbott Laboratories, Pharmaceutical Discovery Division (United States)

    2000-11-15

    An approach is described for rapidly determining protein structures by NMR that utilizes proteins containing {sup 13}C-methyl labeled Val, Leu, and Ile ({delta}1) and protonated Phe and Tyr in a deuterated background. Using this strategy, the key NOEs that define the hydrophobic core and overall fold of the protein are easily obtained. NMR data are acquired using cryogenic probe technology which markedly reduces the spectrometer time needed for data acquisition. The approach is demonstrated by determining the overall fold of the antiapoptotic protein, Bcl-xL, from data collected in only 4 days. Refinement of the Bcl-xL structure to a backbone rmsd of 0.95 A was accomplished with data collected in an additional 3 days. A distance analysis of 180 different proteins and structure calculations using simulated data suggests that our method will allow the global folds of a wide variety of proteins to be determined.

  4. Application of amino acid type-specific 1H- and 14N-labeling in a 2H-, 15N-labeled background to a 47 kDa homodimer: Potential for NMR structure determination of large proteins

    International Nuclear Information System (INIS)

    Kelly, Mark J.S.; Krieger, Cornelia; Ball, Linda J.; Yu Yihua; Richter, Gerald; Schmieder, Peter; Bacher, Adelbert; Oschkinat, Hartmut

    1999-01-01

    NMR investigations of larger macromolecules (>20 kDa) are severely hindered by rapid 1H and 13C transverse relaxation. Replacement of non-exchangeable protons with deuterium removes many efficient 1H-1H and 1H-13C relaxation pathways. The main disadvantage of deuteration is that many of the protons which would normally be the source of NOE-based distance restraints are removed. We report the development of a novel labeling strategy which is based on specific protonation and 14N-labeling of the residues phenylalanine, tyrosine, threonine, isoleucine and valine in a fully deuterated, 15N-labeled background. This allows the application of heteronuclear half-filters, 15N-editing and 1H-TOCSY experiments to select for particular magnetization transfer pathways. Results from investigations of a 47 kDa dimeric protein labeled in this way demonstrated that the method provides useful information for the structure determination of large proteins

  5. Structure of DNA damaged by UV and psoralen

    International Nuclear Information System (INIS)

    Sung-hou Kim; Tomic, M.T.; Wemmer, D.E.; Pearlman, D.; Holbrook, S.

    1988-01-01

    The authors have used NMR methods to determine a three-dimensional model of an 8 base-pair DNA fragment cross-linked with psoralen. The duplex form of the self-complementary deoxyribonucleotide d-GGGTACCC, contains a psoralen cross-linkable site at the center of the duplex. The cross-link was formed by UV irradiation of a mixture of the purified DNA octamer and 4'-(aminomethyl)-4,5',8-trimethylpsoralen (AMT). Structural information was obtained using one and two-dimensional NMR techniques. Two-dimensional NOE experiments were used to assign the spectrum and estimate distances for many pairs of protons in the cross-linked DNA. Structural parameters obtained are qualitatively consistent with a previously proposed model for kinked and unwound cross-linked B-form DNA derived from crystallography and molecular modeling. The NMR derived model has a 53 degree bend into the major groove occuring primarily at the site of drug addition, and a 56 degree unwinding spanning the 8 base pair duplex. (author)

  6. [Influence of straw manuring on the biological activity of a lessivé chernozem (author's transl)].

    Science.gov (United States)

    Heisig, W; Seeboldt, M

    1979-01-01

    In a long-term experiment, the influence of straw manuring in spring and autumn on the biological activity of a lessive chernozem soil was examined. The quantity of carbon dioxide, evolved by the plots during May and June, showed an increase in soil respiration by straw manuring. Increasing amounts of nitrogen, given together with straw, had no significant influence on the quantity of carbon dioxide evolved. The base respiration, however, showed increasing rates proportional to increasing amounts of nitrogen. The variants manured with straw in autumn were superior to those manured in spring. For covering the efficiency of soil respiration, the field method applied noes not seem suitable. With high N-supply (200 kg/ka), the relative respiration rates show good stability of the organic substance, present in soil. This stability is higher with straw manuring in spring than in autumn. Straw supply in autumn influences the yield more favourably. Direct relation between the quantity of carbon dioxide evolved and yield cannot be inferred.

  7. Barn og diabetes type 1

    OpenAIRE

    Ramstad, Marte Elise; Sagbakken, Sina Bekkelund

    2017-01-01

    Bacheloroppgave sykepleie, 2017 Bakgrunn: Vi har valgt denne problemstillingen fordi diabetes type 1 er svært utbredt hos barn i Norge. Videre har vi lite erfaringer med barn og ønsket å lære mer om denne pasientgruppen. Vi ønsket videre å se på hvordan vi kan undervise og veilede for å gi god og hensiktsmessig sykepleie til barn og deres familier. Hensikt: Finne ut hvordan sykepleier kan fremme egenomsorg hos barn med diabetes gjennom veiledning og undervisning. Dette er noe som sykepl...

  8. Informe científico de investigador: Agamennoni, Osvaldo Enrique (2012-2013)

    OpenAIRE

    Agamennoni, Osvaldo Enrique

    2013-01-01

    Entre los principales resultados alcanzados en el período comprendido por el siguiente informe, caben destacarse los siguientes: -Implementación en un ASIC (Application Specific Integrated Circuit) de una técnica de identificación no lineal mediante una estructura de Error de Salida No lineal (NOE) que posibilita un crecimiento gradual de la cantidad de parámetros sin perder la aproximación lograda al incrementar los mismos. -Una técnica de modelado del movimiento de los o...

  9. Structural characterization of the interactions between calmodulin and skeletal muscle myosin light chain kinase: Effect of peptide (576-594)G binding on the Ca2+-binding domains

    International Nuclear Information System (INIS)

    Seeholzer, S.H.; Wand, A.J.

    1989-01-01

    Calcium-containing calmodulin (CaM) and its complex with a peptide corresponding to the calmodulin-binding domain of skeletal muscle myosin light chain kinase [skMLCK(576-594)G] have been studied by one- and two-dimensional 1 H NMR techniques. Resonances arising from the antiparallel β-sheet structures associated with the calcium-binding domains of CaM and their counterparts in the CaM-skMLCK(576-594)G complex have been assigned. The assignments were initiated by application of the main chain directed assignment strategy. It is found that, despite significant changes in chemical shifts of resonances arising from amino acid residues in this region upon binding of the peptide, the β-sheets have virtually the same structure in the complex as in CaM. Hydrogen exchange rates of amide NH within the β-sheet structures are significantly slowed upon binding of peptide. These data, in conjunction with the observed nuclear Overhauser effect (NOE) patterns and relative intensities and the downfield shifts of associated amide and α resonances upon binding of peptide, show that the peptide stabilizes the Ca 2+ -bound state of calmodulin. The observed pattern of NOEs within the β-sheets and their structural similarity correspond closely to those predicted by the crystal structure. These findings imply that the apparent inconsistency of the crystal structure with recently reported low-angle X-ray scattering profiles of CaM may lie within the putative central helix bridging the globular domains

  10. Sequential nearest-neighbor effects on computed {sup 13}C{sup {alpha}} chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Serrano, Pedro; Wuethrich, Kurt [The Scripps Research Institute, Department of Molecular Biology (United States); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

    2010-09-15

    To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of {sup 13}C{sup {alpha}} chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue {alpha}/{beta} protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed {sup 13}C{sup {alpha}} chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical {sup 13}C{sup {alpha}} chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed {sup 13}C{sup {alpha}} chemical shifts, {Delta}{sub ca,i}, for the individual residues along the sequence. This indicates that the {Delta}{sub ca,i} -values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.

  11. ESONET , a milestone towards sustained multidisciplinary ocean observation.

    Science.gov (United States)

    Rolin, J.-F.

    2012-04-01

    At the end of a 4 year project dedicated to the constitution of a Network of Excellence (NoE) on subsea observatories in Europe, large expectations are still in the agenda. The economical crisis changes the infrastructure construction planning in many ways but the objectives are quite clear and may be reached at European scale. The overall objective of the ESONET NoE was to create an organisation able to implement, operate and maintain a sustainable underwater observation network, extending into deep water, capable of monitoring biological, geo-chemical, geological, geophysical and physical processes occurring throughout the water column, sea floor interface and solid earth below. This main objective of ESONET has been met by creating the network of 11 permanent underwater observation sites together with the "ESONET Vi" Virtual Institute organising the exchange of staff and joint experiments on EMSO large research infrastructure observatories. The development of recommendations on best practices, standardization and interoperability concepts concerning underwater observatory equipment, as synthetized by the so called ESONET Label document has been created. The ESONET Label is a set of criteria to be met by the deep-sea observatory equipment as well as recommended solutions and options to guarantee their optimal operation in the ocean over long time periods. ESONET contributes to the fixed point sustained observatory community which extends worldwide, is fully multidisciplinary and in its way may open a new page in ocean sciences history.

  12. Inventory Methods in a Conversion Plant; Methodes d'Inventaire dans un Etablissement de Transformation; Metody inventarizatsij na predpriyatii po pererabotke yadernykh materialov; Metodos de Inventario en una Planta de Transformacion

    Energy Technology Data Exchange (ETDEWEB)

    Billy, G. [Commissariat a l' Energie Atomique, Paris (France)

    1966-02-15

    The main purposes of the inventories are: to safeguard the interests of the Commissariat, to evaluate losses, and to check the measures taken for waste storage. On stocktaking the investigator can either carry out a physical inventory, participate in the inventory, or check the inventory. The latter method gives the best results. The stocktaking operations, preceded by a preparatory meeting to determine the methods to be applied, are carried out in two stages: the weight inventory check and the physical auditing check. Some questions arising in connection with the inventory are disputes between consignors and consignees regarding weight and content; choice of weighing equipment, waste, and evaluation of losses. Inventory methods should not differ greatly from one country to another. It would appear desirable to stress the difficulties which arise during operation and to consider jointly ways of surmounting them. (author) [French] Les inventaires ont notamment pour but de sauvegarder les interets du Commissariat, evaluer le montant des pertes, et controler les mesures prises pour le stockage des dechets. Pour le recensement, l'enqueteur peut effectuer materiellement l'inventaire, V participer, ou le verifier. Cettedernieremethodedonneles meilleurs resultats. Les operations de recensement, precedees d'une reunion preparatoire pour definir les modalites a appliquer, ont lieu en deux temps: la verification de l'inventaire ponderal, et la verification de la comptabilite physique. Les questions qui peuvent etre soulevees en cours d'inventaire sont des contestations sur le poids et les teneurs entre expediteurs et destinataires, le choix du materiel de pesee, les dechets et l'evaluation des pertes. Les methodes d'inventaire ne doivent guere differer d'un pays a l'autre. U semble preferable de souligner les difficultes qui se presentent en cours d'operation et d'etudier, en commun, les moyens qui permettent de les surmonter. (author) [Spanish] La finalidad principal de los

  13. Læring innen toppfotball : en studie av forholdet mellom coaching og mesterlære som læringsteorier, og deres potensial og rolle i toppfotball

    OpenAIRE

    Lindseth, Ole Kristian

    2008-01-01

    Tema og problemstilling Jeg har bakgrunn som fotballspiller og har i den forbindelse vært svært opptatt av hvordan man best kan legge til rette for utvikling av fotballspillere. Gjennom mine pedagogikkstudier har to læringsteorier fasinert meg i forhold til fotball, nemlig coaching og mesterlære. Disse to teoriene skiller seg tydelig fra hverandre og er på mange måter motsetninger. Dette var noe jeg ønsket å gå dypere inn i, og derfor endte denne masteroppgaven opp med en studie av coachin...

  14. 1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

    International Nuclear Information System (INIS)

    Cort, John R.; Cho, Herman M.

    2009-01-01

    Proton and 13C NMR chemical shift assignments and 1H-1H scalar couplings for the two diastereomers of the vitamin K epoxide reductase (VKOR) inhibitor brodifacoum have been determined from acetone solutions containing both diastereomers. Data were obtained from homo- and heteronuclear correlation spectra acquired at 1H frequencies of 750 and 900 MHz over a 268-303 K temperature range. Conformations inferred from scalar coupling and 1-D NOE measurements exhibit large differences between the diastereomers. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  15. Facility management i fremtidens bankdrift

    OpenAIRE

    Vollan, Silje Steen

    2015-01-01

    Facility Management (FM) er et relativt ungt fagområde som er i sterk utvikling. Bank og finansbransjen har hatt en tradisjon med å eie og forvalte egne bygninger, noe som har gitt et underbevisst fokus på FM. Økt digitalisering fører til at bankene står overfor nye utfordringer og muligheter. Nye produkter og tjenester dukker opp og dette fører til at FM enheten utfordres med høyere krav til profesjonalitet og effektivitet. Internasjonale trender i markedet viser at flere facility management...

  16. Analysis of the backbone dynamics of capsicein using 15N NMR relaxation rate measurements

    International Nuclear Information System (INIS)

    Van Heijenoort, C.; Bouaziz, S.; Guittet, E.

    1994-01-01

    15 N relaxation times T 1 and T 1ρ , and heteronuclear steady state nOes, were measured on capsicein, a 98 residue protein. The classical analysis of these data using directly the Lipari and Szabo formalism was shown to give incoherent results, probably due to the presence of a slow exchange along the whole protein. This global exchange broadening made the usual preliminary evaluation of the overall correlation time of capsicein using the Lipari and Szabo expression for the spectral densities impossible. (authors). 2 figs., 23 refs

  17. Solvent Exchange Rates of Side-chain Amide Protons in Proteins

    International Nuclear Information System (INIS)

    Rajagopal, Ponni; Jones, Bryan E.; Klevit, Rachel E.

    1998-01-01

    Solvent exchange rates and temperature coefficients for Asn/Gln side-chain amide protons have been measured in Escherichia coli HPr. The protons of the eight side-chain amide groups (two Asn and six Gln) exhibit varying exchange rates which are slower than some of the fast exchanging backbone amide protons. Differences in exchange rates of the E and Z protons of the same side-chain amide group are obtained by measuring exchange rates at pH values > 8. An NOE between a side-chain amide proton and a bound water molecule was also observed

  18. Using discrepant events in science demonstrations to promote student engagement in scientific investigations: An action research study

    Science.gov (United States)

    Mancuso, Vincent J.

    Students' scientific investigations have been identified in national standards and related reform documents as a critical component of students' learning experiences in school, yet it is not easy to implement them in science classrooms. Could science demonstrations help science teachers put this recommendation into practice? While demonstrations are a common practice in the science classroom and research has documented some positive effects in terms of student motivation and engagement from their use, the literature also shows that, as traditionally presented, science demonstrations do not always achieve their intended outcomes. This, in turn, suggested the value of investigating what design elements of demonstrations could be used to promote specific instructional goals. Employing action research as a methodology, the proposed study was developed to explore how science demonstrations can be designed so as to most effectively promote student engagement in scientific investigations. More specifically, I was interested in examining the effects of using a discrepant event as part of the demonstration, as a way to create cognitive conflict and, thus, increase interest and engagement. I also investigated the relative merit of the well-researched POE (Predict, Observe, Explain) design versus employing demonstrations that appear to the student to be unplanned (what I will refer to as NOE, or a Naturally Occurring Experience). This study was informed by Constructivism, Situated Cognition and Conceptual Change as theoretical frameworks. The project included the design, implementation and study of an intervention consisting of three instructional units designed to support students' learning of the concepts of density, molecular arrangement of gas particles, and cohesion, respectively. In each of these units, lasting a total of two 80-minute class periods, students were asked to design and conduct an investigation to gain a better understanding of the concept under study. In

  19. Gaspar Noé: mu eesmärk pole filmidega solvata / Gaspar Noe ; intervjueerinud Jaanus Noormets

    Index Scriptorium Estoniae

    Noé, Gaspar, 1963-

    2010-01-01

    Prantsusmaal elav ja töötav, Argentiinas sündinud režissöör endast. Gaspar Noé mängufilmidest "Ootamatu tühjus" (Prantsusmaa-Saksamaa-Itaalia, 2009), "Üksi kõigi vastu" (Prantsusmaa 1998), "Ümberpööramatu" (Prantsusmaa 2002)

  20. Vision of Spaces in the Paintings of the Asháninka sheripiare Noe Morales Silva

    Directory of Open Access Journals (Sweden)

    Luisa Elvira Belaunde

    2011-02-01

    Full Text Available Amazonian shamanic painting is a hybrid art born from the coming together of Western figurative techniques, indigenous body painting and visionary shamanic experiences. It is a testimonial art by which painters express their visionary experiences to a foreign public aiming to understand the Amazonian universe. In his watercolors and drawings, the Asháninka healer Noé Silva Morales bears witness to his life as a sheripiare through the construction of visionary spaces carefully painted with skins of luminous designs.

  1. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, Mitsuhiro [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan); Ono, Akira M.; Terauchi, Tsutomu [SAIL Technologies Co., Inc. (Japan); Kainosho, Masatsune, E-mail: kainosho@nmr.chem.metro-u.ac.j [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan)

    2010-01-15

    The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines ({epsilon}- and {zeta}-SAIL Phe) and tyrosine ({epsilon}-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized {delta}-SAIL Phe and {delta}-SAIL Tyr, which allow us to observe and assign {delta}-{sup 13}C/{sup 1}H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the {delta}-, {epsilon}- or {zeta}-{sup 13}C/{sup 1}H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the {delta}-, {epsilon}-, and {zeta}-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly {sup 13}C, {sup 15}N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of {zeta}-SAIL Phe and {epsilon}-SAIL Tyr would be practically the best choice for protein structural determinations.

  2. NMR studies of the interaction of the antibiotic nogalamycin with the hexadeoxyribonucleotide duplex d(5'-GCATGC)2

    International Nuclear Information System (INIS)

    Searle, M.S.; Hall, J.G.; Denny, W.A.; Wakelin, L.P.G.

    1988-01-01

    1 H resonance assignments in the NMR spectra of the self-complementary hexadeoxyribonucleoside pentaphosphate d(5'-GCATGC) 2 and its complex with the antibiotic nogalamycin, together with interproton distance constraints obtained from two-dimensional nuclear Overhauser effect (NOE) spectra, have enabled the authors to characterize the three-dimensional structure of these species in solution. In the complex described, two drug molecules are bound per duplex, in each of two equivalent binding sites, with full retention of the dyad symmetry. Twenty-eight NOE distance constraints between antibiotic and nucleotide protons define the position and orientation of the bound drug molecule. Nogalamycin intercalates at the 5'-CA and 5'-TG steps with the major axis of the anthracycline chromophore aligned approximately at right angles to the major axes of the base pairs. The nogalose sugar occupies the minor groove of the helix and makes many contacts with the deoxyribose moieties of three nucleotides along one strand of the duplex in the 5'-TGC segment. The charged dimethylamino group and hydroxyl functions of the bicyclic sugar lie in the major groove juxtaposed to the guanine base, the bridging atoms of the bicyclic sugar making contacts with the methyl group of the thymine. Thus the antibiotic is not symmetrically disposed in the intercalation site but is in close contact in both grooves with atoms comprising the 5'-TGC strand. The intercalation cavity is wedge-shaped, the major axes of the base pairs forming the site being tilted with respect to one another

  3. Diastereotopic covalent binding of the natural inhibitor leupeptin to trypsin: Detection of two interconverting hemiacetals by solution and solid-state NMR spectroscopy

    International Nuclear Information System (INIS)

    Ortiz, C.; Tellier, C.; Williams, H.; Stolowich, N.J.; Scott, A.I.

    1991-01-01

    The naturally occurring peptidyl protease inhibitor leupeptin (N-acetyl-L-leucyl-L-leucyl-L-argininal) has been prepared labeled with 13 C at the argininal carbonyl. 13 C chemical shift data for the trypsin-leupeptin inhibitor complex in the pH range 3.0-7.6 reveal the presence of two pH-dependent covalent complexes, suggestive of two interconverting diastereomers at the new asymmetric tetrahedral center created by covalent addition of Ser195 to either side of the 13 C-enriched aldehyde of the inhibitor. At pH 7 two signals are observable at δ 98.8 and δ 97.2 (84:16 ratio), while at pH 3.0 the latter signal predominates. In the selective proton 13 C-edited NOE spectrum of the major diastereomer at pH 7.4, a strong NOE is observed between the hemiacetal proton of the inhibitor and the C2 proton of His57 of the enzyme, thus defining the stereochemistry of the high pH complex to the S configuration in which the hemiacetal oxygen resides in the oxyanion hole. pH titration studies further indicate that the 13 C chemical shift of the S diastereomer follows a titration curve with a pK a of 4.69, the magnitude of which is consistent with direct titration of the hemiacetal oxygen. Similar pH-dependent chemical shifts were obtained by using CPMAS 13 C NMR, providing evidence for the existence of the same diastereomeric equilibrium in the solid state

  4. Lærer- og elevmangfold i det livstolkingsplurale norske klasserommet – utfordringer og muligheter for lærerutdanningen

    Directory of Open Access Journals (Sweden)

    Sidsel Lied

    2009-05-01

    Full Text Available Med denne artikkelen ønsker jeg å gi et bidrag til diskusjonen om hvordan lærerutdanningen kan møte utfordringene fra et økt kulturelt mangfold i samfunnet. Siden mitt forsknings- og interessefelt er knyttet til mangfoldet på feltet livstolking, er artikkelens forskningsspørsmål og overordnede problemstilling: Hvordan kan lærerutdanningen møte de utfordringer og muligheter som det livstolkingsplurale norske klasserommet representerer? Delspørsmål jeg utforsker for å svare på dette, er: Hvordan kommer en livstolkingsplural virkelighet til uttrykk i grunnskolens og lærerutdanningens religions- og livssynsfag? Og: Hvordan kan lærerstudenters medvirkning i forskning bidra til å øke deres forståelse for de kravene det livstolkingsplurale norske klasserommet stiller til sine lærere? De empiriske prosjektene som inngår i arbeidet med å besvare forskningsspørsmålene, er utført i norsk offentlig grunnskole og allmenlærerutdanning. Det er naturlig å holde disse prosjektene sammen fordi all norsk lærerutdanning kvalifiserer sine studenter til å arbeide i grunnskolen. Ved å se på hvordan en livstolkingsplural virkelighet kommer til uttrykk i grunnskolens religions- og livssynsfag, vil en følgelig kunne si noe om hvordan deler av den skolehverdagen som norsk lærerutdanning kvalifiserer sine studenter for, ser ut. Dessuten vil en, ved å utforske hvordan en livstolkingsplural virkelighet kommer til uttrykk i lærerutdanningen, kunne si noe om hvordan utdanningen forventes å forberede sine studenter for denne yrkesutfordringen.

  5. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination.

    Science.gov (United States)

    Takeda, Mitsuhiro; Ono, Akira M; Terauchi, Tsutomu; Kainosho, Masatsune

    2010-01-01

    The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines (epsilon- and zeta-SAIL Phe) and tyrosine (epsilon-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized delta-SAIL Phe and delta-SAIL Tyr, which allow us to observe and assign delta-(13)C/(1)H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the delta-, epsilon- or zeta-(13)C/(1)H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the delta-, epsilon-, and zeta-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly (13)C, (15)N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of zeta-SAIL Phe and epsilon-SAIL Tyr would be practically the best choice for protein structural determinations.

  6. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination

    International Nuclear Information System (INIS)

    Takeda, Mitsuhiro; Ono, Akira M.; Terauchi, Tsutomu; Kainosho, Masatsune

    2010-01-01

    The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines (ε- and ζ-SAIL Phe) and tyrosine (ε-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized δ-SAIL Phe and δ-SAIL Tyr, which allow us to observe and assign δ- 13 C/ 1 H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the δ-, ε- or ζ- 13 C/ 1 H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the δ-, ε-, and ζ-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly 13 C, 15 N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of ζ-SAIL Phe and ε-SAIL Tyr would be practically the best choice for protein structural determinations.

  7. A vision and strategy for the virtual physiological human: 2012 update.

    Science.gov (United States)

    Hunter, Peter; Chapman, Tara; Coveney, Peter V; de Bono, Bernard; Diaz, Vanessa; Fenner, John; Frangi, Alejandro F; Harris, Peter; Hose, Rod; Kohl, Peter; Lawford, Pat; McCormack, Keith; Mendes, Miriam; Omholt, Stig; Quarteroni, Alfio; Shublaq, Nour; Skår, John; Stroetmann, Karl; Tegner, Jesper; Thomas, S Randall; Tollis, Ioannis; Tsamardinos, Ioannis; van Beek, Johannes H G M; Viceconti, Marco

    2013-04-06

    European funding under Framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for 5 years. The VPH Network of Excellence (NoE) has been set up to help develop common standards, open source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also working to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by the FP6 STEP project in 2006. In 2010, we wrote an assessment of the accomplishments of the first two years of the VPH in which we considered the biomedical science, healthcare and information and communications technology challenges facing the project (Hunter et al. 2010 Phil. Trans. R. Soc. A 368, 2595-2614 (doi:10.1098/rsta.2010.0048)). We proposed that a not-for-profit professional umbrella organization, the VPH Institute, should be established as a means of sustaining the VPH vision beyond the time-frame of the NoE. Here, we update and extend this assessment and in particular address the following issues raised in response to Hunter et al.: (i) a vision for the VPH updated in the light of progress made so far, (ii) biomedical science and healthcare challenges that the VPH initiative can address while also providing innovation opportunities for the European industry, and (iii) external changes needed in regulatory policy and business models to realize the full potential that the VPH has to offer to industry, clinics and society generally.

  8. Compliance with OSHA record-keeping requirements.

    Science.gov (United States)

    Seligman, P J; Sieber, W K; Pedersen, D H; Sundin, D S; Frazier, T M

    1988-01-01

    The Occupational Safety and Health Act of 1970 requires employers to maintain records of workplace injuries and illnesses. To assess compliance with the law, data from the National Occupational Exposure Survey (NOES) were examined. Of the 4,185 companies with 11 or more employees, 75 per cent maintained OSHA Form 200 designed for recording illnesses and injuries. The number of employees and the presence of a union were positive determinants in the record maintenance. Of companies with 500 or more employees, 95 per cent kept records compared with 60 per cent of companies with between 11 and 99 employees. PMID:3407825

  9. Jernkarbonatutfelling (Sideritt) i myr

    OpenAIRE

    Selmer-Olsen, A. R.; Lie, Ole

    1983-01-01

    I torva langs det NV utløpet fra Glesmyra er det funnet et 15 - 20 cm tykt lyst grått sjikt l, 5 m nede i profilet. Aldersbestemmelse, røntgenbestemmelse og kjemiske analyser viser at dette er jernkarbonat (sideritt) dannet for 5700 år siden. Det er diskutert hvordan dette sjiktet kan ha blitt dannet. Som konklusjon, har en kommet fram til at det har vært en utfelling av jernhydroksyd i bekkeløpet. I løpet av et visst tidsrom har pH i vannet steget noe ved at jernet ha blitt redusert og hydro...

  10. Synthesis and biological evaluation of p,p'-dideuteriophenytoin

    Energy Technology Data Exchange (ETDEWEB)

    Poupaert, J.H.; Guiot, P.; Dumont, P.

    1988-01-01

    A reaction sequence is described to synthesize p,p'-dideuteriophenytoin in three steps from commercially available starting materials. The deuterium content at best reached 99.2% as measured by mass spectrometry. For materials with isotopic content up to 95%, excellent agreement was found between the data obtained by mass spectrometry and /sup 13/C-nuclear magnetic resonance operated in a NOE-suppression mode. p,p'-Dideuteriophenytoin was evaluated comparatively with phenytoin and p-deuteriophenytoin in the maximal electroshock test. While all three compounds exhibited a high degree of antiepileptic activity, none of them demonstrated significant superiority over the others.

  11. Når to mennesker møtes: Hvordan kan sykepleier møte pasienter med selvskadende atferd

    OpenAIRE

    Eikrem, Mats Ulstein

    2017-01-01

    Høgskulen på Vestlandet Institutt for sykepleie Avdeling for helsefag Tittel: Når to mennesker møtes Bakgrunn for val av tema: Bakgrunnen for tema er mine egne erfaringer innenfor legevakts arbeid, og de observasjonene jeg har tilnærmet meg der. Noe som har ført til at jeg opplever at sykepleiere ikke skaper nok rom for pasienter med selvskadende atferd. Jeg ønsker derfor å lære mer om hvordan man bør møte denne pasientgruppen på en god måte. Problemstilling: Hvordan kan syk...

  12. NMR studies on the structure and dynamics of lac operator DNA

    International Nuclear Information System (INIS)

    Lee, S.C.

    1985-01-01

    Nuclear Magnetic Resonance spectroscopy was used to elucidate the relationships between structure, dynamics and function of the gene regulatory sequence corresponding to the lactose operon operator of Escherichia coli. The length of the DNA fragments examined varied from 13 to 36 base pair, containing all or part of the operator sequence. These DNA fragments are either derived genetically or synthesized chemically. Resonances of the imino protons were assigned by one dimensional inter-base pair nuclear Overhauser enhancement (NOE) measurements. Imino proton exchange rates were measured by saturation recovery methods. Results from the kinetic measurements show an interesting dynamic heterogeneity with a maximum opening rate centered about a GTG/CAC sequence which correlates with the biological function of the operator DNA. This particular three base pair sequence occurs frequently and often symmetrically in prokaryotic nd eukaryotic DNA sites where one anticipates specific protein interaction for gene regulation. The observed sequence dependent imino proton exchange rate may be a reflection of variation of the local structure of regulatory DNA. The results also indicate that the observed imino proton exchange rates are length dependent

  13. "Dem vil at barna skal ha noe å gjøre" : En casestudie av Habbo.no

    OpenAIRE

    Kvaale, Torkel

    2012-01-01

    Denne oppgaven er en kvalitativ casestudie av Habbo.no, en virtuell verden der hovedgruppen av brukere er barn og unge. Det kvalitative forskningsintervju representerer metodeverktøyet som er brukt for innsamlingen av data, og datamaterialet består av 10 intervjuer med tilsammen 13 brukere av Habbo.no, i alderen 10-12 år. Habbo ble skapt av det finske selskapet Sulake i 2000 som hevder at denne er verdens største virtuelle verden for tenåringer. Habbo.no er kun én av til sammen 35 unike H...

  14. The spatial data infrastructure for the European Seas Observatory Network (ESONET)

    Science.gov (United States)

    Huber, Robert; Diepenbroek, Michael

    2010-05-01

    ESONET is a Multidisciplinary European Network of Excellence (NoE) in which scientists and engineers from 50 partners and 14 countries cooperate in building the infrastructure for a lasting integration of research and development in deep sea observatories in Europe. This NoE aims to develop strong links between regional nodes of a European network of sub sea observatories and to promote multidiciplinarity and transnationality within each node. Essential for these goals is the provision of an effective data and knowledge infrastructure for both, management and archiving of observatory data as well as knowledge and data sharing among network participants. The ESONET data infrastructure roughly consists of four major components: data policies a common agreement on the data management procedures and prerequisites, data acquisition technologies serve to collect data directly from ESONET observatories, data archives care for long term data management of collected ESONET data and data integration and portal tools which ensure harmonisation of collected data and allow access to the data in a common way. Most critical for ESONET was the development of a spatial data infrastructure (SDI) by using standardised protocols to directly access observatory data in its spatial and temporal context. The ESONET SDI provides means to either access data in quasi real time or harvest locally stored data in order to transfer it to a long term data archive. ESONET SDI largely builds upon the OGC Sensor Web Enablement (SWE) suite of standards. Among those, the Sensor Observation Service (SOS), the Observations & Measurements (O&M), Sensor Markup Language (SensorML) are especially important for the integration of observatory data as well as for the contribution of ESONET data to GEOSS.

  15. Sequence-specific 1H NMR assignments and secondary structure of the Arc repressor of bacteriophage P22, as determined by two-dimensional 1H NMR spectroscopy

    International Nuclear Information System (INIS)

    Breg, J.N.; Boelens, R.; George, A.V.E.; Kaptein, R.

    1989-01-01

    The Arc repressor of bacteriophage P22 is a DNA binding protein that does not belong to any of the known classes of such proteins. The authors have undertaken a 1 H NMR study of the protein with the aim of elucidating its three-dimensional structure in solution and its mode of binding of operator DNA. Here the authors present the 1 H nuclear magnetic resonance (NMR) assignments of all backbone protons an most of the side-chain protons of Arc repressor. Elements of secondary structure have been identified on the basis of networks of characteristics sequential and medium-range nuclear Overhauser enhancements (NOEs). Two α-helical regions have been found in the peptide regions 16-29 and 35-45. The ends of the helices could not yet be firmly established and could extend to residue 31 for the first helix and to residue 49 for the second. Immediately before the first helix, between residues 8 and 14, a region is present with β-sheet characteristics dominated by a close proximity of the α-protons of residues 9 and 13. Because of the dimeric nature of the protein there are still two possible ways in which the NOEs in the β-sheet region can be interpreted. While the data presently do not allow an unambiguous choice between these two possibilities, some evidence is discussed that favors the latter (β-sheet between monomers). Since the N-terminal region of Arc is responsible for the sequence-specific recognition of its operator, the findings suggest the existence of a DNA binding motif in which a β-sheet region is present

  16. Approach for energy saving and pollution reducing by fueling diesel engines with emulsified biosolution/ biodiesel/diesel blends.

    Science.gov (United States)

    Lin, Yuan-Chung; Lee, Wen-Jhy; Chao, How-Ran; Wang, Shu-Li; Tsou, Tsui-Chun; Chang-Chien, Guo-Ping; Tsai, Perng-Jy

    2008-05-15

    The developments of both biodiesel and emulsified diesel are being driven by the need for reducing emissions from diesel engines and saving energy. Artificial chemical additives are also being used in diesel engines for increasing their combustion efficiencies. But the effects associated with the use of emulsified additive/biodiesel/diesel blends in diesel engines have never been assessed. In this research, the premium diesel fuel (PDF) was used as the reference fuel. A soy-biodiesel was selected as the test biodiesel. A biosolution made of 96.5 wt % natural organic enzyme-7F (NOE-7F) and 3.5 wt % water (NOE-7F water) was used as the fuel additive. By adding additional 1 vol % of surfactant into the fuel blend, a nanotechnology was used to form emulsified biosolution/soy-biodiesel/PDF blends for fueling the diesel engine. We found that the emulsified biosolution/soy-biodiesel/PDF blends did not separate after being kept motionless for 30 days. The above stability suggests that the above combinations are suitable for diesel engines as alternative fuels. Particularly, we found that the emulsified biosolution/soy-biodiesel/PDF blends did have the advantage in saving energy and reducing the emissions of both particulate matters (PM) and polycyclic aromatic hydrocarbons (PAHs) from diesel engines as compared with PDF, soy-biodiesel/PDF blends, and emulsified soy-biodiesel/ PDF blends. The results obtained from this study will provide useful approaches for reducing the petroleum reliance, pollution, and global warming. However, it should be noted that NO(x) emissions were not measured in the present study which warrants the need for future investigation.

  17. Estudo espectroscópico em elucidação estrutural de flavonoides de Solanum jabrense Agra & Nee e S. paludosum Moric Spectroscopy study on structural elucidation of flavonoids from Solanum jabrense Agra & Nee e S. paludosum Moric

    Directory of Open Access Journals (Sweden)

    Tania Maria Sarmento da Silva

    2009-01-01

    Full Text Available The NMR (RMN¹H, 13C, COSY, HMQC, HMBC, NOE-DIFF, NOESY and mass spectra data analysis of sixteen flavonoids, including nine natural, 7-O-methylkanferol (ramnocitrin, 3,7-di-O-methylkanferol (kumatakenin, 3-O-methylquercetin, 3,7,3',4'-tetra-O-methylquercetin (retusin, 3,7,8,4'-tetra-O-methylgossipetin, 3,7,8,3',4'-penta-O-methylgossipetin, 7-O-methylapigenin (genkwanin, 3,7,8-tri-O-methylherbacetin, 7,4'- di-O-methylquercetin (ombuine, isolated from Solanum paludosum and S. jabrense, and seven prepared methyl and acetyl derivatives, are discussed according the substitution on the rings A, B and C.

  18. Spectroscopy study on structural elucidation of flavonoids from Solanum jabrense Agra and Nee and S. paludosum Moric; Estudo espectroscopico em elucidacao estrutural de flavonoides de Solanum jabrense Agra and Nee e S. paludosum Moric

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Tania Maria Sarmento da [Universidade Federal Rural de Pernambuco (UFRPE), Recife, PE (Brazil). Dept. de Quimica], e-mail: sarmento@pesquisador.cnpq.br; Carvalho, Mario Geraldo de [Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropedica, RJ (Brazil). Inst. de Ciencias Exatas. Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacazes, RJ (Brazil). Setor de Quimica de Produtos Naturais

    2009-07-01

    The NMR (RMN{sup 1}H, {sup 13}C, COSY, HMQC, HMBC, NOE-DIFF, NOESY) and mass spectra data analysis of sixteen flavonoids, including nine natural, 7-O-methylkanferol (rhamnocitrin), 3,7-di-O-methylkanferol (kumatakenin), 3-O-methylquercetin, 3,7,3',4'-tetra-O-methylquercetin (retusin), 3,7,8,4'-tetra-O-methylgossipetin, 3,7,8,3',4'-penta-O-methylgossipetin, 7-O-methylapigenin (genkwanin), 3,7,8-tri-O-methylherbacetin, 7,4'- di-O-methylquercetin (ombuine), isolated from Solanum paludosum and S. jabrense, and seven prepared methyl and acetyl derivatives, are discussed according the substitution on the rings A, B and C. (author)

  19. Uniform and selective deuteration in two-dimensional NMR of proteins

    International Nuclear Information System (INIS)

    LeMaster, D.M.

    1990-01-01

    This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

  20. Nanooptics for high efficient photon managment

    Science.gov (United States)

    Wyrowski, Frank; Schimmel, Hagen

    2005-09-01

    Optical systems for photon management, that is the generation of tailored electromagnetic fields, constitute one of the keys for innovation through photonics. An important subfield of photon management deals with the transformation of an incident light field into a field of specified intensity distribution. In this paper we consider some basic aspects of the nature of systems for those light transformations. It turns out, that the transversal redistribution of energy (TRE) is of central concern to achieve systems with high transformation efficiency. Besides established techniques nanostructured optical elements (NOE) are demanded to implement transversal energy redistribution. That builds a bridge between the needs of photon management, optical engineering, and nanooptics.

  1. Hvordan fungerer samvirke mellom landbaserte nødetater og maritime ressurser ved ulykker i umiddelbar nærhet til land? Et kvalitativt blikk på redningsarbeidet etter helikopterulykken ved Turøy.

    OpenAIRE

    Haugen, Eirik Solheim; Løvskogen, Tom Arild; Røstgård, Synne Elise

    2017-01-01

    Bacheloroppgave i beredskap og krisehåndtering 2017 Vi har valgt samvirke, og konkret samvirke mellom landbaserte nødetater og maritime ressurser, som tema for vår oppgave. Utfordringer knyttet til samordning og koordinering har vært tilbakevendende i flere av fagene i studiet, noe som gjør at vi synes dette både er interessant og aktuelt å se nærmere på. Vi mener også at det kan finnes en slags gråsone i grensesnittet mellom land og sjø, og håper derfor at vår avhandling kan være med på å...

  2. Improving the Accuracy of NMR Structures of Large Proteins Using Pseudocontact Shifts as Long-Range Restraints

    Energy Technology Data Exchange (ETDEWEB)

    Gaponenko, Vadim [National Cancer Institute, Structural Biophysics Laboratory (United States); Sarma, Siddhartha P. [Indian Institute of Science, Molecular Biophysics Unit (India); Altieri, Amanda S. [National Cancer Institute, Structural Biophysics Laboratory (United States); Horita, David A. [Wake Forest University School of Medicine, Department of Biochemistry (United States); Li, Jess; Byrd, R. Andrew [National Cancer Institute, Structural Biophysics Laboratory (United States)], E-mail: rabyrd@ncifcrf.gov

    2004-03-15

    We demonstrate improved accuracy in protein structure determination for large ({>=}30 kDa), deuterated proteins (e.g. STAT4{sub NT}) via the combination of pseudocontact shifts for amide and methyl protons with the available NOEs in methyl-protonated proteins. The improved accuracy is cross validated by Q-factors determined from residual dipolar couplings measured as a result of magnetic susceptibility alignment. The paramagnet is introduced via binding to thiol-reactive EDTA, and multiple sites can be serially engineered to obtain data from alternative orientations of the paramagnetic anisotropic susceptibility tensor. The technique is advantageous for systems where the target protein has strong interactions with known alignment media.

  3. Feasibility study for ergonomic analysis and design of future helicopter cockpit systems

    Science.gov (United States)

    Hawkins, H. L.

    1985-01-01

    The Army's light scout-attack helicopters (LHXs), planned for deployment in the 1990's, will fly nap-of-the-earth (NOE) missions in high threat environments, often under poor visibility and adverse atmospheric conditions, and probably with a one man crew. A procedure for the analysis of pilot workload that will identify and explicate the main characteristics of those LHX mission components holding overload potential is described. A principled, in-depth, explication of the cognitive demans of LHX piloting is essential to any effective effort to address the human factors issues. A task-analytic procedure that will yield the detail and organizstion needed to achieve these goals is examined.

  4. Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes.

    Science.gov (United States)

    Jayalakshmi, V; Krishna, N Rama

    2002-03-01

    A couple of recent applications of intermolecular NOE (INOE) experiments as applied to biomolecular systems involve the (i) saturation transfer difference NMR (STD-NMR) method and (ii) the intermolecular cross-saturation NMR (ICS-NMR) experiment. STD-NMR is a promising tool for rapid screening of a large library of compounds to identify bioactive ligands binding to a target protein. Additionally, it is also useful in mapping the binding epitopes presented by a bioactive ligand to its target protein. In this latter application, the STD-NMR technique is essentially similar to the ICS-NMR experiment, which is used to map protein-protein or protein-nucleic acid contact surfaces in complexes. In this work, we present a complete relaxation and conformational exchange matrix (CORCEMA) theory (H. N. B. Moseley et al., J. Magn. Reson. B 108, 243-261 (1995)) applicable for these two closely related experiments. As in our previous work, we show that when exchange is fast on the relaxation rate scale, a simplified CORCEMA theory can be formulated using a generalized average relaxation rate matrix. Its range of validity is established by comparing its predictions with those of the exact CORCEMA theory which is valid for all exchange rates. Using some ideal model systems we have analyzed the factors that influence the ligand proton intensity changes when the resonances from some protons on the receptor protein are saturated. The results show that the intensity changes in the ligand signals in an intermolecular NOE experiment are very much dependent upon: (1) the saturation time, (2) the location of the saturated receptor protons with respect to the ligand protons, (3) the conformation of the ligand-receptor interface, (4) the rotational correlation times for the molecular species, (5) the kinetics of the reversibly forming complex, and (6) the ligand/receptor ratio. As an example of a typical application of the STD-NMR experiment we have also simulated the STD effects for a

  5. Conformation of glycomimetics in the free and protein-bound state: structural and binding features of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man.

    Science.gov (United States)

    Mikkelsen, Lise Munch; Hernáiz, María José; Martín-Pastor, M; Skrydstrup, Troels; Jiménez-Barbero, Jesús

    2002-12-18

    The conformational properties of the C-glycosyl analogue of the core trisaccharide alpha-D-Man-(1 --> 3)-[alpha-D-Man-(1 --> 6)]-D-Man in solution have been carefully analyzed by a combination of NMR spectroscopy and time-averaged restrained molecular dynamics. It has been found that both the alpha-1,3- and the alpha-1,6-glycosidic linkages show a major conformational averaging. Unusual Phi ca. 60 degrees orientations for both Phi torsion angles are found. Moreover, a major conformational distinction between the natural compound and the glycomimetic affects to the behavior of the omega(16) torsion angle around the alpha-1 --> 6-linkage. Despite this increased flexibility, the C-glycosyl analogue is recognized by three mannose binding lectins, as shown by NMR (line broadening, TR-NOE, and STD) and surface plasmon resonance (SPR) methods. Moreover, a process of conformational selection takes place, so that these lectins probably bind the glycomimetic similarly to the way they recognize the natural analogue. Depending upon the architecture and extension of the binding site of the lectin, loss or gain of binding affinity with respect to the natural analogue is found.

  6. Structural Studies of Bcl-xL/ligand Complexes using {sup 19}F NMR

    Energy Technology Data Exchange (ETDEWEB)

    Yu Liping; Hajduk, Philip J.; Mack, Jamey; Olejniczak, Edward T. [GPRD, Abbott Laboratories, Pharmaceutical Discovery Division (United States)], E-mail: Edward.olejniczak@abbott.com

    2006-04-15

    Fluorine atoms are often incorporated into drug molecules as part of the lead optimization process in order to improve affinity or modify undesirable metabolic and pharmacokinetic profiles. From an NMR perspective, the abundance of fluorinated drug leads provides an exploitable niche for structural studies using {sup 19}F NMR in the drug discovery process. As {sup 19}F has no interfering background signal from biological sources, {sup 19}F NMR studies of fluorinated drugs bound to their protein receptors can yield easily interpretable and unambiguous structural constraints. {sup 19}F can also be selectively incorporated into proteins to obtain additional constraints for structural studies. Despite these advantages, {sup 19}F NMR has rarely been exploited for structural studies due to its broad lines in macromolecules and their ligand complexes, leading to weak signals in {sup 1}H/{sup 19}F heteronuclear NOE experiments. Here we demonstrate several different experimental strategies that use {sup 19}F NMR to obtain ligand-protein structural constraints for ligands bound to the anti-apoptotic protein Bcl-xL, a drug target for anti-cancer therapy. These examples indicate the applicability of these methods to typical structural problems encountered in the drug development process.

  7. The development and application of composite complexity models and a relative complexity metric in a software maintenance environment

    Science.gov (United States)

    Hops, J. M.; Sherif, J. S.

    1994-01-01

    A great deal of effort is now being devoted to the study, analysis, prediction, and minimization of software maintenance expected cost, long before software is delivered to users or customers. It has been estimated that, on the average, the effort spent on software maintenance is as costly as the effort spent on all other software costs. Software design methods should be the starting point to aid in alleviating the problems of software maintenance complexity and high costs. Two aspects of maintenance deserve attention: (1) protocols for locating and rectifying defects, and for ensuring that noe new defects are introduced in the development phase of the software process; and (2) protocols for modification, enhancement, and upgrading. This article focuses primarily on the second aspect, the development of protocols to help increase the quality and reduce the costs associated with modifications, enhancements, and upgrades of existing software. This study developed parsimonious models and a relative complexity metric for complexity measurement of software that were used to rank the modules in the system relative to one another. Some success was achieved in using the models and the relative metric to identify maintenance-prone modules.

  8. Spectroscopic and immunochemical characterization of left-handed Z RNA under physiological conditions

    International Nuclear Information System (INIS)

    Hardin, C.C.; Zarling, D.A.; Tinoco, I. Jr.

    1986-01-01

    Limited chemical brominination of poly[r(C-G)] results in partial modification of guanine C8 and cytosine C5 producing a mixture of A and Z RNA forms in 110 mM NaCl buffer at 37 0 C. 1 H NMR of Br-poly[r(C-G)] shows a 1:1 mixture of A and Z RNAs. Nuclear Overhauser effect (NOE) experiments permit complete assignments of GH8, CH6, CH5, GH1' and CH1 resonances in both the A and Z forms. Distance estimates obtained from GH8 to GH1' NOEs demonstrate that even unbrominated guanine residues in these polynucleotides undergo a transition to the syn conformation (Z form). The Z form of Br-poly[r(C-G)] in 110 mM NaCl has a guanine Raman scattering band at 643 cm -1 in agreement with the band in the Z form of poly[r(C-G)] stabilized by 6 M NaClO 4 . In A RNA the band is at 671 cm -1 . The corresponding shift in DNA is from 682 cm -1 (B DNA) to 625 cm -1 (Z DNA). This suggests different glycosidic torsion angles in Z RNA and Z DNA. Inoculating rabbits with Br-poly[r(C-G)] produces polyclonal antibodies specific for the Z forms of RNA and DNA (i.e., poly[d(br 5 C-G)] or poly[d(io 5 C-G)] as judged by radioimmunoassay in 100 mM NaCl buffers. Phosphate buffer or certain high ionic strength conditions affect the recognition of Z RNA and Z DNA by anti-Z RNA or anti-Z DNA IgGs suggesting that one determinant recognized by these antibodies is the zig-zag phosphodiester backbone

  9. Structural studies of SpoIIAA using NMR

    International Nuclear Information System (INIS)

    Comfort, D.M.

    1998-01-01

    The protein SpoIIAA participates, via phosphorylation and dephosphorylation, in the four-component system that regulates the sporulation sigma factor e. Differential gene expression depends on specialised transcription factors called sigma factors, which direct the RNA polymerase to transcribe specific genes in one or other of the two chambers at various stages of sporulation. The first sporulation-specific sigma factor to be activated is 4 transcription that depends on σ F is essential for the remaining sigma factors to become active in turn. Early in sporulation SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase, SpoIIAB. About 80 minutes after the initiation of sporulation a specific phosphatase, SpoIIE, begins to hydrolyse SpoIIAA-P, and the resulting SpoIIAA again becomes a substrate for SpoIIAB. SpoIIAB is also an anti-sigma factor which in its free form inhibits a F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases e activity. The three-dimensional structure of SpoIIAA has been determined using high resolution NMR. SpoIIAA has a novel fold, composed of a-helices and P-strand elements. The structural differences between SpoIIAA and its inactive form, SpoIIAA-P, were also investigated by NMR. Tentative evidence points to the observation that phosphorylation of SpoIIAA results in a minor conformational change near the site of phosphorylation, which interferes with the hydrophobic interaction between SpoIIAA and SpoIIAB. Further NMR studies helped to predict the location of SpoIIAA-, GTP-, and ATP-binding sites on the SpoIIAA structure. In addition, the automated iterative NOE assignment algorithm, ARIA, was used to obtain additional NOE-based distance constraints and to calculate a refined structure. (author)

  10. Structural studies of SpoIIAA using NMR

    Energy Technology Data Exchange (ETDEWEB)

    Comfort, D.M

    1998-07-01

    The protein SpoIIAA participates, via phosphorylation and dephosphorylation, in the four-component system that regulates the sporulation sigma factor e. Differential gene expression depends on specialised transcription factors called sigma factors, which direct the RNA polymerase to transcribe specific genes in one or other of the two chambers at various stages of sporulation. The first sporulation-specific sigma factor to be activated is 4 transcription that depends on {sigma}{sup F} is essential for the remaining sigma factors to become active in turn. Early in sporulation SpoIIAA is in the phosphorylated state (SpoIIAA-P), as a result of the activity of the ATP-dependent protein kinase, SpoIIAB. About 80 minutes after the initiation of sporulation a specific phosphatase, SpoIIE, begins to hydrolyse SpoIIAA-P, and the resulting SpoIIAA again becomes a substrate for SpoIIAB. SpoIIAB is also an anti-sigma factor which in its free form inhibits a F by binding to it. Competition by SpoIIAA (the anti-anti-sigma factor) for binding to SpoIIAB releases e activity. The three-dimensional structure of SpoIIAA has been determined using high resolution NMR. SpoIIAA has a novel fold, composed of a-helices and P-strand elements. The structural differences between SpoIIAA and its inactive form, SpoIIAA-P, were also investigated by NMR. Tentative evidence points to the observation that phosphorylation of SpoIIAA results in a minor conformational change near the site of phosphorylation, which interferes with the hydrophobic interaction between SpoIIAA and SpoIIAB. Further NMR studies helped to predict the location of SpoIIAA-, GTP-, and ATP-binding sites on the SpoIIAA structure. In addition, the automated iterative NOE assignment algorithm, ARIA, was used to obtain additional NOE-based distance constraints and to calculate a refined structure. (author)

  11. NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating.

    Science.gov (United States)

    Shenkarev, Zakhar O; Paramonov, Alexander S; Lyukmanova, Ekaterina N; Shingarova, Lyudmila N; Yakimov, Sergei A; Dubinnyi, Maxim A; Chupin, Vladimir V; Kirpichnikov, Mikhail P; Blommers, Marcel J J; Arseniev, Alexander S

    2010-04-28

    The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein domain solubilized in DPC/LDAO (2:1) mixed micelles. Secondary and tertiary structures of the VSD were characterized using secondary chemical shifts and NOE contacts. These data indicate that the spatial structure of the VSD solubilized in micelles corresponds to the structure of the domain in an open state of the channel. NOE contacts and secondary chemical shifts of amide protons indicate the presence of tightly bound water molecule as well as hydrogen bond formation involving an interhelical salt bridge (Asp62-R133) that stabilizes the overall structure of the domain. The backbone dynamics of the VSD was studied using (15)N relaxation measurements. The loop regions S1-S2 and S2-S3 were found mobile, while the S3-S4 loop (voltage-sensor paddle) was found stable at the ps-ns time scale. The moieties of S1, S2, S3, and S4 helices sharing interhelical contacts (at the level of the Asp62-R133 salt bridge) were observed in conformational exchange on the micros-ms time scale. Similar exchange-induced broadening of characteristic resonances was observed for the VSD solubilized in the membrane of lipid-protein nanodiscs composed of DMPC, DMPG, and POPC/DOPG lipids. Apparently, the observed interhelical motions represent an inherent property of the VSD of the KvAP channel and can play an important role in the voltage gating.

  12. Solution structure of the Equine Infectious Anemia Virus p9 protein: a rationalization of its different ALIX binding requirements compared to the analogous HIV-p6 protein

    Directory of Open Access Journals (Sweden)

    Henklein Peter

    2009-12-01

    Full Text Available Abstract Background The equine infection anemia virus (EIAV p9 Gag protein contains the late (L- domain required for efficient virus release of nascent virions from the cell membrane of infected cell. Results In the present study the p9 protein and N- and C-terminal fragments (residues 1-21 and 22-51, respectively were chemically synthesized and used for structural analyses. Circular dichroism and 1H-NMR spectroscopy provide the first molecular insight into the secondary structure and folding of this 51-amino acid protein under different solution conditions. Qualitative 1H-chemical shift and NOE data indicate that in a pure aqueous environment p9 favors an unstructured state. In its most structured state under hydrophobic conditions, p9 adopts a stable helical structure within the C-terminus. Quantitative NOE data further revealed that this α-helix extends from Ser-27 to Ser-48, while the N-terminal residues remain unstructured. The structural elements identified for p9 differ substantially from that of the functional homologous HIV-1 p6 protein. Conclusions These structural differences are discussed in the context of the different types of L-domains regulating distinct cellular pathways in virus budding. EIAV p9 mediates virus release by recruiting the ALG2-interacting protein X (ALIX via the YPDL-motif to the site of virus budding, the counterpart of the YPXnL-motif found in p6. However, p6 contains an additional PTAP L-domain that promotes HIV-1 release by binding to the tumor susceptibility gene 101 (Tsg101. The notion that structures found in p9 differ form that of p6 further support the idea that different mechanisms regulate binding of ALIX to primary versus secondary L-domains types.

  13. Solution structure of the luzopeptin-DNA complex

    International Nuclear Information System (INIS)

    Zhang, Xiaolu; Patel, D.J.

    1991-01-01

    The luzopeptin-d(C-A-T-G) complex (1 drug/duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. Once equivalent of luzopeptin binds to the self-complementary tetranucleotide duplex with the 2-fold symmetry of the antitumor agent and the DNA oligomer retained on complex formation. The authors have assigned the exchangeable and nonexchangeable proton resonances of luzopeptin and the d(C-A-T-G) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site in duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the luzopeptin and the DNA in the complex. The formation of cis peptide bonds for luzopeptin in the complex results in an increased separation of the long sides of the rectangular cyclic depsipeptide backbone and reorients in the glycine amide proton so that it can form an intermolecular hydrogen bond with the 2-carbonyl of T3 in the complex. This observation explains, in part, the requirement for Watson-Crick A·T pairs to be sandwiched between the quinolines at the bisintercalation site in the luzopeptin-DNA complex. The NMR studies on the luzopeptin-d(C-A-T-G) complex unequivocally establish that antitumor agents can undergo conformational transitions on complex formation with DNA, and it is the conformation of the drug in the complex that should serve as the starting point for drug design studies. The above structural details on the solution structure of the luzopeptin-DNA complex also explain the sequence selectivity of luzopeptin for bisintercalation at d(C-A)·d(T-G) steps in the d(C-A-T-G) duplex in solution

  14. Monomeric Aβ(1-40) and Aβ(1-42) Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil.

    Science.gov (United States)

    Roche, Julien; Shen, Yang; Lee, Jung Ho; Ying, Jinfa; Bax, Ad

    2016-02-09

    The pathogenesis of Alzheimer's disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ(1-40) and Aβ(1-42) into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ(1-42) compared to that of Aβ(1-40) are poorly understood. To explore in detail the structural propensity of the monomeric Aβ(1-40) and Aβ(1-42) peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ(1-40) and Aβ(1-42) peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings ((3)JHNHα, (3)JC'C', (3)JC'Hα, (1)JHαCα, (2)JNCα, and (1)JNCα) recorded for Aβ(1-40) were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ(1-42), suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process.

  15. Optimization of number and signal to noise ratio radiographs for defects 3D reconstruction in industrial control

    International Nuclear Information System (INIS)

    Bruandet, J.-P.

    2001-01-01

    Among numerous techniques for non-destructive evaluation (NOE), X-rays systems are well suited to inspect inner objects. Acquiring several radiographs of inspected objects under different points of view enables to recover a three dimensional structural information. In this NOE application, a tomographic testing is considered. This work deals with two tomographic testing optimizations in order to improve the characterization of defects that may occur into metallic welds. The first one consists in the optimization of the acquisition strategy. Because tomographic testing is made on-line, the total duration for image acquisition is fixed, limiting the number of available views. Hence, for a given acquisition duration, it is possible either to acquire a very limited number of radiographs with a good signal to noise ratio in each single acquisition or a larger number of radiographs with a limited signal to noise ratio. The second one consists in optimizing the 3D reconstruction algorithms from a limited number of cone-beam projections. To manage the lack of data, we first used algebraic reconstruction algorithms such as ART or regularized ICM. In terms of acquisition strategy optimization, an increase of the number of projections was proved to be valuable. Taking into account specific prior knowledge such as support constraint or physical noise model in attenuation images also improved reconstruction quality. Then, a new regularized region based reconstruction approach was developed. Defects to reconstruct are binary (lack of material in a homogeneous object). As a consequence, they are entirely described by their shapes. Because the number of defects to recover is unknown and is totally arbitrary, a level set formulation allowing handling topological changes was used. Results obtained with a regularized level-set reconstruction algorithm are optimistic in the proposed context. (author) [fr

  16. Structural and dynamical characterization of the Miz-1 zinc fingers 5-8 by solution-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, David; Bedard, Mikaeel; Bilodeau, Josee; Lavigne, Pierre, E-mail: pierre.lavigne@usherbrooke.ca [Universite de Sherbrooke, Departement de Biochimie, Faculte de Medecine et des Sciences de la Sante, Institut de Pharmacologie de Sherbrooke (Canada)

    2013-10-15

    Myc-interacting zinc finger protein-1 (Miz-1) is a BTB/POZ transcription factor that activates the transcription of cytostatic genes, such as p15{sup INK4B} or p21{sup CIP1}. The C-terminus of Miz-1 contains 13 consensus C{sub 2}H{sub 2} zinc finger domains (ZF). ZFs 1-4 have been shown to interact with SMAD3/4, while the remaining ZFs are expected to bind the promoters of target genes. We have noted unusual features in ZF 5 and the linker between ZFs 5 and 6. Indeed, a glutamate is found instead of the conserved basic residue two positions before the second zinc-coordinating histidine on the ZF 5 helix, and the linker sequence is DTDKE in place of the classical TGEKP sequence. In a canonical {beta}{beta}{alpha} fold, such unusual primary structure elements should cause severe electrostatic repulsions. In this context, we have characterized the structure and the dynamics of a Miz-1 construct comprising ZFs 5-8 (Miz 5-8) by solution-state NMR. Whilst ZFs 5, 7 and 8 were shown to adopt the classical {beta}{beta}{alpha} fold for C{sub 2}H{sub 2} ZFs, the number of long-range NOEs was insufficient to define a classical fold for ZF 6. We show by using {sup 15}N-relaxation dispersion experiments that this lack of NOEs is due to the presence of extensive motions on the {mu}s-ms timescale. Since this negatively charged region would have to be located near the phosphodiester backbone in a DNA complex, we propose that in addition to promoting conformational searches, it could serve as a hinge region to keep ZFs 1-4 away from DNA.

  17. Computer vision techniques for rotorcraft low altitude flight

    Science.gov (United States)

    Sridhar, Banavar

    1990-01-01

    Rotorcraft operating in high-threat environments fly close to the earth's surface to utilize surrounding terrain, vegetation, or manmade objects to minimize the risk of being detected by an enemy. Increasing levels of concealment are achieved by adopting different tactics during low-altitude flight. Rotorcraft employ three tactics during low-altitude flight: low-level, contour, and nap-of-the-earth (NOE). The key feature distinguishing the NOE mode from the other two modes is that the whole rotorcraft, including the main rotor, is below tree-top whenever possible. This leads to the use of lateral maneuvers for avoiding obstacles, which in fact constitutes the means for concealment. The piloting of the rotorcraft is at best a very demanding task and the pilot will need help from onboard automation tools in order to devote more time to mission-related activities. The development of an automation tool which has the potential to detect obstacles in the rotorcraft flight path, warn the crew, and interact with the guidance system to avoid detected obstacles, presents challenging problems. Research is described which applies techniques from computer vision to automation of rotorcraft navigtion. The effort emphasizes the development of a methodology for detecting the ranges to obstacles in the region of interest based on the maximum utilization of passive sensors. The range map derived from the obstacle-detection approach can be used as obstacle data for the obstacle avoidance in an automatic guidance system and as advisory display to the pilot. The lack of suitable flight imagery data presents a problem in the verification of concepts for obstacle detection. This problem is being addressed by the development of an adequate flight database and by preprocessing of currently available flight imagery. The presentation concludes with some comments on future work and how research in this area relates to the guidance of other autonomous vehicles.

  18. Structural and dynamic characterization of eukaryotic gene regulatory protein domains in solution

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Andrew Loyd [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    Solution NMR was primarily used to characterize structure and dynamics in two different eukaryotic protein systems: the δ-Al-ε activation domain from c-jun and the Drosophila RNA-binding protein Sex-lethal. The second system is the Drosophila Sex-lethal (Sxl) protein, an RNA-binding protein which is the ``master switch`` in sex determination. Sxl contains two adjacent RNA-binding domains (RBDs) of the RNP consensus-type. The NMR spectrum of the second RBD (Sxl-RBD2) was assigned using multidimensional heteronuclear NMR, and an intermediate-resolution family of structures was calculated from primarily NOE distance restraints. The overall fold was determined to be similar to other RBDs: a βαβ-βαβ pattern of secondary structure, with the two helices packed against a 4-stranded anti-parallel β-sheet. In addition 15N T1, T2, and 15N/1H NOE relaxation measurements were carried out to characterize the backbone dynamics of Sxl-RBD2 in solution. RNA corresponding to the polypyrimidine tract of transformer pre-mRNA was generated and titrated into 3 different Sxl-RBD protein constructs. Combining Sxl-RBD1+2 (bht RBDs) with this RNA formed a specific, high affinity protein/RNA complex that is amenable to further NMR characterization. The backbone 1H, 13C, and 15N resonances of Sxl-RBD1+2 were assigned using a triple-resonance approach, and 15N relaxation experiments were carried out to characterize the backbone dynamics of this complex. The changes in chemical shift in Sxl-RBD1+2 upon binding RNA are observed using Sxl-RBD2 as a substitute for unbound Sxl-RBD1+2. This allowed the binding interface to be qualitatively mapped for the second domain.

  19. T.C.G triplet in an antiparallel purine.purine.pyrimidine DNA triplex. Conformational studies by NMR.

    Science.gov (United States)

    Dittrich, K; Gu, J; Tinder, R; Hogan, M; Gao, X

    1994-04-12

    The antiparallel purine.purine.pyrimidine DNA triplex, RRY6, which contains a T.C.G inverted triplet in the center of the sequence, was examined by proton and phosphorous two-dimensional NMR spectroscopy. The local conformation of the T.C.G triplet (T4.C11.G18) and the effect of this triplet on the global helical structure were analyzed in detail. The formation of the T.C.G triplet is confirmed by a set of cross-strand NOEs, including unusual cross-strand NOEs between the third strand and the pyrimidine strand as opposed to the purine strand of the duplex. NMR data suggest that the T.C.G triplet may be present in an equilibrium between a non-hydrogen-bonded form and a T(O4)-C(NH2) hydrogen-bonded form and that there is a distortion of the in-plane alignment of the three bases. The flanking G.G.C base triplets are well-defined on the 5'-side of T4, but somewhat interrupted on the 3'-side of T4. The effect of the third strand binding on the Watson-Crick duplex was probed by an NMR study of the free duplex RY6. NMR parameters are affected mostly around the T.C.G inversion site. The perturbations extend to at least two adjacent base triplets on either side. The binding of the third purine strand and the accommodation of a central T.C.G inversion in RRY6 does not require a readjustment in sugar pucker, which remains in the range of C2'-endo. 31P resonances of RRY6 distribute over a range of 2.2 ppm. The H-P coupling patterns of the third strand differ from those of the duplex. General spectral patterns defined by the marker protons of the RRY and YRY triplexes are compared.

  20. Elforbrug på e-mail & sms

    DEFF Research Database (Denmark)

    Christiansen, Ellen Tove; Kanstrup, Anne Marie; Grønhøj, Alice

    Feedback Project: 'Dansk Energi, Projekt nr. 338-020', http://feedback.noe.dk, reported in Kibsgaard 2008; Junge 2008). The main finding in this follow-up study is that customers demand knowledge about their electricity consumption independent of their attitude towards electricity conservation. We find...... consumption just for the sake of knowing, monitoring, comparing and competing. Interest in this information seemed unrelated to the actual electricity savings accomplished during the year of feedback, attitude to saving, and priority given to conservation behavior. This finding suggests that electricity......, which in turn may increase awareness among those less aware, and support and ease the awareness of those already aware, in this way supporting conservation behavior....

  1. Konfliktperspektiver i religionsundervisning og religionsdidaktikk - en bredere og bedre tilnærming til religion?

    Directory of Open Access Journals (Sweden)

    Bengt Ove Andreassen

    2008-12-01

    Full Text Available Artikkelen drøfter ulike sider ved eksplisitt å åpne for konfliktperspektiver i religionsundervisningen. En slik tilnærming er faglig utfordrende, men gir innblikk i en side ved religion som i norsk religionsdidaktisk sammenheng har vært lite utforsket. Norske religionsdidaktikere er i all hovedsak rekruttert fra teologiske fagmiljøer og har hentet perspektiver fra økumenikk og religionsdidalog i stedet for å kunne utforske konflikter der religion inngår, for å lære noe om religioner. Artikkelen trekker inn bidrag fra religionsvitenskapen og legger til grunn en forståelse av religion som i noen grad skiller seg fra etablerte perspektiver i norsk religionsdidaktikk.

  2. Constituintes químicos de Capraria biflora (Scrophulariaceae e atividade larvicida de seu óleo essencial

    Directory of Open Access Journals (Sweden)

    Luciana Gregório da S. Souza

    2012-01-01

    Full Text Available Analysis of essential oil from fresh leaves of Capraria biflora allowed identification of fourteen essential oil constituents among which thirteen are sesquiterpene compounds, and α-humulene (43.0% the major constituent. The essential oil was tested for larvicidal activity against Aedes aegypti showing good activity, with LC50 73.39 µg/mL (2.27 g/mL. Chromatographic studies of extracts from roots and stems allowed the isolation of five compounds: naphthoquinone biflorin, sesquiterpene caprariolide B, the steroid β-sitosterol, the carbohydrate D-mannitol and iridoid myopochlorin first reported in the species C. biflora. The structures of compounds were characterized by spectroscopic data, IR, MS, NMR13C, NMR¹H, NOE, HSQC and HMBC.

  3. Chemical constituents of Capraria biflora (Scrophulariaceae) and larvicidal activity of essential oil

    International Nuclear Information System (INIS)

    Souza, Luciana Gregorio da S.; Almeida, Macia Cleane S.; Monte, Francisco Jose Q.; Santiago, Gilvandete Maria P.; Braz-Filho, Raimundo; Lemos, Telma Leda G.; Gomes, Clerton L.; Nascimento, Ronaldo F. do

    2012-01-01

    . Analysis of essential oil from fresh leaves of Capraria biflora allowed identification of fourteen essential oil constituents among which thirteen are sesquiterpene compounds, and α-humulene (43.0%) the major constituent. The essential oil was tested for larvicidal activity against Aedes aegypyti showing good activity, with LC 50 73.39 μg/mL (2.27 g/mL). Chromatographic studies of extracts from roots and stems allowed the isolation of five compounds: naphthoquinone biflorin, sesquiterpene caprariolide B, the steroid β-sitosterol, the carbohydrate D-mannitol and iridoid myopochlorin first reported in the species C. biflora. The structures of compounds were characterized by spectroscopic data, IR, MS, NMR 13 C, NMR 1 H, NOE, HSQC and HMBC. (author)

  4. 13C-NMR assignment, structure, and dynamics of deoxyoligonucleotides

    International Nuclear Information System (INIS)

    Zanatta, N.; Borer, P.N.; Levy, G.C.

    1986-01-01

    The unique spectral properties of 13 C-NMR for studying nucleic acids and some of the important features of 13 C-NMR in oligonucleotide studies are demostrated. The main difficulty in studying oligonucleotides by 13 C-NMR and recent improvements in NMR instrumentation and advances in oligonucleotide synthesis are presented. The high resolution 13 C-NMR spectra, T 1 relaxation times and NOEs were measured for duplex of the self-complementary oligo-DNAs: d(CG) 3 and d(GGTATACC) are studied. The target of this study is to developed a systematic 13 C-NMR spectral assignment and to investigate the structure and dynamics of these two sequences by this techniques. (M.J.C.) [pt

  5. Den koreanske bølgen - En kulturvitenskapelig studie av sørkoreansk populærkultur, og hvordan den har nådd Vesten

    OpenAIRE

    Kvinge, Kristin Øyvindsdatter

    2016-01-01

    Hensikten med denne oppgaven er å se på den koreanske bølgen, som ofte refereres til som Hallyu. Den tar for seg både Hallyu som innhold og Hallyu som fenomen. Den koreanske bølgen har spredd seg hurtig i løpet av de siste 20 årene, noe som har bidratt til å gjøre Korea til en av de hurtigst økende økonomiene i den moderne tid. Denne oppgaven forsøker å se nærmere på hvordan Hallyu har nådd Vesten, med fokus på Europa og Norge. Før analysen vil oppgaven se nærmere på hv...

  6. Målinger i Norge fra 1960 og frem til Tsjernobyl

    Directory of Open Access Journals (Sweden)

    Torolf Berthelsen

    1986-06-01

    Full Text Available I Norge var målekapasiteten svært dårlig i forhold til situasjonen i Sverige. Vi hadde nesten ingen målekapasitet, heller ikke ved Institutt for Strålehygiene. Imidlertid hadde vi opprettholdt en undersøkelse som startet i 1965, da nedfallssituasjonen var noe av den samme som i dag. Vi visste også da at spesielle befolkningsgrupper var mer utsatt for stråling enn andre. Det var spesielt reindriftssamene som var knyttet til næringskjeden lav-reinkjøtt-menneske. Undersøkelser i Sverige, Finland og i Nord-Amerika hadde vist at det var betydelige mengder radioaktivitet i visse befolkningsgrupper. Kautokeino ble valgt som målingssted.

  7. Exact nonparametric confidence bands for the survivor function.

    Science.gov (United States)

    Matthews, David

    2013-10-12

    A method to produce exact simultaneous confidence bands for the empirical cumulative distribution function that was first described by Owen, and subsequently corrected by Jager and Wellner, is the starting point for deriving exact nonparametric confidence bands for the survivor function of any positive random variable. We invert a nonparametric likelihood test of uniformity, constructed from the Kaplan-Meier estimator of the survivor function, to obtain simultaneous lower and upper bands for the function of interest with specified global confidence level. The method involves calculating a null distribution and associated critical value for each observed sample configuration. However, Noe recursions and the Van Wijngaarden-Decker-Brent root-finding algorithm provide the necessary tools for efficient computation of these exact bounds. Various aspects of the effect of right censoring on these exact bands are investigated, using as illustrations two observational studies of survival experience among non-Hodgkin's lymphoma patients and a much larger group of subjects with advanced lung cancer enrolled in trials within the North Central Cancer Treatment Group. Monte Carlo simulations confirm the merits of the proposed method of deriving simultaneous interval estimates of the survivor function across the entire range of the observed sample. This research was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada. It was begun while the author was visiting the Department of Statistics, University of Auckland, and completed during a subsequent sojourn at the Medical Research Council Biostatistics Unit in Cambridge. The support of both institutions, in addition to that of NSERC and the University of Waterloo, is greatly appreciated.

  8. Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of 13C chemical shifts

    Directory of Open Access Journals (Sweden)

    Simone Di Micco

    2013-12-01

    Full Text Available In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of 13C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of 13C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.

  9. {sup 13}C relaxation in an RNA hairpin

    Energy Technology Data Exchange (ETDEWEB)

    King, G.C. [Univ. of South Wales, Kensington (Australia)]|[Rice Univ., Houston, TX (United States); Akratos, C. [Univ. of South Wales, Kensington (Australia); Xi, Z.; Michnica, M.J. [Rice Univ., Houston, TX (United States)

    1994-12-01

    This initial survey of {sup 13}C relaxation in the {triangle}TAR RNA element has generated a number of interesting results that should prove generally useful for future studies. The most readily comparable study in the literature monitored {sup 13}C relaxation of the methyl groups from unusual bases in tRNA{sup Phe}. The study, which used T{sub 1} and NOE data only, reported order parameters for the methyl group axis that ranged between 0.51 and 0.97-a range similar to that observed here. However, they reported a breakdown of the standard order parameter analysis at higher (118-MHz {sup 13}C) frequencies, which should serve to emphasize the need for a thorough exploration of suitable motional models.

  10. Separation and identification of phenolic compounds of extra virgin olive oil from Olea europaea L. by HPLC-DAD-SPE-NMR/MS. Identification of a new diastereoisomer of the aldehydic form of oleuropein aglycone.

    Science.gov (United States)

    Pérez-Trujillo, Míriam; Gómez-Caravaca, Ana María; Segura-Carretero, Antonio; Fernández-Gutiérrez, Alberto; Parella, Teodor

    2010-08-25

    The phenolic fraction of a monovarietal extra virgin olive oil (EVOO) from Olea europaea L. var. Cornezuelo was studied by the hyphenated HPLC-DAD-SPE-NMR/MS techniques. This survey led to the identification of 25 main compounds. One was identified as a new diastereoisomer of the aldehydic form of oleuropein aglycone (AOA) and characterized by 1D and 2D NMR techniques. The relative configuration of this new AOA was determined as 5R*,8S*,9S* on the basis of the results obtained from the combination of NOE experiments and Monte Carlo conformational search calculations. Assuming, as for the described diastereoisomers, that the new AOA comes from the natural oleuropein aglycone (OA), the absolute configuration was proposed as 5S,8R,9R.

  11. Stereochemical Analysis of Leubethanol, an Anti-TB Active Serrulatane, from Leucophyllum frutescens

    Science.gov (United States)

    Molina-Salinas, Gloria M.; Rivas-Galindo, Verónica M.; Said-Fernández, Salvador; Lankin, David C.; Muñoz, Marcelo A.; Joseph-Nathan, Pedro; Pauli, Guido F.; Waksman, Noemí

    2013-01-01

    Bioactivity-guided fractionation of the methanolic root bark extract of Leucophyllum frutescens (Berl.) I.M. Johnst. led to the identification of leubethanol (1), a new serrulatane-type diterpene with activity against both multi drug-resistant and drug-sensitive strains of virulent Mycobacterium tuberculosis. Leubethanol (1) was identified by 1D/2D NMR data, as a serrulatane closely related to erogorgiane (2), and exhibited anti-TB activity with minimum inhibitory concentrations in the range 6.25–12.50 µg/mL. Stereochemical evidence for 1 was gleaned from 1D and 2D NOE experiments, 1H-NMR full spin analysis, as well as by comparison of the experimental vibrational circular dichroism (VCD) spectrum to density functional theory calculated VCD spectra of two diastereomers. PMID:21859082

  12. Chemical constituents of Capraria biflora (Scrophulariaceae) and larvicidal activity of essential oil; Constituintes quimicos de Capraria biflora (Scrophulariaceae) e atividade larvicida de seu oleo essencial

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Luciana Gregorio da S.; Almeida, Macia Cleane S.; Monte, Francisco Jose Q.; Santiago, Gilvandete Maria P.; Braz-Filho, Raimundo; Lemos, Telma Leda G. [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica; Gomes, Clerton L.; Nascimento, Ronaldo F. do, [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Analitica e Fisico-Quimica

    2012-07-01

    . Analysis of essential oil from fresh leaves of Capraria biflora allowed identification of fourteen essential oil constituents among which thirteen are sesquiterpene compounds, and {alpha}-humulene (43.0%) the major constituent. The essential oil was tested for larvicidal activity against Aedes aegypyti showing good activity, with LC{sub 50} 73.39 {mu}g/mL (2.27 g/mL). Chromatographic studies of extracts from roots and stems allowed the isolation of five compounds: naphthoquinone biflorin, sesquiterpene caprariolide B, the steroid {beta}-sitosterol, the carbohydrate D-mannitol and iridoid myopochlorin first reported in the species C. biflora. The structures of compounds were characterized by spectroscopic data, IR, MS, NMR{sup 13}C, NMR{sup 1}H, NOE, HSQC and HMBC. (author)

  13. Una nueva lectura de Razón de amor

    Directory of Open Access Journals (Sweden)

    Francisco Manuel Gómez Domingo

    1996-12-01

    Full Text Available Razón de Amor es un poema de difícil explicación. Es un poema medieval de autor desconocido que se nos da a conocer por primera vez en 1887 por Morel-Fatio. Desde esa fecha, se han escrito diversos artículos de todo tipo, intentando encontrar o descubrir su sentido último, su estructura, su unidad, etc. La mayoría de la crítica ha fijado su interés en intentar encontrar su unidad compositiva o en negársela. Noes extraño que esto haya sido así porque, no es normal encontramos dos composiciones tan distintas, como lo son un poema de amor y un debate goliardesco, en una sola obra.

  14. NMR-Assisted Structure Elucidation of an Anticancer Steroid-β-Enaminone Derivative

    Directory of Open Access Journals (Sweden)

    Donald Poirier

    2017-11-01

    Full Text Available The fortuitous modification of a quinoline-proline-piperazine side chain linked to a steroid in the presence of lithium (trimethylsilyl acetylide has generated an unknown product that is more active than its precursor. After having characterized two β-enaminones (two-carbon homologation compounds that were generated from a simplified model side chain, we have identified the unknown product as being the β-enaminone steroid derivative 1. NMR analysis, especially two-dimensional (2D experiments (correlation spectroscopy (COSY, NOE spectroscopy (NOESY, heteronuclear single-quantum correlation (HSQC and heteronuclear multiple-bond correlation (HMBC provided crucial information that was found essential in the characterization of enaminone 1. We also proposed a mechanism to rationalize the formation of this biologically active compound.

  15. Uniform 15N- and 15N/13C-labeling of proteins in mammalian cells and solution structure of the amino terminal fragment of u-PA

    International Nuclear Information System (INIS)

    Hansen, A.P.; Petros, A.M.; Meadows, R.P.; Mazar, A.P.; Nettesheim, D.G.; Pederson, T.M.; Fesik, S.W.

    1994-01-01

    Urokinase-type plasminogen activator (u-PA) is a 54-kDa glycoprotein that catalyzes the conversion of plasminogen to plasmin, a broad-specificity protease responsible for the degradation of fibrin clots and extracellular matrix components. The u-PA protein consists of three individual modules: a growth factor domain (GFD), a kringle, and a serine protease domain. The amino terminal fragment (ATF) includes the GFD-responsible for u-PA binding to its receptor-and the kringle domains. This protein was expressed and uniformly 15 N-and 15 N/ 13 C-labeled in mammalian cells by methods that will be described. In addition, we present the three-dimensional structure of ATF that was derived from 1299 NOE-derived distance restraints along with the φ angle and hydrogen bonding restraints. Although the individual domains in the structures were highly converged, the two domains are structurally independent. The overall structures of the individual domains are very similar to the structures of homologous proteins. However, important structural differences between the growth factor domain of u-PA and other homologous proteins were observed in the region that has been implicated in binding the urokinase receptor. These results may explain, in part, why other growth factors show no appreciable affinity for the urokinase receptor

  16. Uniform {sup 15}N- and {sup 15}N/{sup 13}C-labeling of proteins in mammalian cells and solution structure of the amino terminal fragment of u-PA

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, A.P.; Petros, A.M.; Meadows, R.P.; Mazar, A.P.; Nettesheim, D.G.; Pederson, T.M.; Fesik, S.W. [Abbott Laboratories, Abbott Park, IL (United States)

    1994-12-01

    Urokinase-type plasminogen activator (u-PA) is a 54-kDa glycoprotein that catalyzes the conversion of plasminogen to plasmin, a broad-specificity protease responsible for the degradation of fibrin clots and extracellular matrix components. The u-PA protein consists of three individual modules: a growth factor domain (GFD), a kringle, and a serine protease domain. The amino terminal fragment (ATF) includes the GFD-responsible for u-PA binding to its receptor-and the kringle domains. This protein was expressed and uniformly {sup 15}N-and {sup 15}N/{sup 13}C-labeled in mammalian cells by methods that will be described. In addition, we present the three-dimensional structure of ATF that was derived from 1299 NOE-derived distance restraints along with the {phi} angle and hydrogen bonding restraints. Although the individual domains in the structures were highly converged, the two domains are structurally independent. The overall structures of the individual domains are very similar to the structures of homologous proteins. However, important structural differences between the growth factor domain of u-PA and other homologous proteins were observed in the region that has been implicated in binding the urokinase receptor. These results may explain, in part, why other growth factors show no appreciable affinity for the urokinase receptor.

  17. Spin Choreography: Basic Steps in High Resolution NMR (by Ray Freeman)

    Science.gov (United States)

    Minch, Michael J.

    1998-02-01

    There are three orientations that NMR courses may take. The traditional molecular structure course focuses on the interpretation of spectra and the use of chemical shifts, coupling constants, and nuclear Overhauser effects (NOE) to sort out subtle details of structure and stereochemistry. Courses can also focus on the fundamental quantum mechanics of observable NMR parameters and processes such a spin-spin splitting and relaxation. More recently there are courses devoted to the manipulation of nuclear spins and the basic steps of one- and two-dimensional NMR experiments. Freeman's book is directed towards the latter audience. Modern NMR methods offer a myriad ways to extract information about molecular structure and motion by observing the behavior of nuclear spins under a variety of conditions. In Freeman's words: "We can lead the spins through an intricate dance, carefully programmed in advance, to enhance, simplify, correlate, decouple, edit or assign NMR spectra." This is a carefully written, well-illustrated account of how this dance is choreographed by pulse programming, double resonance, and gradient effects. Although well written, this book is not an easy read; every word counts. It is recommended for graduate courses that emphasize the fundamentals of magnetic resonance. It is not a text on interpretation of spectra.

  18. A robust algorithm for optimizing protein structures with NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2015-11-15

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca.

  19. Bovine pancreatic polypeptide (bPP) undergoes significant changes in conformation and dynamics upon binding to DPC micelles.

    Science.gov (United States)

    Lerch, Mirjam; Gafner, Verena; Bader, Reto; Christen, Barbara; Folkers, Gerd; Zerbe, Oliver

    2002-10-04

    The pancreatic polypeptide (PP), a 36-residue, C-terminally amidated polypeptide hormone is a member of the neuropeptide Y (NPY) family. Here, we have studied the structure and dynamics of bovine pancreatic polypeptide (bPP) when bound to DPC-micelles as a membrane-mimicking model as well as the dynamics of bPP in solution. The comparison of structure and dynamics of bPP in both states reveals remarkable differences. The overall correlation time of 5.08ns derived from the 15N relaxation data proves unambiguously that bPP in solution exists as a dimer. Therein, intermolecular as well as intramolecular hydrophobic interactions from residues of both the amphiphilic helix and of the back-folded N terminus contribute to the stability of the PP fold. The overall rigidity is well-reflected in positive values for the heteronuclear NOE for residues 4-34. The membrane-bound species displays a partitioning into a more flexible N-terminal region and a well-defined alpha-helical region comprising residues 17-31. The average RMSD value for residues 17-31 is 0.22(+/-0.09)A. The flexibility of the N terminus is compatible with negative values of the heteronuclear NOE observed for the N-terminal residues 4-12 and low values of the generalized order parameter S(2). The membrane-peptide interface was investigated by micelle-integrating spin-labels and H,2H exchange measurements. It is formed by those residues which make contacts between the C-terminal alpha-helix and the polyproline helix. In contrast to pNPY, also residues from the N terminus display spatial proximity to the membrane interface. Furthermore, the orientation of the C terminus, that presumably contains residues involved in receptor binding, is different in the two environments. We speculate that this pre-positioning of residues could be an important requirement for receptor activation. Moreover, we doubt that the PP fold is of functional relevance for binding at the Y(4) receptor.

  20. Conformational study of C8 diazocine turn mimics using {sup 3}J{sub CH} coupling constants with {sup 13}C in natural abundance

    Energy Technology Data Exchange (ETDEWEB)

    Bean, J.W.; Briand, J.; Burgess, J.L.; Callahan, J.F. [SmithKline Beecham Pharmaceuticals, King of Prussia, PA (United States)

    1994-12-01

    The conformations of two diazocine turn mimics, which were later incorporated into GPIIb/IIIa peptide antagonists, were investigated using nuclear magnetic resonance techniques. The two compounds, methyl (2,5-dioxo-3-(S)-(3-{omega}-tosylguanidino-propyl)-4-methyl-octahydro-1,4-dazocin-1-yl)acetate (1) and methyl (2,5-dioxo-3-(S)-(3-{omega}-tosyl-guanidino-propyl)-octahydro-1,5-diazocin-1-yl)acetate (2), differ only in their substituent at the diazocine position 4 nitrogen, yet this substitution results in a marked difference in the affinity of the resulting analogs for the GPIIb/IIIa receptor. It was of interest to determine if the difference observed in the antagonistic potency between these analogs was related to constitutional or, perhaps, conformational differences. The backbone conformations of these two molecules can be determined by measuring vicinal coupling constants along the trimethylene portion of the C8 ring backbone and by measuring interproton NOE intensities between the diazocine methine proton and the protons of the trimethylene group. For compound 1, {sup 3}J{sub HH} values measured from a P.E.COSY spectrum and interproton distances calculated from ROESY buildup curves indicated the presence of a single C8 ring backbone conformation where the trimethylene bridge adopted a staggered conformation and the H{alpha}1 and H{gamma}1 protons of the trimethylene group were 2.2 A from the methine proton. For compound 2, however, partial overlap of the central H{beta}1 and H{beta}2 protons made it impossible to measure {sup 3}J{sub HH} values from the P.E.COSY spectrum. We therefore used a {sup 13}C-filtered TOCSY experiment to measure the {sup 3}J{sub CH} values in both compounds 1 and 2. These heteronuclear vicinal coupling constants measured with {sup 13}C in natural abundance in conjunction with measured interproton NOE intensities indicate that these compounds share a common C8 ring backbone conformation.

  1. Quantitative measurement of water diffusion lifetimes at a protein/DNA interface by NMR

    International Nuclear Information System (INIS)

    Gruschus, James M.; Ferretti, James A.

    2001-01-01

    Hydration site lifetimes of slowly diffusing water molecules at the protein/DNA interface of the vnd/NK-2 homeodomain DNA complex were determined using novel three-dimensional NMR techniques. The lifetimes were calculated using the ratios of ROE and NOE cross-relaxation rates between the water and the protein backbone and side chain amides. This calculation of the lifetimes is based on a model of the spectral density function of the water-protein interaction consisting of three timescales of motion: fast vibrational/rotational motion, diffusion into/out of the hydration site, and overall macromolecular tumbling. The lifetimes measured ranged from approximately 400 ps to more than 5 ns, and nearly all the slowly diffusing water molecules detected lie at the protein/DNA interface. A quantitative analysis of relayed water cross-relaxation indicated that even at very short mixing times, 5 ms for ROESY and 12 ms for NOESY, relay of magnetization can make a small but detectable contribution to the measured rates. The temperature dependences of the NOE rates were measured to help discriminate direct dipolar cross-relaxation from chemical exchange. Comparison with several X-ray structures of homeodomain/DNA complexes reveals a strong correspondence between water molecules in conserved locations and the slowly diffusing water molecules detected by NMR. A homology model based on the X-ray structures was created to visualize the conserved water molecules detected at the vnd/NK-2 homeodomain DNA interface. Two chains of water molecules are seen at the right and left sides of the major groove, adjacent to the third helix of the homeodomain. Two water-mediated hydrogen bond bridges spanning the protein/DNA interface are present in the model, one between the backbone of Phe8 and a DNA phosphate, and one between the side chain of Asn51 and a DNA phosphate. The hydrogen bond bridge between Asn51 and the DNA might be especially important since the DNA contact made by the invariant

  2. Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil

    Science.gov (United States)

    2016-01-01

    The pathogenesis of Alzheimer’s disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ1–42 compared to that of Aβ1–40 are poorly understood. To explore in detail the structural propensity of the monomeric Aβ1–40 and Aβ1–42 peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ1–40 and Aβ1–42 peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JNCα, and 1JNCα) recorded for Aβ1–40 were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ1–42, suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process. PMID:26780756

  3. Advanced information processing system: The Army fault tolerant architecture conceptual study. Volume 2: Army fault tolerant architecture design and analysis

    Science.gov (United States)

    Harper, R. E.; Alger, L. S.; Babikyan, C. A.; Butler, B. P.; Friend, S. A.; Ganska, R. J.; Lala, J. H.; Masotto, T. K.; Meyer, A. J.; Morton, D. P.

    1992-01-01

    Described here is the Army Fault Tolerant Architecture (AFTA) hardware architecture and components and the operating system. The architectural and operational theory of the AFTA Fault Tolerant Data Bus is discussed. The test and maintenance strategy developed for use in fielded AFTA installations is presented. An approach to be used in reducing the probability of AFTA failure due to common mode faults is described. Analytical models for AFTA performance, reliability, availability, life cycle cost, weight, power, and volume are developed. An approach is presented for using VHSIC Hardware Description Language (VHDL) to describe and design AFTA's developmental hardware. A plan is described for verifying and validating key AFTA concepts during the Dem/Val phase. Analytical models and partial mission requirements are used to generate AFTA configurations for the TF/TA/NOE and Ground Vehicle missions.

  4. IRMA iterative relaxation matrix approach for NMR structure determination application to DNA fragments

    International Nuclear Information System (INIS)

    Koning, M.M.G.

    1990-01-01

    The subject of this thesis is the structure determination of DNA molecules in solution with the use of NMR. For this purpose a new relaxation matrix approach is introduced. The emphasis is on the interpretation of nuclear Overhauser effects (NOEs) in terms of proton-proton distances and related three dimensional structures. The DNA molecules studied are obligonucleotides, unmodifief as well as modified molecules bu UV radiation. From comparison with unmodified molecules it turned out that UV irradiation scarcely influences the helical structure of the DNA string. At one place of the string a nucleotide is rotated towards the high-ANTI conformation which results in a slight unwinding of the DNA string but sufficient for blocking of the normal reading of genetic information. (H.W.). 456 refs.; 50 figs.; 30 tabs

  5. Conformation of an Shc-derived phosphotyrosine-containing peptide complexed with the Grb2 SH2 domain

    International Nuclear Information System (INIS)

    Ogura, Kenji; Tsuchiya, Shigeo; Terasawa, Hiroaki; Yuzawa, Satoru; Hatanaka, Hideki; Mandiyan, Valsan; Schlessinger, Joseph; Inagaki, Fuyuhiko

    1997-01-01

    We have determined the structure of an Shc-derived phosphotyrosine-containing peptide complexed with Grb2 SH2 based on intra-and intermolecular NOE correlations observed by a series of isotope-filtered NMR experiments using a PFG z-filter. In contrast to an extended conformation of phosphotyrosine-containing peptides bound to Src, Syp and PLC γ SH2s, the Shc-derived peptide formed a turn at the +1 and +2 positions next to the phosphotyrosine residue. Trp 121 , located at the EF1 site of Grb2 SH2, blocked the peptide binding in an extended conformation. The present study confirms that each phosphotyrosine-containing peptide binds to the cognate SH2 with a specific conformation, which gives the structural basis for the binding specificity between SH2s and target proteins

  6. Cost structure and profitability of Assaf dairy sheep farms in Spain.

    Science.gov (United States)

    Milán, M J; Frendi, F; González-González, R; Caja, G

    2014-01-01

    Twenty dairy sheep farms of Assaf breed, located in the Spanish autonomous community of Castilla y León and included in a group receiving technical support, were used to study their production cost structure and to assess their economic profitability during 2009. On average, farms had 89.2±38.0 ha (own, 38%), 592±63 ewes, yielded 185.9±21.1×10(3) L/yr (i.e., 316±15 L/ewe), and were attended by 2.3±0.2 annual working units (family, 72%). Total annual income was €194.4±23.0×10(3)/yr (€1.0=$1.3) from milk (78.6%), lamb (13.2%), culled ewes (0.5%), and other sales (0.8%, wool and manure), and completed with the European Union sheep subsidy (6.9%). Total costs were €185.9±19.0×10(3)/yr to attend to feeding (61.6%), labor (18.2%), equipment maintenance and depreciation (7.6%), finances (3.0%), animal health (2.5%), energy, water and milking supplies (2.2%), milk recording (0.5%), and other costs (4.4%; assurances, shearing, association fees, and so on). Mean dairy sheep farm profit was €8.5±5.8×10(3)/yr (€7.4±8.3/ewe) on average, and varied between -€40.6 and €81.1/ewe among farms. Only 60% of farms were able to pay all costs, the rest had negative balances. Nevertheless, net margin was €31.0±6.5×10(3)/yr on average, varying between €0.6 and €108.4×10(3)/yr among farms. In this case, without including the opportunity costs, all farms had positive balances. Total annual cost (TAC; €/ewe) and total annual income (TAI; €/ewe) depended on milk yield (MY; L/ewe) and were TAC=161.6 + 0.502 MY (R(2)=0.50), and TAI=78.13 + 0.790 MY (R(2)=0.88), respectively, with the break-even point being 291 L/ewe. Conversely, farm TAC (€/yr) and farm TAI (€/yr) were also predicted as a function of the number of ewes (NOE) per flock, as TAC=18,401 + 282.8 NOE (R(2)=0.89) and TAI=330.9 NOE (R(2)=0.98), with the break-even point being 383 ewes/flock. Finally, according to the increasing trend expected for agricultural commodity prices, it was

  7. Sequence-specific 1H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

    International Nuclear Information System (INIS)

    Wittekind, M.; Klevit, R.E.; Reizer, J.

    1990-01-01

    On the basis of an analysis of two-dimensional 1 H NMR spectra, the complete sequence-specific 1 H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four β-strands that form a single antiparallel β-sheet and two well-defined α-helices. There are two stretches of extended backbone structure, one of which contains the active site His 15 . The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies

  8. Selective backbone labelling of ILV methyl labelled proteins

    International Nuclear Information System (INIS)

    Sibille, Nathalie; Hanoulle, Xavier; Bonachera, Fanny; Verdegem, Dries; Landrieu, Isabelle; Wieruszeski, Jean-Michel; Lippens, Guy

    2009-01-01

    Adding the 13 C labelled 2-keto-isovalerate and 2-oxobutanoate precursors to a minimal medium composed of 12 C labelled glucose instead of the commonly used ( 2 D, 13 C) glucose leads not only to the 13 C labelling of (I, L, V) methyls but also to the selective 13 C labelling of the backbone C α and CO carbons of the Ile and Val residues. As a result, the backbone ( 1 H, 15 N) correlations of the Ile and Val residues and their next neighbours in the (i + 1) position can be selectively identified in HN(CA) and HN(CO) planes. The availability of a selective HSQC spectrum corresponding to the sole amide resonances of the Ile and Val residues allows connecting them to their corresponding methyls by the intra-residue NOE effect, and should therefore be applicable to larger systems

  9. An antibacterial ortho-quinone diterpenoid and its derivatives from Caryopteris mongolica.

    Science.gov (United States)

    Saruul, Erdenebileg; Murata, Toshihiro; Selenge, Erdenechimeg; Sasaki, Kenroh; Yoshizaki, Fumihiko; Batkhuu, Javzan

    2015-06-15

    To identify antibacterial components in traditional Mongolian medicinal plant Caryopteris mongolica, an ortho-quinone abietane caryopteron A (1) and three its derivatives caryopteron B-D (2-4) were isolated from the roots of the plant together with three known abietanes demethylcryptojaponol (5), 6α-hydroxydemethyl cryptojaponol (6), and 14-deoxycoleon U (7). The chemical structures of these abietane derivatives were elucidated on the basis of spectroscopic data. Compounds 1-4 had C-13 methylcyclopropane substructures, and 2-4 had a hexanedioic anhydride ring C instead of ortho-quinone in 1. The stereochemistry of these compound was assumed from NOE spectra and ECD Cotton effects. Compounds 1 and 5-7 showed antibacterial activities against the Gram-positive bacteria Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, and Micrococcus luteus, being 1 the more potent. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. A molecular receptor selective for zwitterionic alanine.

    Science.gov (United States)

    Rubio, Omayra H; Taouil, Rachid; Muñiz, Francisco M; Monleón, Laura M; Simón, Luis; Sanz, Francisca; Morán, Joaquín R

    2017-01-04

    A molecular receptor has been synthesized joining an aza-crown ether with a chiral chromane which mimics the oxyanion hole of the enzymes. With this receptor an apolar host-guest complex with zwitterionic alanine has been achieved through the formation of up to seven H-bonds. This complex allows the extraction of aqueous alanine to a chloroform phase, while other natural amino acids are poorly extracted or are not extracted at all. Due to the chiral nature of the receptor, enantioselective extraction from the aqueous alanine solution to a chloroform phase takes place. X-Ray analysis combined with anisotropic effects, NOE and CD studies revealed the absolute configuration of both strong and weak complexes. Modelling studies also support the proposed structures. The presence of an oxyanion-hole motif in this structure was corroborated by X-ray diffraction studies.

  11. Mesodynamics in the SARS nucleocapsid measured by NMR field cycling

    Energy Technology Data Exchange (ETDEWEB)

    Clarkson, Michael W.; Lei Ming; Eisenmesser, Elan Z.; Labeikovsky, Wladimir [MS009 Brandeis University, Department of Biochemistry and Howard Hughes Medical Institute (United States); Redfield, Alfred [MS009 Brandeis University, Department of Biochemistry (United States)], E-mail: redfield@brandeis.edu; Kern, Dorothee [MS009 Brandeis University, Department of Biochemistry and Howard Hughes Medical Institute (United States)], E-mail: dkern@brandeis.edu

    2009-09-15

    Protein motions on all timescales faster than molecular tumbling are encoded in the spectral density. The dissection of complex protein dynamics is typically performed using relaxation rates determined at high and ultra-high field. Here we expand this range of the spectral density to low fields through field cycling using the nucleocapsid protein of the SARS coronavirus as a model system. The field-cycling approach enables site-specific measurements of R{sub 1} at low fields with the sensitivity and resolution of a high-field magnet. These data, together with high-field relaxation and heteronuclear NOE, provide evidence for correlated rigid-body motions of the entire {beta}-hairpin, and corresponding motions of adjacent loops with a time constant of 0.8 ns (mesodynamics). MD simulations substantiate these findings and provide direct verification of the time scale and collective nature of these motions.

  12. High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions

    International Nuclear Information System (INIS)

    Chou, Shanho; Flynn, P.; Wang, A.; Reid, B.

    1991-01-01

    Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(AACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3'-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3' end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1'-H2' J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2'-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but these results differ somewhat from previous theoretical model studies

  13. Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

    Science.gov (United States)

    Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

    2018-05-10

    Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

  14. The research strategy of the Swedish Nuclear Power Inspectorate

    International Nuclear Information System (INIS)

    2002-06-01

    such projects in future. Furthermore, in the safeguards area, important joint work is underway in ESARDA. Experience has shown that a prerequisite for taking advantage of international research and expertise is that activities on the national level should be of an adequate scope within each area. In SKI's opinion, the increased co-operation offers the possibility of gaining access to important research information at a relatively modest cost. In recent years, concerns have been expressed regarding the possibility of maintaining adequate strategic expertise in the nuclear field. To explore this issue, SKI has investigated the needs in the strategic expertise areas today and within a ten-year perspective. The investigation shows that the annual university recruitment need is a total of about 50 people within the strategic nuclear areas. In SKI's opinion, the education capacity in these areas is adequate at present and is assured for the foreseeable future as a result of the measures taken by SKI and the nuclear industry through the Swedish Nuclear Centre (SKC). There is also concern regarding expertise and resources for conducting qualified experiments. Over the past ten years, several of the world's research reactors and experimental facilities in thermohydraulics have been decommissioned. The OECD/NEA has therefore taken the initiative to support 'Centres of Excellence' (CoE), which are defined as international research groups associated with important experimental facilities. In parallel, within the Sixth Framework Programme, which is starting in 2003, the EU has used the term 'Networks of Excellence' (NoE), where the aim is to achieve co-operation between researchers within a specific research discipline. SKI has investigated the possibility of proposing a CoE in Sweden or of participating in NoE, in order to support important research conducted in Sweden. SKI sees a possibility that Studsvik's R2 reactor and the fuel experiments that can be conducted and analysed at

  15. International Conference eXtended Discretization MethodS

    CERN Document Server

    Benvenuti, Elena

    2016-01-01

    This book gathers selected contributions on emerging research work presented at the International Conference eXtended Discretization MethodS (X-DMS), held in Ferrara in September 2015. It highlights the most relevant advances made at the international level in the context of expanding classical discretization methods, like finite elements, to the numerical analysis of a variety of physical problems. The improvements are intended to achieve higher computational efficiency and to account for special features of the solution directly in the approximation space and/or in the discretization procedure. The methods described include, among others, partition of unity methods (meshfree, XFEM, GFEM), virtual element methods, fictitious domain methods, and special techniques for static and evolving interfaces. The uniting feature of all contributions is the direct link between computational methodologies and their application to different engineering areas.

  16. The EU Emissions Trading Scheme and Biomass. Final Report

    International Nuclear Information System (INIS)

    Schwaiger, H.; Tuerk, A.; Arasto, A.; Vehlow, J.; Kautto, N.; Sijm, J.; Hunder, M.; Brammer, J.

    2009-02-01

    Within its Energy and Climate Package, adopted by the European Parliament in December 2008, the European commission set a 10% minimum for the market share of renewables in the transport sector in 2020. To find the appropriate instruments to reach this target and the instrument mix with which biomass use in general could be best stimulated are the main questions of this project. An important instrument of the European Climate Policy is the European Emissions Trading Scheme (EU-ETS), which started operation in 2005. Previous work done within Bioenergy NoE showed that only a high share of auctioning of allowances and a high CO2 price provide necessary incentives for a higher biomass use. According to the Energy and Climate Package, all allowances will be auctioned in the energy sector from 2013 on, with exceptions for a few CEE countries. Based on work done within the project, a model has been developed to analyse at which CO2 price biomass becomes competitive in case of 100 per cent auctioning or at a lower level. The European Commission furthermore decided not to include the road transport sector into the EU-ETS until 2020. Whether the inclusion of the road transport sector in the EU-ETS, could help introducing biofuels, a separate trading scheme for biofuels should be set up, or biofuels should be addressed with other policy instruments, was another main question of this project. The first result shows that an integrated scheme would hardly have any effects on the use of liquid biofuels in the transportation sector, but might cause higher CO2 prices for the energy and industry sector. A separate trading scheme has been implemented in the UK in 2008, California is planning such as scheme in addition to include the road transport sector into the future ETS. Within this project the design of such as system has been elaborated based on the comparison of several policy instruments to increase the use of liquid biofuels in the transportation sector. Policy interaction

  17. Measurement of {sup 1}H-{sup 15}N and {sup 1}H-{sup 13}C residual dipolar couplings in nucleic acids from TROSY intensities

    Energy Technology Data Exchange (ETDEWEB)

    Ying Jinfa [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Wang Jinbu [National Cancer Institute, National Institutes of Health, Structural Biophysics Laboratory (United States); Grishaev, Alex [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Yu Ping; Wang Yunxing [National Cancer Institute, National Institutes of Health, Structural Biophysics Laboratory (United States); Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2011-09-15

    Analogous to the recently introduced ARTSY method for measurement of one-bond {sup 1}H-{sup 15}N residual dipolar couplings (RDCs) in large perdeuterated proteins, we introduce methods for measurement of base {sup 13}C-{sup 1}H and {sup 15}N-{sup 1}H RDCs in protonated nucleic acids. Measurements are based on quantitative analysis of intensities in {sup 1}H-{sup 15}N and {sup 13}C-{sup 1}H TROSY-HSQC spectra, and are illustrated for a 71-nucleotide adenine riboswitch. Results compare favorably with those of conventional frequency-based measurements in terms of completeness and convenience of use. The ARTSY method derives the size of the coupling from the ratio of intensities observed in two TROSY-HSQC spectra recorded with different dephasing delays, thereby minimizing potential resonance overlap problems. Precision of the RDC measurements is limited by the signal-to-noise ratio, S/N, achievable in the 2D TROSY-HSQC reference spectrum, and is approximately given by 30/(S/N) Hz for {sup 15}N-{sup 1}H and 65/(S/N) Hz for {sup 13}C-{sup 1}H. The signal-to-noise ratio of both {sup 1}H-{sup 15}N and {sup 1}H-{sup 13}C spectra greatly benefits when water magnetization during the experiments is not perturbed, such that rapid magnetization transfer from bulk water to the nucleic acid, mediated by rapid amino and hydroxyl hydrogen exchange coupled with {sup 1}H-{sup 1}H NOE transfer, allows for fast repetition of the experiment. RDCs in the mutated helix 1 of the riboswitch are compatible with nucleotide-specifically modeled, idealized A-form geometry and a static orientation relative to the helix 2/3 pair, which differs by ca 6 Degree-Sign relative to the X-ray structure of the native riboswitch.

  18. Transition Processes in Superconducting Magnetic Systems; ПЕРЕХОДНЫЕ ПРОЦЕССЫ В СВЕРХПРОВОДЯЩИХ МАГНИТНЫХ СИСТЕМАХ

    Energy Technology Data Exchange (ETDEWEB)

    Sychev, V. V.; Zenkevich, V. B.; Andrianov, V. V. [Nauchno-Issledovatel' skij Institut Vysokih Temperatur, Moskva, SSSR (Russian Federation)

    1966-12-15

    processami, svjazannymi s perehodom chasti obmotki v normal'noe sostojanie. V svjazi s jetim programma rabot po sozdaniju sverhprovodjashhej magnitnoj sistemy MGD generatora predusmatrivala issledovanie processov, v kotoryh ukazannaja specifika projavljaetsja naibolee polno. Jeksperimenty provodilis' s nebol'shimi solenoidami. Poluchennye rezul'taty vyjavljajut nekotorye zakonomernosti processa perehoda sverhprovodjashhej obmotki v normal'noe sostojanie. Issledovany takzhe processy, svjazannye s izmeneniem toka v sverhprovodjashhem solenoide. V chastnosti, jeksperimental'no opredeljalis' zavisimost' mezhdu potokoscepleniem solenoida i tokom, ostatochnoe potokosceplenie, svjaz' mezhdu induktivnost'ju i tokom, poteri pri peremagnichivanii solenoida i dr. Rassmatrivaetsja vozmozhnost' teoreticheskogo obob- shhenija poluchennyh rezul'tatov. (author)

  19. Glioblastoma (GBM) effects on quantitative MRI of contralateral normal appearing white matter.

    Science.gov (United States)

    Mehrabian, Hatef; Lam, Wilfred W; Myrehaug, Sten; Sahgal, Arjun; Stanisz, Greg J

    2018-03-28

    The objective was to investigate (with quantitative MRI) whether the normal appearing white matter (NAWM) of glioblastoma (GBM) patients on the contralateral side (cNAWM) was different from NAWM of healthy controls. Thirteen patients with newly diagnosed GBM and nine healthy age-matched controls were MRI-scanned with quantitative magnetization transfer (qMT), chemical exchange saturation transfer (CEST), and transverse relaxation time (T 2 )-mapping. MRI scans were performed after surgery and before chemo-radiation treatment. Comprehensive qMT, CEST, T 2 data were acquired. A two-pool MT model was fit to qMT data in transient state, to calculate MT model parameters [Formula: see text]. CEST signal was isolated by removing the contributions from the MT and direct water saturation, and CEST signal was calculated for Amide (CEST Amide ), Amine (CEST Amine ) and nuclear overhauser effect, NOE (CEST NOE ). There was no difference between GBM patients and normal controls in the qMT properties of the macromolecular pool [Formula: see text]. However, their free water pool spectrum was different (1/R a T 2a , patient  = 28.1 ± 3.9, 1/R a T 2a , control  = 25.0 ± 1.1, p = 0.03). This difference could be attributed to the difference in their T 2 time ([Formula: see text] = 83 ± 4, [Formula: see text] = 88 ± 1, p = 0.004). CEST signals were statistically significantly different with the CEST Amide having the largest difference between the two cohorts (CEST Amide,patient  = 2.8 ± 0.4, CEST Amide,control  = 3.4 ± 0.5, p = 0.009). CEST in cNAWM of GBM patients was lower than healthy controls which could be caused by modified brain metabolism due to tumor cell infiltration. There was no difference in MT properties of the patients and controls, however, the differences in free water pool properties were mainly due to reduced T 2 in cNAWM of the patients (resulting from structural changes and increased cellularity).

  20. NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-oxo-7H-dG(syn)·dA(anti) alignment at lesion site

    International Nuclear Information System (INIS)

    Kouchakdjian, M.; Patel, D.J.; Bodepudi, V.; Shibutani, S.; Eisenberg, M.; Johnson, F.; Grollman, A.P.

    1991-01-01

    Proton NMR studies are reported on the complementary d(C1-C2-A3-C4-T5-A6-oxo-G7-T8-C9-A10-C11-C12)·d(G13-G14-T15-G16-A17-A18-T19-A20-G21-T22-G23-G24) dodecanucleotide duplex (designated 8-oxo-7H-dG·dA 12-mer), which contains a centrally located 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) residue, a group commonly found in DNA that has been exposed to ionizing radiation or oxidizing free radicals. From the NMR spectra it can be deduced that this moiety exists as two tautomers, or gives rise to two DNA conformations, that are in equilibrium and that exchange slowly. The present study focuses on the major component of the equilibrium that originates in the 6,8-dioxo tautomer of 8-oxo-7H-dG. The authors have assigned the exchangeable NH1, NH7, and NH 2 -2 base protons located on the Watson-Crick and Hoogsteen edges of 8-oxo-7H-dG7 in the 8-oxo-7H-dG·dA 12-mer duplex, using an analysis of one- and two-dimensional nuclear Overhauser enhancement (NOE) data in H 2 O solution. They were able to detect a set of intra- and interstrand NOEs between protons (exchangeable and nonexchangeable) on adjacent residues in the d(A6-oxo-G7-T8)·d(A17-A18-T19) trinucleotide segment centered about the lesion site that establishes stacking of the oxo-dG7(syn)·dA(anti) pair between stable Watson-Crick dA6·dT19 and dT8·A17 base pairs with minimal perturbation of the helix. The structural studies demonstrate that 8-oxo-7H-dG(syn)·dA(anti) forms a stable pair in the interior of the helix, providing a basis for the observed incorporation of dA opposite 8-oxo-7H-dG when readthrough occurs past this oxidized nucleoside base

  1. Method

    Directory of Open Access Journals (Sweden)

    Ling Fiona W.M.

    2017-01-01

    Full Text Available Rapid prototyping of microchannel gain lots of attention from researchers along with the rapid development of microfluidic technology. The conventional methods carried few disadvantages such as high cost, time consuming, required high operating pressure and temperature and involve expertise in operating the equipment. In this work, new method adapting xurography method is introduced to replace the conventional method of fabrication of microchannels. The novelty in this study is replacing the adhesion film with clear plastic film which was used to cut the design of the microchannel as the material is more suitable for fabricating more complex microchannel design. The microchannel was then mold using polymethyldisiloxane (PDMS and bonded with a clean glass to produce a close microchannel. The microchannel produced had a clean edge indicating good master mold was produced using the cutting plotter and the bonding between the PDMS and glass was good where no leakage was observed. The materials used in this method is cheap and the total time consumed is less than 5 hours where this method is suitable for rapid prototyping of microchannel.

  2. Method Points: towards a metric for method complexity

    Directory of Open Access Journals (Sweden)

    Graham McLeod

    1998-11-01

    Full Text Available A metric for method complexity is proposed as an aid to choosing between competing methods, as well as in validating the effects of method integration or the products of method engineering work. It is based upon a generic method representation model previously developed by the author and adaptation of concepts used in the popular Function Point metric for system size. The proposed technique is illustrated by comparing two popular I.E. deliverables with counterparts in the object oriented Unified Modeling Language (UML. The paper recommends ways to improve the practical adoption of new methods.

  3. Identification and estimation ot carbohydrates using radioisotopic methods; Identification et dosage des hydrates de carbone a l'aide des radioisotopes; Identifikatsiya i opredelenie karbogidratov s pomoshch'yu radioizotopnykh metodov; Identificacion u valoracion de hidratos de carbono con ayuda de radioisotopos

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, G O; Criddle, W J [Department of Chemistry, University College, Cardiff (United Kingdom)

    1962-01-15

    Isotope-dilution methods have been developed to identify and estimate the small amount of products formed when carbohydrates are irradiated in aqueous solution with Co{sup 60} gamma-radiation. Conventional analytical methods proved inadequate. After irradiation of C{sup 14}-sugar solutions, the autoradiographs prepared after paper chromatography indicated extensive degradation. Using a reverse isotope-dilution procedure involving the addition of known carriers, and conversion of the fragments into crystalline derivatives, various constituents were quantitatively determined. It is possible to distinguish between d- and Z-isomers, and estimate each isomer independently. The method is applicable to other analytical problems in carbohydrate chemistry. A new method for scanning and recording the radioactivity along paper-chromatogram strips, which involves an inexpensive modification to conventional counting equipment, is described. (author) [French] On a mis au point des methodes de dilution isotopique destinees a identifier et a doser les menues quantites de produits qui se forment lorsque des hydrates de carbone en solution aqueuse sont irradies par les rayons gamma du cobalt-60. A cet egard, les methodes d'analyse classiques se sont revelees inadequates. Apres irradiation de solutions de sucre marque au carbone-14, les autoradiogrammes etablis a la suite d'une chromatographic sur papier indiquaient une forte degradation. En recourant a une methode de dilution isotopique inverse, avec adjonction d'entraineurs connus, et en operant une conversion des fragments en derives cristallins, on a pu determiner quantitativement plusieurs elements constitutifs. Il est possible de distinguer les isomeres dextrogyres des isomeres levogyres et de doser chaque isomere independamment. La methode peut etre appliquee a d'autres problemes d'analyse dans la chimie des hydrates de carbone. Le memoire decrit une nouvelle methode permettant d'explorer et d'enregistrer la radioactivite de

  4. A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data

    International Nuclear Information System (INIS)

    Spyracopoulos, Leo

    2006-01-01

    A suite of Mathematica notebooks has been designed to ease the analysis of protein main chain 15 N NMR relaxation data collected at a single magnetic field strength. Individual notebooks were developed to perform the following tasks: nonlinear fitting of 15 N-T 1 and -T 2 relaxation decays to a two parameter exponential decay, calculation of the principal components of the inertia tensor from protein structural coordinates, nonlinear optimization of the principal components and orientation of the axially symmetric rotational diffusion tensor, model-free analysis of 15 N-T 1 , -T 2 , and { 1 H}- 15 N NOE data, and reduced spectral density analysis of the relaxation data. The principle features of the notebooks include use of a minimal number of input files, integrated notebook data management, ease of use, cross-platform compatibility, automatic visualization of results and generation of high-quality graphics, and output of analyses in text format

  5. Conformational studies of human [15-2-aminohexanoic acid]little gastrin in sodium dodecyl sulfate micelles by 1H NMR

    International Nuclear Information System (INIS)

    Mammi, S.; Peggion, E.

    1990-01-01

    Human little gastrin is a 17 amino acid peptide that adopts a random conformation in water and an ordered structure in sodium dodecyl sulfate (SDS) micelles as well as in trifluoroethanol (TFE). The circular dichroism spectra in these two media have the same shape, indicative of a similar preferred conformation. The authors describe here the assignment of the proton NMR resonances and the conformational analysis of [Ahx 15 ] little gastrin in SDS micelles. Two-dimensional correlation techniques form the basis for the assignment. The conformational analysis utilizes NOE's, NH to C α H coupling constants, and the temperature coefficients of the amide chemical shifts. The NMR data indicate a helical structure in the N-terminal portion of the peptide. These results are compared with the conformation that the authors recently proposed for a minigastrin analogue (fragment 5-17 of [Ahx 15 ] little gastrin) in TFE

  6. Practical aspects of NMR signal assignment in larger and challenging proteins

    Science.gov (United States)

    Frueh, Dominique P.

    2014-01-01

    NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis techniques traditionally employed for resonance assignment and describes alternative protocols necessary for overcoming challenges in large protein spectra. In particular, simultaneous analysis of multiple spectra may help overcome ambiguities or may reveal correlations in an indirect manner. Similarly, visualization of orthogonal planes in a multidimensional spectrum can provide alternative assignment procedures. We describe examples of such strategies for assignment of backbone, methyl, and nOe resonances. We describe experimental aspects of data acquisition for the related experiments and provide guidelines for preliminary studies. Focus is placed on large folded monomeric proteins and examples are provided for 37, 48, 53, and 81 kDa proteins. PMID:24534088

  7. BDF-methods

    DEFF Research Database (Denmark)

    Hostrup, Astrid Kuijers

    1999-01-01

    An introduction to BDF-methods is given. The use of these methods on differential algebraic equations (DAE's) with different indexes with respect to order, stability and convergens of the BDF-methods is presented.......An introduction to BDF-methods is given. The use of these methods on differential algebraic equations (DAE's) with different indexes with respect to order, stability and convergens of the BDF-methods is presented....

  8. Methods for evaluating imaging methods of limited reproducibility

    International Nuclear Information System (INIS)

    Krummenauer, F.

    2005-01-01

    Just like new drugs, new or modified imaging methods must be subjected to objective clinical tests, including tests on humans. In this, it must be ensured that the principle of Good Clinical Practice (GCP) are followed with regard to medical, administrative and methodical quality. Innovative methods fo clinical epidemiology and medical biometry should be applied from the planning stage to the final statistical evaluation. The author presents established and new methods for planning, evaluation and reporting of clinical tests of diagnostic methods, and especially imaging methods, in clinical medicine and illustrates these by means of current research projects in the various medical disciplines. The strategies presented are summarized in a recommendation based on the concept of phases I - IV of clinical drug testing in order to enable standardisation of the clinical evaluation of imaging methods. (orig.)

  9. Distillation methods

    International Nuclear Information System (INIS)

    Konecny, C.

    1975-01-01

    Two main methods of separation using the distillation method are given and evaluated, namely evaporation and distillation in carrier gas flow. Two basic apparatus are described for illustrating the methods used. The use of the distillation method in radiochemistry is documented by a number of examples of the separation of elements in elemental state, volatile halogenides and oxides. Tables give a survey of distillation methods used for the separation of the individual elements and give conditions under which this separation takes place. The suitability of the use of distillation methods in radiochemistry is discussed with regard to other separation methods. (L.K.)

  10. Solution structure of the 45-residue MgATP-binding peptide of adenylate kinase as examined by 2-D NMR, FTIR, and CD spectroscopy

    International Nuclear Information System (INIS)

    Fry, D.C.; Byler, D.M.; Susi, H.; Brown, M.; Kuby, S.A.; Mildvan, A.S.

    1988-01-01

    The structure of a synthetic peptide corresponding to residues 1-45 of rabbit muscle adenylate kinase has been studied in aqueous solution by two-dimensional NMR, FTIR, and CD spectroscopy. This peptide, which binds MgATP and is believed to represent most of the MgATP-binding site of the enzyme, appears to maintain a conformation similar to that of residues 1-45 in the X-ray structure of intact porcine adenylate kinase, with 42% of the residues of the peptide showing NOEs indicative of phi and psi angles corresponding to those found in the protein. The NMR studies suggest that the peptide is composed of two helical regions of residues 4-7 and 23-29, and three stretches of β-strand at residues 8-15, 30-32, and 35-40, yielding an overall secondary structure consisting of 24% α-helix, 38% β-structure, and 38% aperiodic. Although the resolution-enhanced amide I band of the peptide FTIR spectrum is broad and rather featureless, possible due to disorder, it can be fit by using methods developed on well-characterized globular proteins. The CD spectrum is best fit by assuming the presence of at most 13% α-helix in the peptide, 24 +/- 2% β-structure, and 66 +/- 4% aperiodic. The inability of the high-frequency FTIR and CD methods to detect helices in the amount found by NMR may result from the short helical lengths as well as from static and dynamic disorder in the peptide. Upon binding of MgATP, numerous conformation changes in the backbone of the peptide are detected by NMR, with smaller alterations in the overall secondary structure as assess by CD

  11. Hybrid-hybrid matrix structural refinement of a DNA three-way junction from 3D NOESY-NOESY

    International Nuclear Information System (INIS)

    Thiviyanathan, Varatharasa; Luxon, Bruce A.; Leontis, Neocles B.; Illangasekare, Nishantha; Donne, David G.; Gorenstein, David G.

    1999-01-01

    Homonuclear 3D NOESY-NOESY has shown great promise for the structural refinement of large biomolecules. A computationally efficient hybrid-hybrid relaxation matrix refinement methodology, using 3D NOESY-NOESY data, was used to refine the structure of a DNA three-way junction having two unpaired bases at the branch point of the junction. The NMR data and the relaxation matrix refinement confirm that the DNA three-way junction exists in a folded conformation with two of the helical stems stacked upon each other. The third unstacked stem extends away from the junction, forming an acute angle (∼60 deg.) with the stacked stems. The two unpaired bases are stacked upon each other and are exposed to the solvent. Helical parameters for the bases in all three strands show slight deviations from typical values expected for right-handed B-form DNA. Inter-nucleotide imino-imino NOEs between the bases at the branch point of the junction show that the junction region is well defined. The helical stems show mobility (± 20 deg.) indicating dynamic processes around the junction region. The unstacked helical stem adjacent to the unpaired bases shows greater mobility compared to the other two stems. The results from this study indicate that the 3D hybrid-hybrid matrix MORASS refinement methodology, by combining the spectral dispersion of 3D NOESY-NOESY and the computational efficiency of 2D refinement programs, provides an accurate and robust means for structure determination of large biomolecules. Our results also indicate that the 3D MORASS method gives higher quality structures compared to the 2D complete relaxation matrix refinement method

  12. Mining Method

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Young Shik; Lee, Kyung Woon; Kim, Oak Hwan; Kim, Dae Kyung [Korea Institute of Geology Mining and Materials, Taejon (Korea, Republic of)

    1996-12-01

    The reducing coal market has been enforcing the coal industry to make exceptional rationalization and restructuring efforts since the end of the eighties. To the competition from crude oil and natural gas has been added the growing pressure from rising wages and rising production cost as the workings get deeper. To improve the competitive position of the coal mines against oil and gas through cost reduction, studies to improve mining system have been carried out. To find fields requiring improvements most, the technologies using in Tae Bak Colliery which was selected one of long running mines were investigated and analyzed. The mining method appeared the field needing improvements most to reduce the production cost. The present method, so-called inseam roadway caving method presently is using to extract the steep and thick seam. However, this method has several drawbacks. To solve the problems, two mining methods are suggested for a long term and short term method respectively. Inseam roadway caving method with long-hole blasting method is a variety of the present inseam roadway caving method modified by replacing timber sets with steel arch sets and the shovel loaders with chain conveyors. And long hole blasting is introduced to promote caving. And pillar caving method with chock supports method uses chock supports setting in the cross-cut from the hanging wall to the footwall. Two single chain conveyors are needed. One is installed in front of chock supports to clear coal from the cutting face. The other is installed behind the supports to transport caved coal from behind. This method is superior to the previous one in terms of safety from water-inrushes, production rate and productivity. The only drawback is that it needs more investment. (author). 14 tabs., 34 figs.

  13. Perturbation methods

    CERN Document Server

    Nayfeh, Ali H

    2008-01-01

    1. Introduction 1 2. Straightforward Expansions and Sources of Nonuniformity 23 3. The Method of Strained Coordinates 56 4. The Methods of Matched and Composite Asymptotic Expansions 110 5. Variation of Parameters and Methods of Averaging 159 6. The Method of Multiple Scales 228 7. Asymptotic Solutions of Linear Equations 308 References and Author Index 387 Subject Index 417

  14. Rearrangement of the distal pocket accompanying E7 His → Gln substitution in elephant carbonmonoxy- and oxymyoglobin: 1H NMR identification of a new aromatic residue in the heme pocket

    International Nuclear Information System (INIS)

    Yu, L.P.; La Mar, G.N.; Mizukami, H.

    1990-01-01

    Two-dimensional 1 H NMR methods have been used to assign side-chain resonances for the residues in the distal heme pocket of elephant carbonmonoxymyoglobin (MbCO) and oxymyoglobin (MbO 2 ). It is shown that, while the other residues in the heme pocket are minimally perturbed, the Phe CD4 residue in elephant MbCO and MbO 2 resonates considerably upfield compared to the corresponding residue in sperm whale MbCO. The new NOE connectivities to Val E11 and heme-induced ring current calculations indicate that Phe CD4 has been inserted into the distal heme pocket by reorienting the aromatic side chain and moving the CD corner closer to the heme. The CζH proton of the Phe CD4 was found to move toward the iron of the heme by ∼4 angstrom relative to the position in sperm whale MbCO, requiring minimally a 3-angstrom movement of the CD helical backbone. The significantly altered distal conformation in elephant myoglobin, rather than the single distal E7 substitution, forms a plausible basis for its altered functional properties of lower autoxidation rate, higher redox potential, and increased affinity for CO ligand. These results demonstrate that one-to-one interpretation of amino acid residue substitution (E7 His → Gln) is oversimplified and that conformational changes of substituted proteins which are not readily predicted have to be considered for interpretation of their functional properties

  15. A Novel Polygonal Finite Element Method: Virtual Node Method

    Science.gov (United States)

    Tang, X. H.; Zheng, C.; Zhang, J. H.

    2010-05-01

    Polygonal finite element method (PFEM), which can construct shape functions on polygonal elements, provides greater flexibility in mesh generation. However, the non-polynomial form of traditional PFEM, such as Wachspress method and Mean Value method, leads to inexact numerical integration. Since the integration technique for non-polynomial functions is immature. To overcome this shortcoming, a great number of integration points have to be used to obtain sufficiently exact results, which increases computational cost. In this paper, a novel polygonal finite element method is proposed and called as virtual node method (VNM). The features of present method can be list as: (1) It is a PFEM with polynomial form. Thereby, Hammer integral and Gauss integral can be naturally used to obtain exact numerical integration; (2) Shape functions of VNM satisfy all the requirements of finite element method. To test the performance of VNM, intensive numerical tests are carried out. It found that, in standard patch test, VNM can achieve significantly better results than Wachspress method and Mean Value method. Moreover, it is observed that VNM can achieve better results than triangular 3-node elements in the accuracy test.

  16. Method Engineering: Engineering of Information Systems Development Methods and Tools

    NARCIS (Netherlands)

    Brinkkemper, J.N.; Brinkkemper, Sjaak

    1996-01-01

    This paper proposes the term method engineering for the research field of the construction of information systems development methods and tools. Some research issues in method engineering are identified. One major research topic in method engineering is discussed in depth: situational methods, i.e.

  17. Enhancing the (MSLDIP) image steganographic method (ESLDIP method)

    Science.gov (United States)

    Seddik Saad, Al-hussien

    2011-10-01

    Message transmissions over the Internet still have data security problem. Therefore, secure and secret communication methods are needed for transmitting messages over the Internet. Cryptography scrambles the message so that it cannot be understood. However, it makes the message suspicious enough to attract eavesdropper's attention. Steganography hides the secret message within other innocuous-looking cover files (i.e. images, music and video files) so that it cannot be observed [1].The term steganography originates from the Greek root words "steganos'' and "graphein'' which literally mean "covered writing''. It is defined as the science that involves communicating secret data in an appropriate multimedia carrier, e.g., image, audio text and video files [3].Steganographic techniques allow one party to communicate information to another without a third party even knowing that the communication is occurring. The ways to deliver these "secret messages" vary greatly [3].Our proposed method called Enhanced SLDIP (ESLDIP). In which the maximmum hiding capacity (MHC) of proposed ESLDIP method is higher than the previously proposed MSLDIP methods and the PSNR of the ESLDIP method is higher than the MSLDIP PSNR values', which means that the image quality of the ESLDIP method will be better than MSLDIP method and the maximmum hiding capacity (MHC) also improved. The rest of this paper is organized as follows. In section 2, steganography has been discussed; lingo, carriers and types. In section 3, related works are introduced. In section 4, the proposed method will be discussed in details. In section 5, the simulation results are given and Section 6 concludes the paper.

  18. Method Engineering: Engineering of Information Systems Development Methods and Tools

    OpenAIRE

    Brinkkemper, J.N.; Brinkkemper, Sjaak

    1996-01-01

    This paper proposes the term method engineering for the research field of the construction of information systems development methods and tools. Some research issues in method engineering are identified. One major research topic in method engineering is discussed in depth: situational methods, i.e. the configuration of a project approach that is tuned to the project at hand. A language and support tool for the engineering of situational methods are discussed.

  19. Numerical Methods for Stochastic Computations A Spectral Method Approach

    CERN Document Server

    Xiu, Dongbin

    2010-01-01

    The first graduate-level textbook to focus on fundamental aspects of numerical methods for stochastic computations, this book describes the class of numerical methods based on generalized polynomial chaos (gPC). These fast, efficient, and accurate methods are an extension of the classical spectral methods of high-dimensional random spaces. Designed to simulate complex systems subject to random inputs, these methods are widely used in many areas of computer science and engineering. The book introduces polynomial approximation theory and probability theory; describes the basic theory of gPC meth

  20. Mining method selection by integrated AHP and PROMETHEE method.

    Science.gov (United States)

    Bogdanovic, Dejan; Nikolic, Djordje; Ilic, Ivana

    2012-03-01

    Selecting the best mining method among many alternatives is a multicriteria decision making problem. The aim of this paper is to demonstrate the implementation of an integrated approach that employs AHP and PROMETHEE together for selecting the most suitable mining method for the "Coka Marin" underground mine in Serbia. The related problem includes five possible mining methods and eleven criteria to evaluate them. Criteria are accurately chosen in order to cover the most important parameters that impact on the mining method selection, such as geological and geotechnical properties, economic parameters and geographical factors. The AHP is used to analyze the structure of the mining method selection problem and to determine weights of the criteria, and PROMETHEE method is used to obtain the final ranking and to make a sensitivity analysis by changing the weights. The results have shown that the proposed integrated method can be successfully used in solving mining engineering problems.

  1. An E-learning Tool as Living Book for Knowledge Preservation in Neutron Activation Analysis

    International Nuclear Information System (INIS)

    Bode, P.; Landsberger, S.; Ridikas, D.; Iunikova, A.

    2016-01-01

    Full text: Neutron activation analysis (NAA) is one of the most common activities in research reactors, irrespective of their power size. Although being a well-established technique, it has been observed that retirement and/or departure of experienced staff often results in gaps in knowledge of methodological principles and metrological aspects of the NAA technique employed, both within the remaining NAA team and for new recruits. Existing books are apparently not sufficient to timely transfer the knowledge on the practice of NAA. As such, the IAEA has launched a project resulting in an E-learning tool for NAA, consisting of lecture noes, animations, practical exercises and self-assessments. The tool includes more than 30 modules and has been reviewed and tested during an IAEA workshop by experienced and new coming practitioners. It is expected that the tool will be developed as a ‘living book’ which can be permanently updated and extended and serve as an archive, fostering unpublished experimental experiences. (author

  2. Fluctuating partially native-like topologies in the acid denatured ensemble of autolysis resistant HIV-1 protease.

    Science.gov (United States)

    Rout, Manoj Kumar; Hosur, Ramakrishna V

    2009-02-01

    Folding, in-vivo, starts from a denatured state and thus the nature of the denatured state would play an important role in directing the folding of a protein. We report here NMR characterization of the acid-denatured state of a mutant of HIV-1 protease, designed to prevent autolysis (Q7K, L33I, L63I) and to prevent cysteine oxidation (C67A and C95A). Secondary chemical shifts, TALOS analysis of chemical shifts and (15)N relaxation data (R(1), R(2), NOE) coupled with AABUF and hydrophobicity calculations, suggest formation of hydrophobic clusters and possibility of some partially native-like topologies in the acid denatured state of the protease. The structural and dynamics characteristics of the acid denatured PR seem to be considerably different from those of the guanidine or urea denatured states of some variants of PR. These would have implications for the folding and auto-processing of the enzyme in-vivo.

  3. Ungdom med innvandringsbakgrunn etter overgangen til videregående opplæring – tapte nettverk og svekket skoletrivsel?

    Directory of Open Access Journals (Sweden)

    Kristinn Hegna

    2014-10-01

    Full Text Available Nylig publisert forskning har vist at de sosioøkonomiske forskjellene i ungdomsskolekarakterer har økt noe etter at Kunnskapsløftet ble innført i 2006/2007. Denne artikkelen undersøker om det samme har skjedd i Oslo – landets eneste virkelige storby med betydelig sosial ulikhet og en særskilt stor andel innvandrere. På tross av slike trekk får Oslos ungdomsskoleelever litt bedre gjennomsnittskarakterer enn landsgjennomsnittet, og «Oslo-forspranget» har økt de siste årene. På midten av 2000-tallet var karakterforskjellene mellom «høy» og «lav» sosioøkonomisk familiebakgrunn mindre i Oslo enn i resten av landet, men etter at Kunnskapsløftet ble innført, er det ikke lenger slik. I 2010/2011 var den sosiale ulikheten i eksamenskarakterer den samme i Oslo som i resten av landet. I artikkelen diskuterer vi forskjellige årsaker til at ulikhetene i skolen øker.

  4. Structural Biology in the context of EGEE

    CERN Document Server

    García, D; Carazo, J M; Valverde, J R; Moscicki, J; Muraru, A

    2007-01-01

    Electron microscopy (EM) is a crucial technique, which allows Structural Biology researchers to characterize macromolecular assemblies in distinct functional states. Image processing in three dimensional EM (3D-EM) is used by a flourishing community (exemplarized by the EU funded 3D-EM NoE) and is characterized by voluminous data and large computing requirements, making this a problem well suited for Grid computing and the EGEE infrastructure. There are various steps in the 3D-EM refinement process that may benefit from Grid computing. To start with, large numbers of experimental images need to be averaged. Nowadays, typically tens of thousands of images are used, while future studies may routinely employ millions of images. Our group has been developing Xmipp, a package for single-particle 3D-EM image processing. Using Xmipp, the classification of 91,000 ribosome projections into 4 classes took more than 2500 CPU hours using the resources of the MareNostrum supercomputer at the Barcelona Supercomputing Centr...

  5. Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance {sup 13}C NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Daley, Margaret E.; Sykes, Brian D. [University of Alberta, Department of Biochemistry, CIHR Group in Protein Structure and Function and Protein Engineering Network of Centres of Excellence (Canada)

    2004-06-15

    The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance {sup 13}C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible for conferring its ability to bind crystalline ice and inhibit its growth. Heteronuclear longitudinal and transverse relaxation rates and the {sup 1}H-{sup 13}C NOE were determined in this study. The C{alpha}H relaxation measurements were compared to the previously measured {sup 15}N backbone parameters and these are found to be in agreement. For the analysis of the threonine side chain motions, the model of restricted rotational diffusion about the {chi}{sub 1} dihedral angle was employed [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. We demonstrate that the motion experienced by the ice binding threonine side chains is highly restricted, with an approximate upper limit of less than {+-}25 deg.

  6. Characterization of threonine side chain dynamics in an antifreeze protein using natural abundance 13C NMR spectroscopy

    International Nuclear Information System (INIS)

    Daley, Margaret E.; Sykes, Brian D.

    2004-01-01

    The dynamics of threonine side chains of the Tenebrio molitor antifreeze protein (TmAFP) were investigated using natural abundance 13 C NMR. In TmAFP, the array of threonine residues on one face of the protein is responsible for conferring its ability to bind crystalline ice and inhibit its growth. Heteronuclear longitudinal and transverse relaxation rates and the 1 H- 13 C NOE were determined in this study. The CαH relaxation measurements were compared to the previously measured 15 N backbone parameters and these are found to be in agreement. For the analysis of the threonine side chain motions, the model of restricted rotational diffusion about the χ 1 dihedral angle was employed [London and Avitabile (1978) J. Am. Chem. Soc., 100, 7159-7165]. We demonstrate that the motion experienced by the ice binding threonine side chains is highly restricted, with an approximate upper limit of less than ±25 deg

  7. 1H NMR of High-Potential Iron-Sulfur Protein from the Purple Non-Sulfur Bacterium Rhodoferax fermentans

    DEFF Research Database (Denmark)

    Ciurli, Stefano; Cremonini, Mauro Andrea; Kofod, Pauli

    1996-01-01

    residues bound to the [4Fe-4S]3+/2+ cluster have been performed using one-dimensional NOE and exchange spectroscopy experiments. 1H-NMR hyperfine shifts and relaxation rates of cluster-bound Cys β-CH2 protons indicate that in the [4Fe-4S]3+ cluster one iron ion can be formally described as Fe(III), while......Oxidized and reduced forms of high-potential iron-sulfur protein (HiPIP) from the purple non-sulfur photosynthetic bacterium Rhodoferux fermentans have been characterized using 1H-NMR spectroscopy. Pairwise and sequence-specific assignments of hyperfine-shifted 1H-NMR signals to protons of cysteine...... longitudinal relaxation rates of Cys β-CH2 protons in HiPIPs from six different sources as a function of the Fe-S-Cβ-Cα dihedral angle, indicate that the major contribution is due to a dipolar metal-centered mechanism, with a non-negligeable contribution from a ligand-centered dipolar mechanism which involves...

  8. Solution structure of the Grb2 SH2 domain complexed with a high-affinity inhibitor

    International Nuclear Information System (INIS)

    Ogura, Kenji; Shiga, Takanori; Yokochi, Masashi; Yuzawa, Satoru; Burke, Terrence R.; Inagaki, Fuyuhiko

    2008-01-01

    The solution structure of the growth factor receptor-bound protein 2 (Grb2) SH2 domain complexed with a high-affinity inhibitor containing a non-phosphorus phosphate mimetic within a macrocyclic platform was determined by nuclear magnetic resonance (NMR) spectroscopy. Unambiguous assignments of the bound inhibitor and intermolecular NOEs between the Grb2 SH2 domain and the inhibitor was accomplished using perdeuterated Grb2 SH2 protein. The well-defined solution structure of the complex was obtained and compared to those by X-ray crystallography. Since the crystal structure of the Grb2 SH2 domain formed a domain-swapped dimer and several inhibitors were bound to a hinge region, there were appreciable differences between the solution and crystal structures. Based on the binding interactions between the inhibitor and the Grb2 SH2 domain in solution, we proposed a design of second-generation inhibitors that could be expected to have higher affinity

  9. Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

    International Nuclear Information System (INIS)

    Zuiderweg, E.R.P.; Fesik, S.W.

    1989-01-01

    The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of 1 H and 15 N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with 15 N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the 15 N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that 15 N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques

  10. Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a

    Energy Technology Data Exchange (ETDEWEB)

    Zuiderweg, E.R.P.; Fesik, S.W. (Abbott Laboratories, Abbott Park, IL (USA))

    1989-03-21

    The utility of three-dimensional heteronuclear NMR spectroscopy for the assignment of {sup 1}H and {sup 15}N resonances of the inflammatory protein C5a (MW 8500), uniformly labeled with {sup 15}N, is demonstrated at a protein concentration of 0.7 mM. It is shown that dramatic simplification of the 2D nuclear Overhauser effect spectrum (NOESY) is obtained by editing with respect to the frequency of the {sup 15}N heteronucleus in a third dimension. The improved resolution in the 3D experiment largely facilitates the assignment of protein NMR spectra and allows for the determination of distance constraints from otherwise overlapping NOE cross peaks for purposes of 3D structure determination. The results show that {sup 15}N heteronuclear 3D NMR can facilitate the structure determination of small proteins and promises to be a useful tool for the study of larger systems that cannot be studied by conventional 2D NMR techniques.

  11. CGI delay compensation. [Computer Generated Image

    Science.gov (United States)

    Mcfarland, R. E.

    1986-01-01

    Computer-generated graphics in real-time helicopter simulation produces objectionable scene-presentation time delays. In the flight simulation laboratory at Ames Research Center, it has been determined that these delays have an adverse influence on pilot performance during agressive tasks such as nap of the earth (NOE) maneuvers. Using contemporary equipment, computer generated image (CGI) time delays are an unavoidable consequence of the operations required for scene generation. However, providing that magnitude distortions at higher frequencies are tolerable, delay compensation is possible over a restricted frequency range. This range, assumed to have an upper limit of perhaps 10 or 15 rad/sec, conforms approximately to the bandwidth associated with helicopter handling qualities research. A compensation algorithm is introduced here and evaluated in terms of tradeoffs in frequency responses. The algorithm has a discrete basis and accommodates both a large, constant transport delay interval and a periodic delay interval, as associated with asynchronous operations.

  12. MDN-0170, a New Napyradiomycin from Streptomyces sp. Strain CA-271078

    Directory of Open Access Journals (Sweden)

    Rodney Lacret

    2016-10-01

    Full Text Available A new napyradiomycin, MDN-0170 (1, was isolated from the culture broth of the marine-derived actinomycete strain CA-271078, together with three known related compounds identified as 4-dehydro-4a-dechloronapyradiomycin A1 (2, napyradiomycin A1 (3 and 3-chloro-6,8-dihydroxy-8-α-lapachone (4. The structure of the new compound was determined using a combination of spectroscopic techniques, including 1D and 2D NMR and electrospray-time of flight mass spectrometry (ESI-TOF MS. The relative configuration of compound 1, which contains two independent stereoclusters, has been established by molecular modelling in combination with nOe and coupling constant analyses. Biosynthetic arguments also allowed us to propose its absolute stereochemistry. The antimicrobial properties of the compounds isolated were evaluated against methicillin-resistant Staphylococcus aureus (MRSA, Escherichia coli, Aspergillus fumigatus, and Candida albicans. The potent bioactivity previously reported for compounds 2 and 3 against methicillin-sensitive S. aureus has been extended to methicillin-resistant strains in this report.

  13. DNA hairpin structures in solution: 500-MHz two-dimensional 1H NMR studies on d(CGCCGCAGC) and d(CGCCGTAGC)

    International Nuclear Information System (INIS)

    Gupta, G.; Sarma, M.H.; Sarma, R.H.

    1987-01-01

    A hairpin structure contains two conformationally distinct domains: a double-helical stem with Watson-Crick base pairs and a single-stranded loop that connects the two arms of the stem. By extensive 1D and 2D 500-MHz 1 H NMR studies in H 2 O and D 2 O, it has been demonstrated that the DNA oligomers d(CGCCGCAGC) and d(CGCCGTAGC) form hairpin structures under conditions of low concentration, 0.5 mM in DNA strand, and low salt (20 mM NaCl, pH 7). From examination of the nuclear Overhauser effect (NOE) between base protons H8/H6 and sugar protons H1' and H2'/H2'', it was concluded that in D(CGCCGCAGC) and d(CGCCCTAGC) all the nine nucleotides display average (C2'-endo,anti) geometry. The NMR data in conjunction with molecular model building and solvent accessibility studies were used to derive a working model for the hairpins

  14. Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction.

    Science.gov (United States)

    Markowitz, Joseph; Chen, Ijen; Gitti, Rossi; Baldisseri, Donna M; Pan, Yongping; Udan, Ryan; Carrier, France; MacKerell, Alexander D; Weber, David J

    2004-10-07

    The binding of S100B to p53 down-regulates wild-type p53 tumor suppressor activity in cancer cells such as malignant melanoma, so a search for small molecules that bind S100B and prevent S100B-p53 complex formation was undertaken. Chemical databases were computationally searched for potential inhibitors of S100B, and 60 compounds were selected for testing on the basis of energy scoring, commercial availability, and chemical similarity clustering. Seven of these compounds bound to S100B as determined by steady state fluorescence spectroscopy (1.0 microM model of one such inhibitor, pentamidine, bound to Ca(2+)-loaded S100B was calculated using intermolecular NOE data between S100B and the drug, and indicates that pentamidine binds into the p53 binding site on S100B defined by helices 3 and 4 and loop 2 (termed the hinge region).

  15. MDN-0170, a New Napyradiomycin from Streptomyces sp. Strain CA-271078

    Science.gov (United States)

    Lacret, Rodney; Pérez-Victoria, Ignacio; Oves-Costales, Daniel; de la Cruz, Mercedes; Domingo, Elizabeth; Martín, Jesús; Díaz, Caridad; Vicente, Francisca; Genilloud, Olga; Reyes, Fernando

    2016-01-01

    A new napyradiomycin, MDN-0170 (1), was isolated from the culture broth of the marine-derived actinomycete strain CA-271078, together with three known related compounds identified as 4-dehydro-4a-dechloronapyradiomycin A1 (2), napyradiomycin A1 (3) and 3-chloro-6,8-dihydroxy-8-α-lapachone (4). The structure of the new compound was determined using a combination of spectroscopic techniques, including 1D and 2D NMR and electrospray-time of flight mass spectrometry (ESI-TOF MS). The relative configuration of compound 1, which contains two independent stereoclusters, has been established by molecular modelling in combination with nOe and coupling constant analyses. Biosynthetic arguments also allowed us to propose its absolute stereochemistry. The antimicrobial properties of the compounds isolated were evaluated against methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli, Aspergillus fumigatus, and Candida albicans. The potent bioactivity previously reported for compounds 2 and 3 against methicillin-sensitive S. aureus has been extended to methicillin-resistant strains in this report. PMID:27763545

  16. NMR characterization of the DNA binding properties of a novel Hoechst 33258 analogue peptide building block

    DEFF Research Database (Denmark)

    Bunkenborg, Jakob; Behrens, Carsten; Jacobsen, Jens Peter

    2002-01-01

    A novel aryl-bis-benzimidazole amino acid analogue of the DNA-binding compound Hoechst 33258 has recently been designed for incorporation in peptide combinatorial libraries by replacing the N-methylpiperazine group with a carboxyl group and the hydroxy group with an amino-methyl group. The DNA......-binding properties of the aryl-bis-benzimidazole monomer with the C-terminus derivatized with 3-(dimethylamino)-propylamine has been investigated in this paper by (1)H NMR studies of two different complexes with two different DNA sequences: A(5) d(5'-GCCA(5)CG-3'):d(5'-CGT(5)GGC-3') and A(3)T(3) d(5'-CGA(3)T(3)CG-3...... preference with the bis-benzimidazole moiety displaced toward the 3'-end from the center of the duplex. Two families of models of the complexes with A(5) and A(3)T(3) were derived with restrained molecular dynamics based on a large set of 70 and 61, respectively, intermolecular ligand NOEs. Both models give...

  17. A Pattern-Oriented Approach to a Methodical Evaluation of Modeling Methods

    Directory of Open Access Journals (Sweden)

    Michael Amberg

    1996-11-01

    Full Text Available The paper describes a pattern-oriented approach to evaluate modeling methods and to compare various methods with each other from a methodical viewpoint. A specific set of principles (the patterns is defined by investigating the notations and the documentation of comparable modeling methods. Each principle helps to examine some parts of the methods from a specific point of view. All principles together lead to an overall picture of the method under examination. First the core ("method neutral" meaning of each principle is described. Then the methods are examined regarding the principle. Afterwards the method specific interpretations are compared with each other and with the core meaning of the principle. By this procedure, the strengths and weaknesses of modeling methods regarding methodical aspects are identified. The principles are described uniformly using a principle description template according to descriptions of object oriented design patterns. The approach is demonstrated by evaluating a business process modeling method.

  18. Maintenance methods

    International Nuclear Information System (INIS)

    Sanchis, H.; Aucher, P.

    1990-01-01

    The maintenance method applied at the Hague is summarized. The method was developed in order to solve problems relating to: the different specialist fields, the need for homogeneity in the maintenance work, the equipment diversity, the increase of the materials used at the Hague's new facilities. The aim of the method is to create a knowhow formalism, to facilitate maintenance, to ensure the running of the operations and to improve the estimation of the maintenance cost. One of the method's difficulties is the demonstration of the profitability of the maintenance operations [fr

  19. BASIC METHODS OF CLASSIFICATION AND CHARACTERISTICS OF METHODS OF PRICING IN UKRAINE

    Directory of Open Access Journals (Sweden)

    A. Boguslavskiy

    2014-12-01

    Full Text Available The article provided definitions and shows the need to use different methods of pricing of enterprises. Exposed the reasons of the absence of a universal classification of pricing methods. The approaches of different authors to classify groups of pricing methods: 1 the cost method; 2 methods with a focus on competition; 3 methods for pricing based on demand, 4 pricing with a focus on maximum profit, 5 parametric methods, 6 pricing under risk and uncertainty, etc. An improved classification pricing methods with the release of the following groups: 1 the methods of cost pricing; 2 methods based on demand; 3 methods, based on competition; 4 microeconomic methods; 5 methods which are based on product life cycles; 6 methods, depending on economic conditions; 7 econometric and statistical techniques 8 Methods of transfer pricing; 9 methods in accordance with the terms of agreements; 10 Methods of assortment pricing; 11 combined methods of pricing and so on. The basic directions of use of combined methods of pricing and analysis of their possible use in Ukraine are shown.

  20. Comparative law as method and the method of comparative law

    NARCIS (Netherlands)

    Hage, J.C.; Adams, M.; Heirbaut, D.

    2014-01-01

    This article addresses both the justificatory role of comparative law within legal research (comparative law as method) and the method of comparative law itself. In this connection two questions will be answered: 1. Is comparative law a method, or a set of methods, for legal research? 2. Does

  1. Safety training for working youth: Methods used versus methods wanted.

    Science.gov (United States)

    Zierold, Kristina M

    2016-04-07

    Safety training is promoted as a tool to prevent workplace injury; however, little is known about the safety training experiences young workers get on-the-job. Furthermore, nothing is known about what methods they think would be the most helpful for learning about safe work practices. To compare safety training methods teens get on the job to those safety training methods teens think would be the best for learning workplace safety, focusing on age differences. A cross-sectional survey was administered to students in two large high schools in spring 2011. Seventy percent of working youth received safety training. The top training methods that youth reported getting at work were safety videos (42%), safety lectures (25%), and safety posters/signs (22%). In comparison to the safety training methods used, the top methods youth wanted included videos (54%), hands-on (47%), and on-the-job demonstrations (34%). This study demonstrated that there were differences in training methods that youth wanted by age; with older youth seemingly wanting more independent methods of training and younger teens wanting more involvement. Results indicate that youth want methods of safety training that are different from what they are getting on the job. The differences in methods wanted by age may aid in developing training programs appropriate for the developmental level of working youth.

  2. The Monte Carlo method the method of statistical trials

    CERN Document Server

    Shreider, YuA

    1966-01-01

    The Monte Carlo Method: The Method of Statistical Trials is a systematic account of the fundamental concepts and techniques of the Monte Carlo method, together with its range of applications. Some of these applications include the computation of definite integrals, neutron physics, and in the investigation of servicing processes. This volume is comprised of seven chapters and begins with an overview of the basic features of the Monte Carlo method and typical examples of its application to simple problems in computational mathematics. The next chapter examines the computation of multi-dimensio

  3. Catalysts, methods of making catalysts, and methods of use

    KAUST Repository

    Renard, Laetitia; El Eter, Mohamad; Caps, Valerie; Basset, Jean-Marie

    2014-01-01

    Embodiments of the present disclosure provide for catalysts, methods of making catalysts, methods of using catalysts, and the like. In an embodiment, the method of making the catalysts can be performed in a single step with a metal nanoparticle precursor and a metal oxide precursor, where a separate stabilizing agent is not needed.

  4. Catalysts, methods of making catalysts, and methods of use

    KAUST Repository

    Renard, Laetitia

    2014-03-06

    Embodiments of the present disclosure provide for catalysts, methods of making catalysts, methods of using catalysts, and the like. In an embodiment, the method of making the catalysts can be performed in a single step with a metal nanoparticle precursor and a metal oxide precursor, where a separate stabilizing agent is not needed.

  5. A comparison of Ki-67 counting methods in luminal Breast Cancer: The Average Method vs. the Hot Spot Method.

    Science.gov (United States)

    Jang, Min Hye; Kim, Hyun Jung; Chung, Yul Ri; Lee, Yangkyu; Park, So Yeon

    2017-01-01

    In spite of the usefulness of the Ki-67 labeling index (LI) as a prognostic and predictive marker in breast cancer, its clinical application remains limited due to variability in its measurement and the absence of a standard method of interpretation. This study was designed to compare the two methods of assessing Ki-67 LI: the average method vs. the hot spot method and thus to determine which method is more appropriate in predicting prognosis of luminal/HER2-negative breast cancers. Ki-67 LIs were calculated by direct counting of three representative areas of 493 luminal/HER2-negative breast cancers using the two methods. We calculated the differences in the Ki-67 LIs (ΔKi-67) between the two methods and the ratio of the Ki-67 LIs (H/A ratio) of the two methods. In addition, we compared the performance of the Ki-67 LIs obtained by the two methods as prognostic markers. ΔKi-67 ranged from 0.01% to 33.3% and the H/A ratio ranged from 1.0 to 2.6. Based on the receiver operating characteristic curve method, the predictive powers of the KI-67 LI measured by the two methods were similar (Area under curve: hot spot method, 0.711; average method, 0.700). In multivariate analysis, high Ki-67 LI based on either method was an independent poor prognostic factor, along with high T stage and node metastasis. However, in repeated counts, the hot spot method did not consistently classify tumors into high vs. low Ki-67 LI groups. In conclusion, both the average and hot spot method of evaluating Ki-67 LI have good predictive performances for tumor recurrence in luminal/HER2-negative breast cancers. However, we recommend using the average method for the present because of its greater reproducibility.

  6. A comparison of Ki-67 counting methods in luminal Breast Cancer: The Average Method vs. the Hot Spot Method.

    Directory of Open Access Journals (Sweden)

    Min Hye Jang

    Full Text Available In spite of the usefulness of the Ki-67 labeling index (LI as a prognostic and predictive marker in breast cancer, its clinical application remains limited due to variability in its measurement and the absence of a standard method of interpretation. This study was designed to compare the two methods of assessing Ki-67 LI: the average method vs. the hot spot method and thus to determine which method is more appropriate in predicting prognosis of luminal/HER2-negative breast cancers. Ki-67 LIs were calculated by direct counting of three representative areas of 493 luminal/HER2-negative breast cancers using the two methods. We calculated the differences in the Ki-67 LIs (ΔKi-67 between the two methods and the ratio of the Ki-67 LIs (H/A ratio of the two methods. In addition, we compared the performance of the Ki-67 LIs obtained by the two methods as prognostic markers. ΔKi-67 ranged from 0.01% to 33.3% and the H/A ratio ranged from 1.0 to 2.6. Based on the receiver operating characteristic curve method, the predictive powers of the KI-67 LI measured by the two methods were similar (Area under curve: hot spot method, 0.711; average method, 0.700. In multivariate analysis, high Ki-67 LI based on either method was an independent poor prognostic factor, along with high T stage and node metastasis. However, in repeated counts, the hot spot method did not consistently classify tumors into high vs. low Ki-67 LI groups. In conclusion, both the average and hot spot method of evaluating Ki-67 LI have good predictive performances for tumor recurrence in luminal/HER2-negative breast cancers. However, we recommend using the average method for the present because of its greater reproducibility.

  7. Radiochemistry methods in DOE methods for evaluating environmental and waste management samples

    International Nuclear Information System (INIS)

    Fadeff, S.K.; Goheen, S.C.

    1994-08-01

    Current standard sources of radiochemistry methods are often inappropriate for use in evaluating US Department of Energy environmental and waste management (DOE/EW) samples. Examples of current sources include EPA, ASTM, Standard Methods for the Examination of Water and Wastewater and HASL-300. Applicability of these methods is limited to specific matrices (usually water), radiation levels (usually environmental levels), and analytes (limited number). Radiochemistry methods in DOE Methods for Evaluating Environmental and Waste Management Samples (DOE Methods) attempt to fill the applicability gap that exists between standard methods and those needed for DOE/EM activities. The Radiochemistry chapter in DOE Methods includes an ''analysis and reporting'' guidance section as well as radiochemistry methods. A basis for identifying the DOE/EM radiochemistry needs is discussed. Within this needs framework, the applicability of standard methods and targeted new methods is identified. Sources of new methods (consolidated methods from DOE laboratories and submissions from individuals) and the methods review process will be discussed. The processes involved in generating consolidated methods add editing individually submitted methods will be compared. DOE Methods is a living document and continues to expand by adding various kinds of methods. Radiochemistry methods are highlighted in this paper. DOE Methods is intended to be a resource for methods applicable to DOE/EM problems. Although it is intended to support DOE, the guidance and methods are not necessarily exclusive to DOE. The document is available at no cost through the Laboratory Management Division of DOE, Office of Technology Development

  8. METHODS IN THE POST-METHODS ERA. REPORT ON AN INTERNATIONAL SURVEY ON LANGUAGE TEACHING METHODS'

    Directory of Open Access Journals (Sweden)

    Jun Liu

    2004-06-01

    Full Text Available Do methods still have a place in 21" century language teaching? To answer this question, an international survey was conducted in the surnmer of 1999. A sample of 800 language teachers world-wide randomly drawn from 17,800 TESOLers were each given a 2-page survey. The return rate was 58.5% with the actual usable data set of448, which was analyzed by using both descriptive and inferential statistics. Among the ten commonly recognized teaching methods surveyed, both the Communicative Language Teaching Approach and an eclectic method seem to have the highest rate in familiarity, preference, and use. But when multiple factors, such as teaching contexts, instructional settings, learners' proficiency levels, class size, teaching experience and educational backgrounds of the teachers, and the status of being a native or nonnative English speaking professional were taken into consideration, various patterns and themes emerged. One interesting finding is that Grammar Translation is still used in EFL contexts, in larger classes, and with learners at low proficiency levels, though the ratio between the actual use of this method and teachers' preference does not match. Based on the results of the survey, a new theoretical framework is proposed to conceptualize language teaching methods in the post-methods era.

  9. A nodal method based on matrix-response method

    International Nuclear Information System (INIS)

    Rocamora Junior, F.D.; Menezes, A.

    1982-01-01

    A nodal method based in the matrix-response method, is presented, and its application to spatial gradient problems, such as those that exist in fast reactors, near the core - blanket interface, is investigated. (E.G.) [pt

  10. Detection of the sulfhydryl groups in proteins with slow hydrogen exchange rates and determination of their proton/deuteron fractionation factors using the deuterium-induced effects on the 13C(beta) NMR signals.

    Science.gov (United States)

    Takeda, Mitsuhiro; Jee, JunGoo; Terauchi, Tsutomu; Kainosho, Masatsune

    2010-05-05

    A method for identifying cysteine (Cys) residues with sulfhydryl (SH) groups exhibiting slow hydrogen exchange rates has been developed for proteins in aqueous media. The method utilizes the isotope shifts of the C(beta) chemical shifts induced by the deuteration of the SH groups. The 18.2 kDa E. coli peptidyl prolyl cis-trans isomerase b (EPPIb), which was selectively labeled with [3-(13)C;3,3-(2)H(2)]Cys, showed much narrower line widths for the (13)C(beta) NMR signals, as compared to those of the proteins labeled with either [3-(13)C]Cys or (3R)-[3-(13)C;3-(2)H]Cys. The (13)C(beta) signals of the two Cys residues of EPPIb, i.e. Cys-31 and Cys-121, labeled with [3-(13)C;3,3-(2)H(2)]Cys, split into four signals in H(2)O/D(2)O (1:1) at 40 degrees C and pH 7.5, indicating that the exchange rates of the side-chain SH's and the backbone amides are too slow to average the chemical shift differences of the (13)C(beta) signals, due to the two- and three-bond isotope shifts. By virtue of the well-separated signals, the proton/deuteron fractional factors for both the SH and amide groups of the two Cys residues in EPPIb could be directly determined, as approximately 0.4-0.5 for [SD]/[SH] and 0.9-1.0 for [ND]/[NH], by the relative intensities of the NMR signals for the isotopomers. The proton NOE's of the two slowly exchanging SH's were clearly identified in the NOESY spectra and were useful for the determining the local structure of EPPIb around the Cys residues.

  11. A Monte Carlo method and finite volume method coupled optical simulation method for parabolic trough solar collectors

    International Nuclear Information System (INIS)

    Liang, Hongbo; Fan, Man; You, Shijun; Zheng, Wandong; Zhang, Huan; Ye, Tianzhen; Zheng, Xuejing

    2017-01-01

    Highlights: •Four optical models for parabolic trough solar collectors were compared in detail. •Characteristics of Monte Carlo Method and Finite Volume Method were discussed. •A novel method was presented combining advantages of different models. •The method was suited to optical analysis of collectors with different geometries. •A new kind of cavity receiver was simulated depending on the novel method. -- Abstract: The PTC (parabolic trough solar collector) is widely used for space heating, heat-driven refrigeration, solar power, etc. The concentrated solar radiation is the only energy source for a PTC, thus its optical performance significantly affects the collector efficiency. In this study, four different optical models were constructed, validated and compared in detail. On this basis, a novel coupled method was presented by combining advantages of these models, which was suited to carry out a mass of optical simulations of collectors with different geometrical parameters rapidly and accurately. Based on these simulation results, the optimal configuration of a collector with highest efficiency can be determined. Thus, this method was useful for collector optimization and design. In the four models, MCM (Monte Carlo Method) and FVM (Finite Volume Method) were used to initialize photons distribution, as well as CPEM (Change Photon Energy Method) and MCM were adopted to describe the process of reflecting, transmitting and absorbing. For simulating reflection, transmission and absorption, CPEM was more efficient than MCM, so it was utilized in the coupled method. For photons distribution initialization, FVM saved running time and computation effort, whereas it needed suitable grid configuration. MCM only required a total number of rays for simulation, whereas it needed higher computing cost and its results fluctuated in multiple runs. In the novel coupled method, the grid configuration for FVM was optimized according to the “true values” from MCM of

  12. Projection Methods

    DEFF Research Database (Denmark)

    Wagner, Falko Jens; Poulsen, Mikael Zebbelin

    1999-01-01

    When trying to solve a DAE problem of high index with more traditional methods, it often causes instability in some of the variables, and finally leads to breakdown of convergence and integration of the solution. This is nicely shown in [ESF98, p. 152 ff.].This chapter will introduce projection...... methods as a way of handling these special problems. It is assumed that we have methods for solving normal ODE systems and index-1 systems....

  13. Method Mixins

    DEFF Research Database (Denmark)

    Ernst, Erik

    2005-01-01

    The world of programming has been conquered by the procedure call mechanism, including object-oriented method invocation which is a procedure call in context of an object. This paper presents an alternative, method mixin invocations, that is optimized for flexible creation of composite behavior, ...... the call stack, e.g., to a callee's callee. The mechanism has been implemented in the programming language gbeta. Variants of the mechanism could be added to almost any imperative programming language.......The world of programming has been conquered by the procedure call mechanism, including object-oriented method invocation which is a procedure call in context of an object. This paper presents an alternative, method mixin invocations, that is optimized for flexible creation of composite behavior...

  14. Eesti SMEAR-jaama andmete kasutus jätkusuutliku biomassi tootmise jälgimisel / Steffen M. Noe, Alisa Krasnova, Dmitri Krasnov, Ahto Kangur

    Index Scriptorium Estoniae

    2015-01-01

    Atmosfääri ja biosfääri vastastikuse mõju uurimise jaama SMEAR-i abil on võimalik seirata ja pikaajaliselt koguda andmeid metsaökosüsteemi süsinikuringet mõjutavate tunnuste kohta erinevatel ökosüsteemi tasanditel ja suure mõõtmissagedusega

  15. Development of signal processing electronics for self powered neutron detector signal with built-in on-line insulation monitoring [Paper No.:E3

    International Nuclear Information System (INIS)

    Das, Amitabha; Chaganty, S.P.

    1993-01-01

    Self powered neutron detectors (SPNDs) are employed to monitor in-core neutron flux in nuclear reactors for control, safety and mapping of in-core neutron flux. The d.c. current produced by SPND is converted into a proportional d.c. voltage, which in turn is used for various purposes stated above. This paper describes various features of the SPND amplifier developed in the Electronics Division of Bhabha Atomic Research Centre (BARC). It also outlines the principle of working of on-line monitoring of insulation resistance (IR) of the detector and associated mineral insulated (MI) and soft cables. The amplifier generates an alarm in case of the IR of the detector and the cable assembly falls below an accepted value or the cable is not connected to the amplifier and relieves the operator from periodic and manual checking of each of the individual detectors and ensures the validity of the signal for further processing. (author). 3 figs

  16. Mimetic discretization methods

    CERN Document Server

    Castillo, Jose E

    2013-01-01

    To help solve physical and engineering problems, mimetic or compatible algebraic discretization methods employ discrete constructs to mimic the continuous identities and theorems found in vector calculus. Mimetic Discretization Methods focuses on the recent mimetic discretization method co-developed by the first author. Based on the Castillo-Grone operators, this simple mimetic discretization method is invariably valid for spatial dimensions no greater than three. The book also presents a numerical method for obtaining corresponding discrete operators that mimic the continuum differential and

  17. Discipline methods

    OpenAIRE

    Maria Kikila; Ioannis Koutelekos

    2012-01-01

    Child discipline is one of the most important elements of successful parenting. As discipline is defined the process that help children to learn appropriate behaviors and make good choices. Aim: The aim of the present study was to review the literature about the discipline methods. The method οf this study included bibliography research from both the review and the research literature, mainly in the pubmed data base which referred to the discipline methods. Results: In the literature it is ci...

  18. Method Mixins

    DEFF Research Database (Denmark)

    Ernst, Erik

    2002-01-01

    invocation is optimized for as-is reuse of existing behavior. Tight coupling reduces flexibility, and traditional invocation tightly couples transfer of information and transfer of control. Method mixins decouple these two kinds of transfer, thereby opening the doors for new kinds of abstraction and reuse......The procedure call mechanism has conquered the world of programming, with object-oriented method invocation being a procedure call in context of an object. This paper presents an alternative, method mixin invocations, that is optimized for flexible creation of composite behavior, where traditional....... Method mixins use shared name spaces to transfer information between caller and callee, as opposed to traditional invocation which uses parameters and returned results. This relieves a caller from dependencies on the callee, and it allows direct transfer of information further down the call stack, e...

  19. BASIC METHODS OF CLASSIFICATION AND CHARACTERISTICS OF METHODS OF PRICING IN UKRAINE

    OpenAIRE

    A. Boguslavskiy

    2014-01-01

    The article provided definitions and shows the need to use different methods of pricing of enterprises. Exposed the reasons of the absence of a universal classification of pricing methods. The approaches of different authors to classify groups of pricing methods: 1) the cost method; 2) methods with a focus on competition; 3) methods for pricing based on demand, 4) pricing with a focus on maximum profit, 5) parametric methods, 6) pricing under risk and uncertainty, etc. An improved classificat...

  20. Compositions, antibodies, asthma diagnosis methods, and methods for preparing antibodies

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Hongjun; Zangar, Richard C.

    2017-01-17

    Methods for preparing an antibody are provided with the method including incorporating 3-bromo-4-hydroxy-benzoic acid into a protein to form an antigen, immunizing a mammalian host with the antigen, and recovering an antibody having an affinity for the antigen from the host. Antibodies having a binding affinity for a monohalotyrosine are provided as well as composition comprising an antibody bound with monohalotyrosine. Compositions comprising a protein having a 3-bromo-4-hydroxy-benzoic acid moiety are also provided. Methods for evaluating the severity of asthma are provide with the methods including analyzing sputum of a patient using an antibody having a binding affinity for monohalotyrosine, and measuring the amount of antibody bound to protein. Methods for determining eosinophil activity in bodily fluid are also provided with the methods including exposing bodily fluid to an antibody having a binding affinity for monohalotyrosine, and measuring the amount of bound antibody to determine the eosinophil activity.

  1. User interface inspection methods a user-centered design method

    CERN Document Server

    Wilson, Chauncey

    2014-01-01

    User Interface Inspection Methods succinctly covers five inspection methods: heuristic evaluation, perspective-based user interface inspection, cognitive walkthrough, pluralistic walkthrough, and formal usability inspections. Heuristic evaluation is perhaps the best-known inspection method, requiring a group of evaluators to review a product against a set of general principles. The perspective-based user interface inspection is based on the principle that different perspectives will find different problems in a user interface. In the related persona-based inspection, colleagues assume the

  2. galerkin's methods

    African Journals Online (AJOL)

    user

    The assumed deflection shapes used in the approximate methods such as in the Galerkin's method were normally ... to direct compressive forces Nx, was derived by Navier. [3]. ..... tend to give higher frequency and stiffness, as well as.

  3. Radiometric dating methods

    International Nuclear Information System (INIS)

    Bourdon, B.

    2003-01-01

    The general principle of isotope dating methods is based on the presence of radioactive isotopes in the geologic or archaeological object to be dated. The decay with time of these isotopes is used to determine the 'zero' time corresponding to the event to be dated. This paper recalls the general principle of isotope dating methods (bases, analytical methods, validation of results and uncertainties) and presents the methods based on natural radioactivity (Rb-Sr, Sm-Nd, U-Pb, Re-Os, K-Ar (Ar-Ar), U-Th-Ra- 210 Pb, U-Pa, 14 C, 36 Cl, 10 Be) and the methods based on artificial radioactivity with their applications. Finally, the methods based on irradiation damages (thermoluminescence, fission tracks, electron spin resonance) are briefly evoked. (J.S.)

  4. Method Mixins

    DEFF Research Database (Denmark)

    Ernst, Erik

    2002-01-01

    . Method mixins use shared name spaces to transfer information between caller and callee, as opposed to traditional invocation which uses parameters and returned results. This relieves a caller from dependencies on the callee, and it allows direct transfer of information further down the call stack, e......The procedure call mechanism has conquered the world of programming, with object-oriented method invocation being a procedure call in context of an object. This paper presents an alternative, method mixin invocations, that is optimized for flexible creation of composite behavior, where traditional...

  5. The Value of Mixed Methods Research: A Mixed Methods Study

    Science.gov (United States)

    McKim, Courtney A.

    2017-01-01

    The purpose of this explanatory mixed methods study was to examine the perceived value of mixed methods research for graduate students. The quantitative phase was an experiment examining the effect of a passage's methodology on students' perceived value. Results indicated students scored the mixed methods passage as more valuable than those who…

  6. Nondestructive testing method

    International Nuclear Information System (INIS)

    Porter, J.F.

    1996-01-01

    Nondestructive testing (NDT) is the use of physical and chemical methods for evaluating material integrity without impairing its intended usefulness or continuing service. Nondestructive tests are used by manufaturer's for the following reasons: 1) to ensure product reliability; 2) to prevent accidents and save human lives; 3) to aid in better product design; 4) to control manufacturing processes; and 5) to maintain a uniform quality level. Nondestructive testing is used extensively on power plants, oil and chemical refineries, offshore oil rigs and pipeline (NDT can even be conducted underwater), welds on tanks, boilers, pressure vessels and heat exchengers. NDT is now being used for testing concrete and composite materials. Because of the criticality of its application, NDT should be performed and the results evaluated by qualified personnel. There are five basic nondestructive examination methods: 1) liquid penetrant testing - method used for detecting surface flaws in materials. This method can be used for metallic and nonmetallic materials, portable and relatively inexpensive. 2) magnetic particle testing - method used to detect surface and subsurface flaws in ferromagnetic materials; 3) radiographic testing - method used to detect internal flaws and significant variation in material composition and thickness; 4) ultrasonic testing - method used to detect internal and external flaws in materials. This method uses ultrasonics to measure thickness of a material or to examine the internal structure for discontinuities. 5) eddy current testing - method used to detect surface and subsurface flaws in conductive materials. Not one nondestructive examination method can find all discontinuities in all of the materials capable of being tested. The most important consideration is for the specifier of the test to be familiar with the test method and its applicability to the type and geometry of the material and the flaws to be detected

  7. Mapping Mixed Methods Research: Methods, Measures, and Meaning

    Science.gov (United States)

    Wheeldon, J.

    2010-01-01

    This article explores how concept maps and mind maps can be used as data collection tools in mixed methods research to combine the clarity of quantitative counts with the nuance of qualitative reflections. Based on more traditional mixed methods approaches, this article details how the use of pre/post concept maps can be used to design qualitative…

  8. DOE methods compendium

    International Nuclear Information System (INIS)

    Leasure, C.S.

    1992-01-01

    The Department of Energy (DOE) has established an analytical methods compendium development program to integrate its environmental analytical methods. This program is administered through DOE's Laboratory Management Division (EM-563). The primary objective of this program is to assemble a compendium of analytical chemistry methods of known performance for use by all DOE Environmental Restoration and Waste Management program. This compendium will include methods for sampling, field screening, fixed analytical laboratory and mobile analytical laboratory analyses. It will also include specific guidance on the proper selection of appropriate sampling and analytical methods in using specific analytical requirements

  9. The preconditioned Gauss-Seidel method faster than the SOR method

    Science.gov (United States)

    Niki, Hiroshi; Kohno, Toshiyuki; Morimoto, Munenori

    2008-09-01

    In recent years, a number of preconditioners have been applied to linear systems [A.D. Gunawardena, S.K. Jain, L. Snyder, Modified iterative methods for consistent linear systems, Linear Algebra Appl. 154-156 (1991) 123-143; T. Kohno, H. Kotakemori, H. Niki, M. Usui, Improving modified Gauss-Seidel method for Z-matrices, Linear Algebra Appl. 267 (1997) 113-123; H. Kotakemori, K. Harada, M. Morimoto, H. Niki, A comparison theorem for the iterative method with the preconditioner (I+Smax), J. Comput. Appl. Math. 145 (2002) 373-378; H. Kotakemori, H. Niki, N. Okamoto, Accelerated iteration method for Z-matrices, J. Comput. Appl. Math. 75 (1996) 87-97; M. Usui, H. Niki, T.Kohno, Adaptive Gauss-Seidel method for linear systems, Internat. J. Comput. Math. 51(1994)119-125 [10

  10. Methods of evaluating SPECT images. The usefulness of the Matsuda`s method by the Patlak plot method in children

    Energy Technology Data Exchange (ETDEWEB)

    Takaishi, Yasuko [Nippon Medical School, Tokyo (Japan); Hashimoto, Kiyoshi; Fujino, Osamu [and others

    1998-11-01

    Single photon emission computed tomography (SPECT) is a tool to study cerebral blood flow (CBF) kinetics. There are three methods of evaluating SPECT images: visual, semi-quantitative (evaluation of the radioactivity ratio of the cerebral region to the cerebellum (R/CE) or to the thalamus (R/TH)) and quantitative (Matsuda`s method by Patlak plot method using {sup 99m}Tc-hexamethylpropylene amine oxime radionuclide angiography). We evaluated SPECT images by the quantitative method in 14 patients with neurological disorders and examined the correlation of the results to those obtained by the semi-quantitative method. There was no significant correlation between the R/CE or R/TH ratio and regional CBF except two regions. The evaluation by the semi-quantitative method may have been inappropriate, probably because the cerebellar or thalamic blood flow was not constant in each case. Evaluation by the quantitative method, on the other hand, seemed to be useful not only for the comparison of CBF among normal subjects, but also in the demonstration of progressive changes of CBF in the same case. The Matsuda`s method by the Patlak plot method is suitable for examination of children, since it dose not require aortic blood sampling. (author)

  11. Purity-activity relationships of natural products: the case of anti-TB active ursolic acid.

    Science.gov (United States)

    Jaki, Birgit U; Franzblau, Scott G; Chadwick, Lucas R; Lankin, David C; Zhang, Fangqiu; Wang, Yuehong; Pauli, Guido F

    2008-10-01

    The present study explores the variability of biological responses from the perspective of sample purity and introduces the concept of purity-activity relationships (PARs) in natural product research. The abundant plant triterpene ursolic acid (1) was selected as an exemplary natural product due to the overwhelming number yet inconsistent nature of its approximate 120 reported biological activities, which include anti-TB potential. Nine different samples of ursolic acid with purity certifications were obtained, and their purity was independently assessed by means of quantitative 1H NMR (qHNMR). Biological evaluation consisted of determining MICs against two strains of virulent Mycobacterium tuberculosis and IC50 values in Vero cells. Ab initio structure elucidation provided unequivocal structural confirmation and included an extensive 1H NMR spin system analysis, determination of nearly all J couplings and the complete NOE pattern, and led to the revision of earlier reports. As a net result, a sigmoid PAR profile of 1 was obtained, demonstrating the inverse correlation of purity and anti-TB bioactivity. The results imply that synergistic effects of 1 and its varying impurities are the likely cause of previously reported antimycobacterial potential. Generating PARs is a powerful extension of the routinely performed quantitative correlation of structure and activity ([Q]SAR). Advanced by the use of primary analytical methods such as qHNMR, PARs enable the elucidation of cases like 1 when increasing purity voids biological activity. This underlines the potential of PARs as a tool in drug discovery and synergy research and accentuates the need to routinely combine biological testing with purity assessment.

  12. Protein proton-proton dynamics from amide proton spin flip rates

    International Nuclear Information System (INIS)

    Weaver, Daniel S.; Zuiderweg, Erik R. P.

    2009-01-01

    Residue-specific amide proton spin-flip rates K were measured for peptide-free and peptide-bound calmodulin. K approximates the sum of NOE build-up rates between the amide proton and all other protons. This work outlines the theory of multi-proton relaxation, cross relaxation and cross correlation, and how to approximate it with a simple model based on a variable number of equidistant protons. This model is used to extract the sums of K-rates from the experimental data. Error in K is estimated using bootstrap methodology. We define a parameter Q as the ratio of experimental K-rates to theoretical K-rates, where the theoretical K-rates are computed from atomic coordinates. Q is 1 in the case of no local motion, but decreases to values as low as 0.5 with increasing domination of sidechain protons of the same residue to the amide proton flips. This establishes Q as a monotonous measure of local dynamics of the proton network surrounding the amide protons. The method is applied to the study of proton dynamics in Ca 2+ -saturated calmodulin, both free in solution and bound to smMLCK peptide. The mean Q is 0.81 ± 0.02 for free calmodulin and 0.88 ± 0.02 for peptide-bound calmodulin. This novel methodology thus reveals the presence of significant interproton disorder in this protein, while the increase in Q indicates rigidification of the proton network upon peptide binding, confirming the known high entropic cost of this process

  13. Transport equation solving methods

    International Nuclear Information System (INIS)

    Granjean, P.M.

    1984-06-01

    This work is mainly devoted to Csub(N) and Fsub(N) methods. CN method: starting from a lemma stated by Placzek, an equivalence is established between two problems: the first one is defined in a finite medium bounded by a surface S, the second one is defined in the whole space. In the first problem the angular flux on the surface S is shown to be the solution of an integral equation. This equation is solved by Galerkin's method. The Csub(N) method is applied here to one-velocity problems: in plane geometry, slab albedo and transmission with Rayleigh scattering, calculation of the extrapolation length; in cylindrical geometry, albedo and extrapolation length calculation with linear scattering. Fsub(N) method: the basic integral transport equation of the Csub(N) method is integrated on Case's elementary distributions; another integral transport equation is obtained: this equation is solved by a collocation method. The plane problems solved by the Csub(N) method are also solved by the Fsub(N) method. The Fsub(N) method is extended to any polynomial scattering law. Some simple spherical problems are also studied. Chandrasekhar's method, collision probability method, Case's method are presented for comparison with Csub(N) and Fsub(N) methods. This comparison shows the respective advantages of the two methods: a) fast convergence and possible extension to various geometries for Csub(N) method; b) easy calculations and easy extension to polynomial scattering for Fsub(N) method [fr

  14. Ensemble Methods

    Science.gov (United States)

    Re, Matteo; Valentini, Giorgio

    2012-03-01

    Ensemble methods are statistical and computational learning procedures reminiscent of the human social learning behavior of seeking several opinions before making any crucial decision. The idea of combining the opinions of different "experts" to obtain an overall “ensemble” decision is rooted in our culture at least from the classical age of ancient Greece, and it has been formalized during the Enlightenment with the Condorcet Jury Theorem[45]), which proved that the judgment of a committee is superior to those of individuals, provided the individuals have reasonable competence. Ensembles are sets of learning machines that combine in some way their decisions, or their learning algorithms, or different views of data, or other specific characteristics to obtain more reliable and more accurate predictions in supervised and unsupervised learning problems [48,116]. A simple example is represented by the majority vote ensemble, by which the decisions of different learning machines are combined, and the class that receives the majority of “votes” (i.e., the class predicted by the majority of the learning machines) is the class predicted by the overall ensemble [158]. In the literature, a plethora of terms other than ensembles has been used, such as fusion, combination, aggregation, and committee, to indicate sets of learning machines that work together to solve a machine learning problem [19,40,56,66,99,108,123], but in this chapter we maintain the term ensemble in its widest meaning, in order to include the whole range of combination methods. Nowadays, ensemble methods represent one of the main current research lines in machine learning [48,116], and the interest of the research community on ensemble methods is witnessed by conferences and workshops specifically devoted to ensembles, first of all the multiple classifier systems (MCS) conference organized by Roli, Kittler, Windeatt, and other researchers of this area [14,62,85,149,173]. Several theories have been

  15. Performative Schizoid Method

    DEFF Research Database (Denmark)

    Svabo, Connie

    2016-01-01

    is presented and an example is provided of a first exploratory engagement with it. The method is used in a specific project Becoming Iris, making inquiry into arts-based knowledge creation during a three month visiting scholarship at a small, independent visual art academy. Using the performative schizoid......A performative schizoid method is developed as a method contribution to performance as research. The method is inspired by contemporary research in the human and social sciences urging experimentation and researcher engagement with creative and artistic practice. In the article, the method...... method in Becoming Iris results in four audio-visual and performance-based productions, centered on an emergent theme of the scholartist as a bird in borrowed feathers. Interestingly, the moral lesson of the fable about the vain jackdaw, who dresses in borrowed peacock feathers and becomes a castout...

  16. Dimensionality Reduction Methods: Comparative Analysis of methods PCA, PPCA and KPCA

    Directory of Open Access Journals (Sweden)

    Jorge Arroyo-Hernández

    2016-01-01

    Full Text Available The dimensionality reduction methods are algorithms mapping the set of data in subspaces derived from the original space, of fewer dimensions, that allow a description of the data at a lower cost. Due to their importance, they are widely used in processes associated with learning machine. This article presents a comparative analysis of PCA, PPCA and KPCA dimensionality reduction methods. A reconstruction experiment of worm-shape data was performed through structures of landmarks located in the body contour, with methods having different number of main components. The results showed that all methods can be seen as alternative processes. Nevertheless, thanks to the potential for analysis in the features space and the method for calculation of its preimage presented, KPCA offers a better method for recognition process and pattern extraction

  17. Development of nondestructive hybrid measuring method for three-dimensional residual stress distribution of thick welded joint. Hybrid measuring method of inherent strain method and neutron diffraction method

    International Nuclear Information System (INIS)

    Nakacho, Keiji; Kasahara, Norifumi; Tamura, Ryota

    2012-01-01

    The measuring methods of the residual stress are classified into destructive one and nondestructive one. The inherent strain method (ISM) is destructive one. The neutron diffraction method (NDM) is nondestructive one. But the measurable depth is limited within about 20 mm and the method cannot measure the weld zone, without destruction of the object. So, in this study, the hybrid measuring method has been developed, by combining the ISM and the NDM. The theory of the hybrid method is the same as the ISM. In the analysis, the strains measured by the NDM without destruction are used. This hybrid measuring method is a true nondestructive measuring method for a thick welded joint. The applicability of the hybrid method has been verified by simulation, using a butt welded joint of thick pipes. In the simulation, the reliable order of the strains measured by the present NDM is very important, and was considered as 10 micro. The measurable regions by the present NDM were assumed. Under the above conditions, the data (the residual elastic strains assumed to be measured by the NDM) were made, and used in the ISM. As a result of such simulation, it has been cleared that the estimated residual stress has very high accuracy, if enough data are used. The required number of data is less than the ISM. (author)

  18. The surface analysis methods; Les methodes d`analyse des surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Deville, J.P. [Institut de Physique et Chimie, 67 - Strasbourg (France)

    1998-11-01

    Nowadays, there are a lot of surfaces analysis methods, each having its specificity, its qualities, its constraints (for instance vacuum) and its limits. Expensive in time and in investment, these methods have to be used deliberately. This article appeals to non specialists. It gives some elements of choice according to the studied information, the sensitivity, the use constraints or the answer to a precise question. After having recalled the fundamental principles which govern these analysis methods, based on the interaction between radiations (ultraviolet, X) or particles (ions, electrons) with matter, two methods will be more particularly described: the Auger electron spectroscopy (AES) and x-rays photoemission spectroscopy (ESCA or XPS). Indeed, they are the most widespread methods in laboratories, the easier for use and probably the most productive for the analysis of surface of industrial materials or samples submitted to treatments in aggressive media. (O.M.) 11 refs.

  19. Unstructured characteristic method embedded with variational nodal method using domain decomposition techniques

    Energy Technology Data Exchange (ETDEWEB)

    Girardi, E.; Ruggieri, J.M. [CEA Cadarache (DER/SPRC/LEPH), 13 - Saint-Paul-lez-Durance (France). Dept. d' Etudes des Reacteurs; Santandrea, S. [CEA Saclay, Dept. Modelisation de Systemes et Structures DM2S/SERMA/LENR, 91 - Gif sur Yvette (France)

    2005-07-01

    This paper describes a recently-developed extension of our 'Multi-methods,multi-domains' (MM-MD) method for the solution of the multigroup transport equation. Based on a domain decomposition technique, our approach allows us to treat the one-group equation by cooperatively employing several numerical methods together. In this work, we describe the coupling between the Method of Characteristics (integro-differential equation, unstructured meshes) with the Variational Nodal Method (even parity equation, cartesian meshes). Then, the coupling method is applied to the benchmark model of the Phebus experimental facility (Cea Cadarache). Our domain decomposition method give us the capability to employ a very fine mesh in describing a particular fuel bundle with an appropriate numerical method (MOC), while using a much large mesh size in the rest of the core, in conjunction with a coarse-mesh method (VNM). This application shows the benefits of our MM-MD approach, in terms of accuracy and computing time: the domain decomposition method allows us to reduce the Cpu time, while preserving a good accuracy of the neutronic indicators: reactivity, core-to-bundle power coupling coefficient and flux error. (authors)

  20. Unstructured characteristic method embedded with variational nodal method using domain decomposition techniques

    International Nuclear Information System (INIS)

    Girardi, E.; Ruggieri, J.M.

    2005-01-01

    This paper describes a recently-developed extension of our 'Multi-methods,multi-domains' (MM-MD) method for the solution of the multigroup transport equation. Based on a domain decomposition technique, our approach allows us to treat the one-group equation by cooperatively employing several numerical methods together. In this work, we describe the coupling between the Method of Characteristics (integro-differential equation, unstructured meshes) with the Variational Nodal Method (even parity equation, cartesian meshes). Then, the coupling method is applied to the benchmark model of the Phebus experimental facility (Cea Cadarache). Our domain decomposition method give us the capability to employ a very fine mesh in describing a particular fuel bundle with an appropriate numerical method (MOC), while using a much large mesh size in the rest of the core, in conjunction with a coarse-mesh method (VNM). This application shows the benefits of our MM-MD approach, in terms of accuracy and computing time: the domain decomposition method allows us to reduce the Cpu time, while preserving a good accuracy of the neutronic indicators: reactivity, core-to-bundle power coupling coefficient and flux error. (authors)

  1. Color image definition evaluation method based on deep learning method

    Science.gov (United States)

    Liu, Di; Li, YingChun

    2018-01-01

    In order to evaluate different blurring levels of color image and improve the method of image definition evaluation, this paper proposed a method based on the depth learning framework and BP neural network classification model, and presents a non-reference color image clarity evaluation method. Firstly, using VGG16 net as the feature extractor to extract 4,096 dimensions features of the images, then the extracted features and labeled images are employed in BP neural network to train. And finally achieve the color image definition evaluation. The method in this paper are experimented by using images from the CSIQ database. The images are blurred at different levels. There are 4,000 images after the processing. Dividing the 4,000 images into three categories, each category represents a blur level. 300 out of 400 high-dimensional features are trained in VGG16 net and BP neural network, and the rest of 100 samples are tested. The experimental results show that the method can take full advantage of the learning and characterization capability of deep learning. Referring to the current shortcomings of the major existing image clarity evaluation methods, which manually design and extract features. The method in this paper can extract the images features automatically, and has got excellent image quality classification accuracy for the test data set. The accuracy rate is 96%. Moreover, the predicted quality levels of original color images are similar to the perception of the human visual system.

  2. Cooperative method development

    DEFF Research Database (Denmark)

    Dittrich, Yvonne; Rönkkö, Kari; Eriksson, Jeanette

    2008-01-01

    The development of methods tools and process improvements is best to be based on the understanding of the development practice to be supported. Qualitative research has been proposed as a method for understanding the social and cooperative aspects of software development. However, qualitative...... research is not easily combined with the improvement orientation of an engineering discipline. During the last 6 years, we have applied an approach we call `cooperative method development', which combines qualitative social science fieldwork, with problem-oriented method, technique and process improvement....... The action research based approach focusing on shop floor software development practices allows an understanding of how contextual contingencies influence the deployment and applicability of methods, processes and techniques. This article summarizes the experiences and discusses the further development...

  3. Conjugated polymer nanoparticles, methods of using, and methods of making

    KAUST Repository

    Habuchi, Satoshi; Piwonski, Hubert Marek; Michinobu, Tsuyoshi

    2017-01-01

    Embodiments of the present disclosure provide for conjugated polymer nanoparticle, method of making conjugated polymer nanoparticles, method of using conjugated polymer nanoparticle, polymers, and the like.

  4. Conjugated polymer nanoparticles, methods of using, and methods of making

    KAUST Repository

    Habuchi, Satoshi

    2017-03-16

    Embodiments of the present disclosure provide for conjugated polymer nanoparticle, method of making conjugated polymer nanoparticles, method of using conjugated polymer nanoparticle, polymers, and the like.

  5. Numerical method for time-dependent localized corrosion analysis with moving boundaries by combining the finite volume method and voxel method

    International Nuclear Information System (INIS)

    Onishi, Yuki; Takiyasu, Jumpei; Amaya, Kenji; Yakuwa, Hiroshi; Hayabusa, Keisuke

    2012-01-01

    Highlights: ► A novel numerical method to analyze time dependent localized corrosion is developed. ► It takes electromigration, mass diffusion, chemical reactions, and moving boundaries. ► Our method perfectly satisfies the conservation of mass and electroneutrality. ► The behavior of typical crevice corrosion is successfully simulated. ► Both verification and validation of our method are carried out. - Abstract: A novel numerical method for time-dependent localized corrosion analysis is presented. Electromigration, mass diffusion, chemical reactions, and moving boundaries are considered in the numerical simulation of localized corrosion of engineering alloys in an underwater environment. Our method combines the finite volume method (FVM) and the voxel method. The FVM is adopted in the corrosion rate calculation so that the conservation of mass is satisfied. A newly developed decoupled algorithm with a projection method is introduced in the FVM to decouple the multiphysics problem into the electrostatic, mass transport, and chemical reaction analyses with electroneutrality maintained. The polarization curves for the corroding metal are used as boundary conditions for the metal surfaces to calculate the corrosion rates. The voxel method is adopted in updating the moving boundaries of cavities without remeshing and mesh-to-mesh solution mapping. Some modifications of the standard voxel method, which represents the boundaries as zigzag-shaped surfaces, are introduced to generate smooth surfaces. Our method successfully reproduces the numerical and experimental results of a capillary electrophoresis problem. Furthermore, the numerical results are qualitatively consistent with the experimental results for several examples of crevice corrosion.

  6. 76 FR 21673 - Alternative Efficiency Determination Methods and Alternate Rating Methods

    Science.gov (United States)

    2011-04-18

    ... EERE-2011-BP-TP-00024] RIN 1904-AC46 Alternative Efficiency Determination Methods and Alternate Rating Methods AGENCY: Office of Energy Efficiency and Renewable Energy, Department of Energy. ACTION: Notice of... and data related to the use of computer simulations, mathematical methods, and other alternative...

  7. Scalable fast multipole methods for vortex element methods

    KAUST Repository

    Hu, Qi

    2012-11-01

    We use a particle-based method to simulate incompressible flows, where the Fast Multipole Method (FMM) is used to accelerate the calculation of particle interactions. The most time-consuming kernelsâ\\'the Biot-Savart equation and stretching term of the vorticity equationâ\\'are mathematically reformulated so that only two Laplace scalar potentials are used instead of six, while automatically ensuring divergence-free far-field computation. Based on this formulation, and on our previous work for a scalar heterogeneous FMM algorithm, we develop a new FMM-based vortex method capable of simulating general flows including turbulence on heterogeneous architectures, which distributes the work between multi-core CPUs and GPUs to best utilize the hardware resources and achieve excellent scalability. The algorithm also uses new data structures which can dynamically manage inter-node communication and load balance efficiently but with only a small parallel construction overhead. This algorithm can scale to large-sized clusters showing both strong and weak scalability. Careful error and timing trade-off analysis are also performed for the cutoff functions induced by the vortex particle method. Our implementation can perform one time step of the velocity+stretching for one billion particles on 32 nodes in 55.9 seconds, which yields 49.12 Tflop/s. © 2012 IEEE.

  8. method

    Directory of Open Access Journals (Sweden)

    L. M. Kimball

    2002-01-01

    Full Text Available This paper presents an interior point algorithm to solve the multiperiod hydrothermal economic dispatch (HTED. The multiperiod HTED is a large scale nonlinear programming problem. Various optimization methods have been applied to the multiperiod HTED, but most neglect important network characteristics or require decomposition into thermal and hydro subproblems. The algorithm described here exploits the special bordered block diagonal structure and sparsity of the Newton system for the first order necessary conditions to result in a fast efficient algorithm that can account for all network aspects. Applying this new algorithm challenges a conventional method for the use of available hydro resources known as the peak shaving heuristic.

  9. Development of modelling method selection tool for health services management: from problem structuring methods to modelling and simulation methods.

    Science.gov (United States)

    Jun, Gyuchan T; Morris, Zoe; Eldabi, Tillal; Harper, Paul; Naseer, Aisha; Patel, Brijesh; Clarkson, John P

    2011-05-19

    There is an increasing recognition that modelling and simulation can assist in the process of designing health care policies, strategies and operations. However, the current use is limited and answers to questions such as what methods to use and when remain somewhat underdeveloped. The aim of this study is to provide a mechanism for decision makers in health services planning and management to compare a broad range of modelling and simulation methods so that they can better select and use them or better commission relevant modelling and simulation work. This paper proposes a modelling and simulation method comparison and selection tool developed from a comprehensive literature review, the research team's extensive expertise and inputs from potential users. Twenty-eight different methods were identified, characterised by their relevance to different application areas, project life cycle stages, types of output and levels of insight, and four input resources required (time, money, knowledge and data). The characterisation is presented in matrix forms to allow quick comparison and selection. This paper also highlights significant knowledge gaps in the existing literature when assessing the applicability of particular approaches to health services management, where modelling and simulation skills are scarce let alone money and time. A modelling and simulation method comparison and selection tool is developed to assist with the selection of methods appropriate to supporting specific decision making processes. In particular it addresses the issue of which method is most appropriate to which specific health services management problem, what the user might expect to be obtained from the method, and what is required to use the method. In summary, we believe the tool adds value to the scarce existing literature on methods comparison and selection.

  10. Comparison of nuclear analytical methods with competitive methods

    International Nuclear Information System (INIS)

    1987-10-01

    The use of nuclear analytical techniques, especially neutron activation analysis, already have a 50 year old history. Today several sensitive and accurate, non-nuclear trace element analytical techniques are available and new methods are continuously developed. The IAEA is supporting the development of nuclear analytical laboratories in its Member States. In order to be able to advise the developing countries which methods to use in different applications, it is important to know the present status and development trends of nuclear analytical methods, what are their benefits, drawbacks and recommended fields of application, compared with other, non-nuclear techniques. In order to get an answer to these questions the IAEA convened this Advisory Group Meeting. This volume is the outcome of the presentations and discussions of the meeting. A separate abstract was prepared for each of the 21 papers. Refs, figs, tabs

  11. Spectroscopic methods

    International Nuclear Information System (INIS)

    Ivanovich, M.; Murray, A.

    1992-01-01

    The principles involved in the interaction of nuclear radiation with matter are described, as are the principles behind methods of radiation detection. Different types of radiation detectors are described and methods of detection such as alpha, beta and gamma spectroscopy, neutron activation analysis are presented. Details are given of measurements of uranium-series disequilibria. (UK)

  12. Statistical and numerical methods to improve the transient divided bar method

    DEFF Research Database (Denmark)

    Bording, Thue Sylvester; Nielsen, S.B.; Balling, N.

    The divided bar method is a commonly used method to measure thermal conductivity of rock samples in laboratory. We present improvements to this method that allows for simultaneous measurements of both thermal conductivity and thermal diffusivity. The divided bar setup is run in a transient mode...

  13. A European legal method? On European private law and scientific method

    NARCIS (Netherlands)

    Hesselink, M.

    2009-01-01

    This article examines the relationship between European private law and scientific method. It argues that a European legal method is a good idea. Not primarily because it will make European private law scholarship look more scientific, but because a debate on the method of a normative science

  14. Uranium price forecasting methods

    International Nuclear Information System (INIS)

    Fuller, D.M.

    1994-01-01

    This article reviews a number of forecasting methods that have been applied to uranium prices and compares their relative strengths and weaknesses. The methods reviewed are: (1) judgemental methods, (2) technical analysis, (3) time-series methods, (4) fundamental analysis, and (5) econometric methods. Historically, none of these methods has performed very well, but a well-thought-out model is still useful as a basis from which to adjust to new circumstances and try again

  15. Approaches to Mixed Methods Dissemination and Implementation Research: Methods, Strengths, Caveats, and Opportunities.

    Science.gov (United States)

    Green, Carla A; Duan, Naihua; Gibbons, Robert D; Hoagwood, Kimberly E; Palinkas, Lawrence A; Wisdom, Jennifer P

    2015-09-01

    Limited translation of research into practice has prompted study of diffusion and implementation, and development of effective methods of encouraging adoption, dissemination and implementation. Mixed methods techniques offer approaches for assessing and addressing processes affecting implementation of evidence-based interventions. We describe common mixed methods approaches used in dissemination and implementation research, discuss strengths and limitations of mixed methods approaches to data collection, and suggest promising methods not yet widely used in implementation research. We review qualitative, quantitative, and hybrid approaches to mixed methods dissemination and implementation studies, and describe methods for integrating multiple methods to increase depth of understanding while improving reliability and validity of findings.

  16. Comparison of Rice Direct Seeding Methods (Mechanical and Manual with Transplanting Method

    Directory of Open Access Journals (Sweden)

    A Eyvani

    2014-04-01

    Full Text Available The main method of rice planting in Iran is transplanting. Due to poor mechanization of rice production, this method is laborious and costly. The other method is direct seeding in wet lands which is performed in the one third of rice cultivation area of the world. The most important problem in this method is high labor requirement of weed control. In order to compare the different rice planting methods (direct drilling, transplanting, and seed broadcasting a manually operated rice direct seeder (drum seeder was designed and fabricated. The research was conducted using a randomized complete block design with three treatments and three replications. Required draft force, field efficiency, effective field capacity, yield, and yield components were measured and the treatments were compared economically. Results showed that there were significant differences among the treatments from the view point of rice yield at the confidence level of 95% i.e. the transplanting method had the maximum yield. A higher rice yield was obtained from the direct seeder compared to the manual broadcasting method but, the difference between these two methods for crop yield was not significant even at the confidence level of the 95%. The coefficient of variation of seed distribution with direct seeding was more than 20%. The labor and time requirements per hectare reduced to 7 and 20 times, respectively when comparing the newly designed direct seeder with the transplanting method. The direct seeding method had the highest benefit to cost ratio in spite of its lower yield. Therefore, this method could be recommended in the rice growing regions.

  17. Advanced differential quadrature methods

    CERN Document Server

    Zong, Zhi

    2009-01-01

    Modern Tools to Perform Numerical DifferentiationThe original direct differential quadrature (DQ) method has been known to fail for problems with strong nonlinearity and material discontinuity as well as for problems involving singularity, irregularity, and multiple scales. But now researchers in applied mathematics, computational mechanics, and engineering have developed a range of innovative DQ-based methods to overcome these shortcomings. Advanced Differential Quadrature Methods explores new DQ methods and uses these methods to solve problems beyond the capabilities of the direct DQ method.After a basic introduction to the direct DQ method, the book presents a number of DQ methods, including complex DQ, triangular DQ, multi-scale DQ, variable order DQ, multi-domain DQ, and localized DQ. It also provides a mathematical compendium that summarizes Gauss elimination, the Runge-Kutta method, complex analysis, and more. The final chapter contains three codes written in the FORTRAN language, enabling readers to q...

  18. Inflow Turbulence Generation Methods

    Science.gov (United States)

    Wu, Xiaohua

    2017-01-01

    Research activities on inflow turbulence generation methods have been vigorous over the past quarter century, accompanying advances in eddy-resolving computations of spatially developing turbulent flows with direct numerical simulation, large-eddy simulation (LES), and hybrid Reynolds-averaged Navier-Stokes-LES. The weak recycling method, rooted in scaling arguments on the canonical incompressible boundary layer, has been applied to supersonic boundary layer, rough surface boundary layer, and microscale urban canopy LES coupled with mesoscale numerical weather forecasting. Synthetic methods, originating from analytical approximation to homogeneous isotropic turbulence, have branched out into several robust methods, including the synthetic random Fourier method, synthetic digital filtering method, synthetic coherent eddy method, and synthetic volume forcing method. This article reviews major progress in inflow turbulence generation methods with an emphasis on fundamental ideas, key milestones, representative applications, and critical issues. Directions for future research in the field are also highlighted.

  19. Improved radioanalytical methods

    International Nuclear Information System (INIS)

    Erickson, M.D.; Aldstadt, J.H.; Alvarado, J.S.; Crain, J.S.; Orlandini, K.A.; Smith, L.L.

    1995-01-01

    Methods for the chemical characterization of the environment are being developed under a multitask project for the Analytical Services Division (EM-263) within the US Department of Energy (DOE) Office of Environmental Management. This project focuses on improvement of radioanalytical methods with an emphasis on faster and cheaper routine methods. We have developed improved methods, for separation of environmental levels of technetium-99 and strontium-89/90, radium, and actinides from soil and water; and for separation of actinides from soil and water matrix interferences. Among the novel separation techniques being used are element- and class-specific resins and membranes. (The 3M Corporation is commercializing Empore trademark membranes under a cooperative research and development agreement [CRADA] initiated under this project). We have also developed methods for simultaneous detection of multiple isotopes using inductively coupled plasma-mass spectrometry (ICP-MS). The ICP-MS method requires less rigorous chemical separations than traditional radiochemical analyses because of its mass-selective mode of detection. Actinides and their progeny have been isolated and concentrated from a variety of natural water matrices by using automated batch separation incorporating selective resins prior to ICP-MS analyses. In addition, improvements in detection limits, sample volume, and time of analysis were obtained by using other sample introduction techniques, such as ultrasonic nebulization and electrothermal vaporization. Integration and automation of the separation methods with the ICP-MS methodology by using flow injection analysis is underway, with an objective of automating methods to achieve more reproducible results, reduce labor costs, cut analysis time, and minimize secondary waste generation through miniaturization of the process

  20. Project Method, as One of the Basic Methods of Environmental Education

    Science.gov (United States)

    Szállassy, Noémi

    2008-01-01

    Our aim was to present in this paper the one of the most important methods of environmental education, the project method. We present here the steps and phases of project method and we give an example of how to use these elements in planning an activity for celebrating the World Day for Water.

  1. „Мифологические модели и ритуальное поведение в советском и постсоветском пространстве. Сборник статей”, zebrała Aleksandra Archipowa, wydawca: Центр типологиии семиотики фольклора РГГУ, Москва 2013, ss. 472.

    Directory of Open Access Journals (Sweden)

    Dorota Pazio-Wlazłowska

    2014-12-01

    Full Text Available „Mifologicheskie modeli i ritual’noe povedenie v sovetskom i postsovetskom prostranstve: sbornik stateĭ” Arkhipova, A. (Comp., Moskva: TSentr tipologii i semiotiki fol’klora RGGU 2013, pp. 472 The volume under discussion, entitled Мифологические модели и ритуальное поведение в советском и постсоветском пространстве, contains lectures that were delivered during a conference organized by the Centre for Typology and Semiotics of Folklore Studies of the Russian State University for the Humanities in September 2013. In this volume, based on rich source material, which has been shown from different perspectives, the following issues were discussed: visional transformation, celebrating of new rites, creating new rituals, magical practices and leaders’ images.

  2. Structural revision of some recently published iridoid glucosides.

    Science.gov (United States)

    Jensen, Søren R; Caliş, Ihsan; Gotfredsen, Charlotte H; Søtofte, Inger

    2007-01-01

    The structures of six different iridoid glucosides have been revised. Three compounds isolated from Eremostachys glabra and designated 6,9-epi-8-O-acetylshanziside (1), 5,9-epi-penstemoside (2), and 5,9-epi-7,8-didehydropenstemoside (3) have been shown to be identical to the known iridoids barlerin (4, 8-O-acetylshanziside), penstemoside (5), and 7,8-didehydropenstemoside (6), respectively. Another compound named harpagoside-B, isolated from Scrophularia deserti and proposed to be 9-epi-6-O-methylharpagoside (11), was demonstrated from the spectroscopic data given to be the known harpagoside (10b). Finally, two alleged iridoid galactosides from Buddleja crispa named buddlejosides A and B (12a and 12b) have been shown to be the corresponding glucosides; the former is identical to agnuside (13a), while the latter is 3,4-dihydroxybenzoylaucubin (13b), an iridoid glucoside not previously published. This clearly showed that care should be taken with the interpretation of NOEs involving bridgehead protons in iridoid structures because they can be capricious and lead to erroneous structural assignments.

  3. Evasione fiscale e sommerso economico in Italia: fatti stilizzati, differenze tra periodi e puzzles

    Directory of Open Access Journals (Sweden)

    Bruno Chiarini

    2007-09-01

    Full Text Available The availability of official time series of Italian underground employment and VAT tax evasion for the period 1980-2004 allow us to investigate empirical1y the long- and short-run characteristics of two components of the Italian Non Observed Economy (NOE. The analysis focuses on a time span during which major labour market and fiscal reforms occurred in Italy, with an evident impact on long-run dynamics of both underground employment and tax evasion. Our investigation pointed out several interesting short-run regularities. The cyclical behaviour of the non-regular labour input indicates that the resources allocated to the underground economy are mostly motivated by flexibility requirements. Moreover, the dynamic adjustments of employment between the regular and underground market, are inextricably tied one to each other over the cycle, highlighting a reallocation mechanism among labour inputs or a labour drag effect. As to the size of the VAT evasion, its short term dynamic suggests a strategic behaviour by taxpayers, aiming to smooth tax liabilities expressed as a share of revenues.

  4. Otite externa necrotizante com paralisia facial periférica bilateral: relato de caso e revisão da literatura Necrotizing external otitis with periferic bilateral facial palsy: case report and literature review

    Directory of Open Access Journals (Sweden)

    Antonio Antunes

    2004-01-01

    Full Text Available A otite externa necrotizante (OEN, conhecida no passado como otite externa maligna, é uma infecção potencialmente letal que começa usualmente no conduto auditivo externo e se estende à base do crânio ocorrendo, principalmente, em pacientes diabéticos idosos e que a despeito de antibioticoterapia prolongada está associada à morbidade elevada e mortalidade significante. Os autores apresentam o caso de um paciente adulto, diabético, com OEN e paralisia facial periférica bilateral que evoluiu com cura da infecção, porém sem melhora da paralisia.Necrotizing external otitis (NEO, known in the past as malignant external otitis, is a potencial letal infection which begins usually in the external ear canal and spreads to the base of the skull. It occurs mainly in diabetic elderly patients who despite prolonged antibioticotherapy is associated to high morbidity and significant mortality. The authors present a case of an adult diabetic patient who developed NOE associated with bilateral periferic facial palsy evoluting with cure of the infection but without facial improvement.

  5. MR findings of congenital craniocerebral anomaly: correlation with seizures and development delay

    International Nuclear Information System (INIS)

    Ko, Seog Wan; Seo, Jeong Jin; Kim, Yun Hyeon; Yoon, Jong Hun; Kim, Hyun Ju; Kim, Hyeong Kil; Kang, Heoung Keun; Chung, Hyon De

    1995-01-01

    To evaluate characteristic MR findings of craniocerebral anomaly and its relationship with neurologic manifestations. We retrospectively reviewed MR images of 36 patients with craniocerebral anomaly diagnosed by MRI and clinical courses. We correlated the characteristic MR findings in 41 lesions with neurologic manifestations focusing on seizures and developmental delay. Twenty-three patients with seizures consisted of 14 patients(60%) with neuronal migration disorders and seven(30%) with phakomatosis, among which 18 patients(78%) had generalized type of seizures. Locations of the lesions were the parietal lobes in 11 patients(52%) and the subependymal or periventricular regions in seven(33%). Two patients with tuberous sclerosis had the lesions in both parietal and subependymal areas. Nine patients had the signs of developmental delay that were seen in the four(44%) with schizencephaly, two (22%) with tuberous sclerosis, two(22%) with heterotopia, and noe(11%) with pachygyria. Neuronal migration anomaly was relatively common lesion that presented neurologic festations such as seizures and developmental delay. Generalized type of seizures were common. We were able to diagnose these anomalies using the MRI that helped establish therapeutic plans

  6. False-positive axillary lymph node on F-18 FDG PET/CT due to moxibustion therapy

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Shin Young; Lee, Sang Woo; Ahn, Byeong Cheol; Lee, Jae Tae [Kyungpook National University Hospital, Daegu (Korea, Republic of); Seo, Ji Hyoung [Inje University Haeundae Paik Hospital, Busan (Korea, Republic of)

    2010-12-15

    A 30-year-old female was diagnosed with papillary thyroid cancer and underwent total thyroidectomy and high-dose radioiodine ablation. F-18 fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) for recurrence detection of thyroid carcinoma was performed at 3 years after total thyroidectomy. Moxibustion is a traditional Chinese medicine therapy using moxa or the mugwort herb. Moxibustion is the burning of a small, thimble-sized, smoldering plug of dried leaves such as moxa or mugwort on the skin at an acupuncture point. Acupuncture and moxibustion induce hyperemia and a local inflammatory reaction. Complications associated with moxibustion such as skin bums or infection of the site have been reported previously. False-positive FDG uptake in PET may result from inflammation, infection, and variations in physiological uptake. In the present case, the hypermetabolic axillary lymph node disappeared without any treatment. Well-known of false-positive FDG uptake in axillary lymph noes such as arthritis of the upper extremity, extravasation of injected FDG, and vaccination were not found. Thus, left axillary lymph node uptake was

  7. False-positive axillary lymph node on F-18 FDG PET/CT due to moxibustion therapy

    International Nuclear Information System (INIS)

    Jeong, Shin Young; Lee, Sang Woo; Ahn, Byeong Cheol; Lee, Jae Tae; Seo, Ji Hyoung

    2010-01-01

    A 30-year-old female was diagnosed with papillary thyroid cancer and underwent total thyroidectomy and high-dose radioiodine ablation. F-18 fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) for recurrence detection of thyroid carcinoma was performed at 3 years after total thyroidectomy. Moxibustion is a traditional Chinese medicine therapy using moxa or the mugwort herb. Moxibustion is the burning of a small, thimble-sized, smoldering plug of dried leaves such as moxa or mugwort on the skin at an acupuncture point. Acupuncture and moxibustion induce hyperemia and a local inflammatory reaction. Complications associated with moxibustion such as skin bums or infection of the site have been reported previously. False-positive FDG uptake in PET may result from inflammation, infection, and variations in physiological uptake. In the present case, the hypermetabolic axillary lymph node disappeared without any treatment. Well-known of false-positive FDG uptake in axillary lymph noes such as arthritis of the upper extremity, extravasation of injected FDG, and vaccination were not found. Thus, left axillary lymph node uptake was

  8. Plate motions, Gondwana Dinosaurs, Noah's Arks, Beached Viking Funeral Ships, Ghost Ships, and Landspans

    Directory of Open Access Journals (Sweden)

    Louis L. Jacobs

    2011-03-01

    Full Text Available Gondwana landmasses have served as large-scale biogeographic Noah's Arks and Beached Viking Funeral Ships, as defined by McKenna. The latitudinal trajectories of selected Gondwana dinosaur localities were traced through time in order to evaluate their movement through climate zones relative to those in which they originally formed. The dispersal of fauna during the breakup of Gondwana may have been facilitated by the presence of offshelf islands forming landspans (sensu Iturralde-Vinent and MacPhee in the Equatorial Atlantic Gateway and elsewhere.As massas de terra do Gondwana serviram como Arcas de Noe biogeograficas de grande escala e Navios Funerarios Vikings encalhados, conforme definido por McKenna. As trajetorias latitudinais de areas selecionadas de dinossauros do Gondwana foram tracadas ao longo do tempo a fim de avaliar seu movimento atraves de zonas climaticas relativas aquelas nas quais elas foram originalmente formadas. A dispersao da fauna durante a quebra do Gondwana pode ter sido facilitada pela presenca de ilhas oceanicas formando extensoes de terra (sensu Iturralde-Vinent e MacPhee na entrada do Atlantico Equatorial e em outros lugares.

  9. Contemporary sensorimotor theory

    CERN Document Server

    Martin, Andrew

    2014-01-01

    This book analyzes the philosophical foundations of sensorimotor theory and discusses the most recent applications of sensorimotor theory to human computer interaction, child’s play, virtual reality, robotics, and linguistics. Why does a circle look curved and not angular? Why does red not sound like a bell? Why, as I interact with the world, is there something it is like to be me? An analytic philosopher might suggest: ``if we ponder the concept of circle we find that it is the essence of a circle to be round’’. However, where does this definition come from? Was it set in stone by the Gods, in other words by divine arbiters of circleness, redness and consciousness? Particularly, with regard to visual consciousness, a first attempt to explain why our conscious experience of the world appears as it does has been attributed to Kevin O’Regan and Alva Noe, who published their sensorimotor account of vision and visual consciousness in 2001. Starting with a chapter by Kevin O’Regan, Contemporary Sensorimo...

  10. Flavonoids from Lonchocarpus muehlbergianus

    Directory of Open Access Journals (Sweden)

    Magalhães Aderbal F.

    2004-01-01

    Full Text Available The light petroleum extract from the roots of Lonchocarpus muehlbergianus Hassl contained nine flavonoids, including six new ones. These are 2,4-cis-2,4,5,8-tetramethoxy-(2,3:6,7-furanoflavan; 2,4-cis-4-hydroxy-2,5,8-trimethoxy-(2,3:6,7-furanoflavan; 2,4-cis-2-prenyloxy-4,5,8-trimethoxy-(2,3:6,7-fu-ranoflavan; 2,4-cis-2-prenyloxy-4-hydroxy-5,8-dimethoxy-(2,3:6,7-furanoflavan; 2',5',6'-trimethoxy-9-(1,1-dimethylallyoxy-[2,3:3,4]-furanochalcone; 5,6-dimethoxy-(2,3:7,8-furanoflavone, identi-fied by analysis of their spectral data (UV, IR, ¹H and 13C NMR, 2D-NMR, NOE and MS. The natural occurrence of 2,4-dioxygenated flavan derivatives is being reported for the first time. Quantitative analysis of the petrol extract, by using reversed-phase HPLC, showed that the most abundant flavonoid in the extract is 2,4-cis-2,4,5,8- tetramethoxy-(2,3:6,7-furanoflavan.

  11. Isolation of dimeric, trimeric, tetrameric and pentameric procyanidins from unroasted cocoa beans (Theobroma cacao L.) using countercurrent chromatography.

    Science.gov (United States)

    Esatbeyoglu, Tuba; Wray, Victor; Winterhalter, Peter

    2015-07-15

    The main procyanidins, including dimeric B2 and B5, trimeric C1, tetrameric and pentameric procyanidins, were isolated from unroasted cocoa beans (Theobroma cacao L.) using various techniques of countercurrent chromatography, such as high-speed countercurrent chromatography (HSCCC), low-speed rotary countercurrent chromatography (LSRCCC) and spiral-coil LSRCCC. Furthermore, dimeric procyanidins B1 and B7, which are not present naturally in the analysed cocoa beans, were obtained after semisynthesis of cocoa bean polymers with (+)-catechin as nucleophile and separated by countercurrent chromatography. In this way, the isolation of dimeric procyanidin B1 in considerable amounts (500mg, purity>97%) was possible in a single run. This is the first report concerning the isolation and semisynthesis of dimeric to pentameric procyanidins from T. cacao by countercurrent chromatography. Additionally, the chemical structures of tetrameric (cinnamtannin A2) and pentameric procyanidins (cinnamtannin A3) were elucidated on the basis of (1)H NMR spectroscopy. Interflavanoid linkage was determined by NOE-correlations, for the first time. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Structure of human insulin monomer in water/acetonitrile solution

    International Nuclear Information System (INIS)

    Bocian, Wojciech; Sitkowski, Jerzy; Bednarek, Elzbieta; Tarnowska, Anna; Kawecki, Robert; Kozerski, Lech

    2008-01-01

    Here we present evidence that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. An NMR-derived human insulin monomer structure in H 2 O/CD 3 CN, 65/35 vol%, pH 3.6 is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Acta Crystallogr. 2003 Sec. D59, 474) and with NMR structures in water and organic cosolvent. Detailed analysis using PFGSE NMR, temperature-dependent NMR, dilution experiments and CSI proves that the structure is monomeric in the concentration and temperature ranges 0.1-3 mM and 10-30 deg. C, respectively. The presence of long-range interstrand NOEs, as found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Starting from structures calculated by the program CYANA, two different molecular dynamics simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER V C), or including a generalized Born solvent model (AMBER G B)

  13. Synthesis of Chromane Derivatives via Indium-mediated Intramolecular Allenylation and Allylation to Imines

    International Nuclear Information System (INIS)

    Kang, Han Young; Yu, Yeon Kwon

    2004-01-01

    The results of preparing chromans by intramolecular allylation are shown in Table 2. The results indicated that the indium-mediated allylation was not as efficient as the allenylation. About 10-20% decrease in yields was observed. As mentioned above, in each case only a single isomer was observed, and the stereochemistry of the product was determined as cis by analysis of 1 H NMR and NOE spectra. There are, however, still some limitations in these transformations. Especially, in the case of allylation mixtures of cis and trans isomers are always produced in about 2 : 1 ratio (cis/trans). The ratio was not improved under the various reaction conditions we attempted. Since the indium-mediated addition to carbonyl groups has been successful, it occurred to us that it would be worthwhile to test the addition to carbon-nitrogen double bonds, that is, imine groups. We wish to report here the results of the investigations on allylation and allenylation to C=N bond to provide the chromane structures. The whole transformations

  14. NMR structure of the N-terminal domain of the replication initiator protein DnaA

    Energy Technology Data Exchange (ETDEWEB)

    Wemmer, David E.; Lowery, Thomas J.; Pelton, Jeffrey G.; Chandonia, John-Marc; Kim, Rosalind; Yokota, Hisao; Wemmer, David E.

    2007-08-07

    DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1-100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/- 0.2 Angstrom based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.

  15. On the calculation of {sup 3}J{sub {alpha}{beta}}-coupling constants for side chains in proteins

    Energy Technology Data Exchange (ETDEWEB)

    Steiner, Denise [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland); Allison, Jane R. [Massey University Albany, Centre for Theoretical Chemistry and Physics, Institute for Natural Sciences (New Zealand); Eichenberger, Andreas P.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH (Switzerland)

    2012-07-15

    Structural knowledge about proteins is mainly derived from values of observables, measurable in NMR spectroscopic or X-ray diffraction experiments, i.e. absorbed or scattered intensities, through theoretically derived relationships between structural quantities such as atom positions or torsional angles on the one hand and observable quantities such as squared structure factor amplitudes, NOE intensities or {sup 3}J-coupling constants on the other. The standardly used relation connecting {sup 3}J-couplings to torsional angles is the Karplus relation, which is used in protein structure refinement as well as in the evaluation of simulated properties of proteins. The accuracy of the simple and generalised Karplus relations is investigated using side-chain structural and {sup 3}J{sub {alpha}{beta}}-coupling data for three different proteins, Plastocyanin, Lysozyme, and FKBP, for which such data are available. The results show that the widely used Karplus relations are only a rough estimate for the relation between {sup 3}J{sub {alpha}{beta}}-couplings and the corresponding {chi}{sub 1}-angle in proteins.

  16. Interaction of the Saccharomyces cerevisiae α-factor with phospholipid vesicles as revealed by proton and phosphorus NMR

    International Nuclear Information System (INIS)

    Jelicks, L.A.; Broido, M.S.; Becker, J.M.; Naider, F.R.

    1989-01-01

    Proton and phosphorus-31 nuclear magnetic resonance ( 1 H and 31 P NMR) studies of the interaction between a tridecapeptide pheromone, the α-factor of Saccharomyces cerevisiae, and sonicated lipid vesicles are reported. 31 P NMR studies demonstrate that there is interaction of the peptide with the phosphorus headgroups, and quasielastic light scattering (QLS) studies indicate that lipid vesicles increase in size upon addition of peptide. Previous solution (aqueous and DMSO) studies from this laboratory indicate that α-factor is highly flexible with only one long-lived identifiable structural feature, a type II β-turn spanning the central portion of the peptide. Two-dimensional (2D) 1 H nuclear Overhauser effect spectroscopy (NOESY) studies demonstrate a marked ordering of the peptide upon interaction with lipid, suggesting a compact N-terminus, in addition to a stabilized β-turn. In contrast to these results in both solution and lipid environment, Wakamatsu et al. proposed a lipid environment conformation, on the basis of one-dimensional transferred NOE studies in D 2 O, which does not include the β-turn

  17. J-UNIO protocol used for NMR structure determination of the 206-residue protein NP-346487.1 from Streptococcus pneumoniae TIGR4

    Energy Technology Data Exchange (ETDEWEB)

    Jaudzems, Kristaps [Latvian Institute of Organic Synthesis (Latvia); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Geralt, Michael; Serrano, Pedro; Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    The NMR structure of the 206-residue protein NP-346487.1 was determined with the J-UNIO protocol, which includes extensive automation of the structure determination. With input from three APSY-NMR experiments, UNIO-MATCH automatically yielded 77 % of the backbone assignments, which were interactively validated and extended to 97 %. With an input of the near-complete backbone assignments and three 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra, automated side chain assignment with UNIO-ATNOS/ASCAN resulted in 77 % of the expected assignments, which was extended interactively to about 90 %. Automated NOE assignment and structure calculation with UNIO-ATNOS/CANDID in combination with CYANA was used for the structure determination of this two-domain protein. The individual domains in the NMR structure coincide closely with the crystal structure, and the NMR studies further imply that the two domains undergo restricted hinge motions relative to each other in solution. NP-346487.1 is so far the largest polypeptide chain to which the J-UNIO structure determination protocol has successfully been applied.

  18. Methods of nonlinear analysis

    CERN Document Server

    Bellman, Richard Ernest

    1970-01-01

    In this book, we study theoretical and practical aspects of computing methods for mathematical modelling of nonlinear systems. A number of computing techniques are considered, such as methods of operator approximation with any given accuracy; operator interpolation techniques including a non-Lagrange interpolation; methods of system representation subject to constraints associated with concepts of causality, memory and stationarity; methods of system representation with an accuracy that is the best within a given class of models; methods of covariance matrix estimation;methods for low-rank mat

  19. Differential modulation of binding loop flexibility and stability by Arg50 and Arg52 in Cucurbita maxima trypsin inhibitor-V deduced by trypsin-catalyzed hydrolysis and NMR spectroscopy.

    Science.gov (United States)

    Cai, M; Huang, Y; Prakash, O; Wen, L; Dunkelbarger, S P; Huang, J K; Liu, J; Krishnamoorthi, R

    1996-04-16

    The side chains of Arg50 and Arg52 iin Cucurbita maxima trypsin inhibitor-V (CMTI-V) anchor the binding loop to the scaffold region [Cai, M., Gong, Y., Kao, J.L-F., & Krishnamoorthi, R. (1995) Biochemistry 34, 5201-5211]. The consequences of these hydrogen-bonding and electrostatic interactions on the conformational flexibility and stability of the binding loop were evaluated by trypsin-catalyzed hydrolysis of CMTI-V mutants, in which each of the arginines was individually replaced with Ala, Lys, or Gln by genetic engineering methods. All mutants exhibited significantly increased vulnerability to the protease attack at many sites, including the reactive-site (Lys44-Asp45 peptide bond), with the R50 mutants showing much more pronounced effects than the R52 counterparts. For CmTI-V and the mutants studied, a qualitative correlation was inferred between binding loop flexibility and retention time on a reverse-phase high-pressure liquid chromatography C-18 column. The R50 mutants were found to be more flexible than the corresponding R52 versions. These results demonstrate that Arg50 contributes more to the stability and function of CMTI-V. The differing strengths of the hydrogen bonds made by Arg50 and Arg52 were characterized by determining the internal dynamics of their side chains at pH 5.0 and 2.5: 15N NMR longitudinal and transverse relaxation rates and 15N-1H nuclear Overhauser effect (NOE) enhancements were measured for the main-chain and side-chain NH groups in 15N-labeled recombinant CMTI-V (rCMTI-V) and the model-free parameters [Lipari, G., & Szabo, A.(1982) J. Am. Chem. Soc. 104, 4546-59; 4559-4570] were calculated. At both pH 5.0 and 2.5, the arginines at positions 26, 47, 58 and 66 are found to be highly mobile, as the caluculated general order parameters, S2 values, of their NepsilonH groups fall in the range 0.03-0.18. The corresponding values for Arg50 amd Arg52 are 0.73 and 0.63, respectively, at pH 5.0, thus confirming that the two arginines are

  20. Transport methods: general. 1. The Analytical Monte Carlo Method for Radiation Transport Calculations

    International Nuclear Information System (INIS)

    Martin, William R.; Brown, Forrest B.

    2001-01-01

    We present an alternative Monte Carlo method for solving the coupled equations of radiation transport and material energy. This method is based on incorporating the analytical solution to the material energy equation directly into the Monte Carlo simulation for the radiation intensity. This method, which we call the Analytical Monte Carlo (AMC) method, differs from the well known Implicit Monte Carlo (IMC) method of Fleck and Cummings because there is no discretization of the material energy equation since it is solved as a by-product of the Monte Carlo simulation of the transport equation. Our method also differs from the method recently proposed by Ahrens and Larsen since they use Monte Carlo to solve both equations, while we are solving only the radiation transport equation with Monte Carlo, albeit with effective sources and cross sections to represent the emission sources. Our method bears some similarity to a method developed and implemented by Carter and Forest nearly three decades ago, but there are substantive differences. We have implemented our method in a simple zero-dimensional Monte Carlo code to test the feasibility of the method, and the preliminary results are very promising, justifying further extension to more realistic geometries. (authors)

  1. Two different hematocrit detection methods: Different methods, different results?

    Directory of Open Access Journals (Sweden)

    Schuepbach Reto A

    2010-03-01

    Full Text Available Abstract Background Less is known about the influence of hematocrit detection methodology on transfusion triggers. Therefore, the aim of the present study was to compare two different hematocrit-assessing methods. In a total of 50 critically ill patients hematocrit was analyzed using (1 blood gas analyzer (ABLflex 800 and (2 the central laboratory method (ADVIA® 2120 and compared. Findings Bland-Altman analysis for repeated measurements showed a good correlation with a bias of +1.39% and 2 SD of ± 3.12%. The 24%-hematocrit-group showed a correlation of r2 = 0.87. With a kappa of 0.56, 22.7% of the cases would have been transfused differently. In the-28%-hematocrit group with a similar correlation (r2 = 0.8 and a kappa of 0.58, 21% of the cases would have been transfused differently. Conclusions Despite a good agreement between the two methods used to determine hematocrit in clinical routine, the calculated difference of 1.4% might substantially influence transfusion triggers depending on the employed method.

  2. Method Mixins

    DEFF Research Database (Denmark)

    Ernst, Erik

    2005-01-01

    The world of programming has been conquered by the procedure call mechanism, including object-oriented method invocation which is a procedure call in context of an object. This paper presents an alternative, method mixin invocations, that is optimized for flexible creation of composite behavior...... of abstraction and reuse. Method mixins use shared name spaces to transfer information between caller and callee, as opposed to traditional invocation which uses parameters and returned results. This relieves the caller from dependencies on the callee, and it allows direct transfer of information further down...... the call stack, e.g., to a callee's callee. The mechanism has been implemented in the programming language gbeta. Variants of the mechanism could be added to almost any imperative programming language....

  3. Dianhydrides, polyimides, methods of making each, and methods of use

    KAUST Repository

    Ma, Xiaohua; Pinnau, Ingo; Ghanem, Bader

    2015-01-01

    Embodiments of the present disclosure provide for an aromatic dianhydride, a method of making an aromatic dianhydride, an aromatic dianhydride-based polyimide, a method of making an aromatic dianhydride-based polyimide, and the like.

  4. Dianhydrides, polyimides, methods of making each, and methods of use

    KAUST Repository

    Ma, Xiaohua

    2015-01-08

    Embodiments of the present disclosure provide for an aromatic dianhydride, a method of making an aromatic dianhydride, an aromatic dianhydride-based polyimide, a method of making an aromatic dianhydride-based polyimide, and the like.

  5. The Method of Manufactured Universes for validating uncertainty quantification methods

    KAUST Repository

    Stripling, H.F.; Adams, M.L.; McClarren, R.G.; Mallick, B.K.

    2011-01-01

    The Method of Manufactured Universes is presented as a validation framework for uncertainty quantification (UQ) methodologies and as a tool for exploring the effects of statistical and modeling assumptions embedded in these methods. The framework

  6. Design Methods in Practice

    DEFF Research Database (Denmark)

    Jensen, Torben Elgaard; Andreasen, Mogens Myrup

    2010-01-01

    The paper challenges the dominant and widespread view that a good design method will guarantee a systematic approach as well as certain results. First, it explores the substantial differences between on the one hand the conception of methods implied in Pahl & Beitz’s widely recognized text book...... on engineering design, and on the other hand the understanding of method use, which has emerged from micro-sociological studies of practice (ethnomethodology). Second, it reviews a number of case studies conducted by engineering students, who were instructed to investigate the actual use of design methods...... in Danish companies. The paper concludes that design methods in practice deviate substantially from Pahl & Beitz’s description of method use: The object and problems, which are the starting points for method use, are more contested and less given than generally assumed; The steps of methods are often...

  7. FPGA Implementation of the Coupled Filtering Method and the Affine Warping Method.

    Science.gov (United States)

    Zhang, Chen; Liang, Tianzhu; Mok, Philip K T; Yu, Weichuan

    2017-07-01

    In ultrasound image analysis, the speckle tracking methods are widely applied to study the elasticity of body tissue. However, "feature-motion decorrelation" still remains as a challenge for the speckle tracking methods. Recently, a coupled filtering method and an affine warping method were proposed to accurately estimate strain values, when the tissue deformation is large. The major drawback of these methods is the high computational complexity. Even the graphics processing unit (GPU)-based program requires a long time to finish the analysis. In this paper, we propose field-programmable gate array (FPGA)-based implementations of both methods for further acceleration. The capability of FPGAs on handling different image processing components in these methods is discussed. A fast and memory-saving image warping approach is proposed. The algorithms are reformulated to build a highly efficient pipeline on FPGA. The final implementations on a Xilinx Virtex-7 FPGA are at least 13 times faster than the GPU implementation on the NVIDIA graphic card (GeForce GTX 580).

  8. Methods for assessing geodiversity

    Science.gov (United States)

    Zwoliński, Zbigniew; Najwer, Alicja; Giardino, Marco

    2017-04-01

    The accepted systematics of geodiversity assessment methods will be presented in three categories: qualitative, quantitative and qualitative-quantitative. Qualitative methods are usually descriptive methods that are suited to nominal and ordinal data. Quantitative methods use a different set of parameters and indicators to determine the characteristics of geodiversity in the area being researched. Qualitative-quantitative methods are a good combination of the collection of quantitative data (i.e. digital) and cause-effect data (i.e. relational and explanatory). It seems that at the current stage of the development of geodiversity research methods, qualitative-quantitative methods are the most advanced and best assess the geodiversity of the study area. Their particular advantage is the integration of data from different sources and with different substantive content. Among the distinguishing features of the quantitative and qualitative-quantitative methods for assessing geodiversity are their wide use within geographic information systems, both at the stage of data collection and data integration, as well as numerical processing and their presentation. The unresolved problem for these methods, however, is the possibility of their validation. It seems that currently the best method of validation is direct filed confrontation. Looking to the next few years, the development of qualitative-quantitative methods connected with cognitive issues should be expected, oriented towards ontology and the Semantic Web.

  9. Mixed methods research.

    Science.gov (United States)

    Halcomb, Elizabeth; Hickman, Louise

    2015-04-08

    Mixed methods research involves the use of qualitative and quantitative data in a single research project. It represents an alternative methodological approach, combining qualitative and quantitative research approaches, which enables nurse researchers to explore complex phenomena in detail. This article provides a practical overview of mixed methods research and its application in nursing, to guide the novice researcher considering a mixed methods research project.

  10. Recent Advances in the Method of Forces: Integrated Force Method of Structural Analysis

    Science.gov (United States)

    Patnaik, Surya N.; Coroneos, Rula M.; Hopkins, Dale A.

    1998-01-01

    Stress that can be induced in an elastic continuum can be determined directly through the simultaneous application of the equilibrium equations and the compatibility conditions. In the literature, this direct stress formulation is referred to as the integrated force method. This method, which uses forces as the primary unknowns, complements the popular equilibrium-based stiffness method, which considers displacements as the unknowns. The integrated force method produces accurate stress, displacement, and frequency results even for modest finite element models. This version of the force method should be developed as an alternative to the stiffness method because the latter method, which has been researched for the past several decades, may have entered its developmental plateau. Stress plays a primary role in the development of aerospace and other products, and its analysis is difficult. Therefore, it is advisable to use both methods to calculate stress and eliminate errors through comparison. This paper examines the role of the integrated force method in analysis, animation and design.

  11. Test Methods for Evaluating Solid Waste, Physical/Chemical Methods. First Update. (3rd edition)

    International Nuclear Information System (INIS)

    Friedman; Sellers.

    1988-01-01

    The proposed Update is for Test Methods for Evaluating Solid Waste, Physical/Chemical Methods, SW-846, Third Edition. Attached to the report is a list of methods included in the proposed update indicating whether the method is a new method, a partially revised method, or a totally revised method. Do not discard or replace any of the current pages in the SW-846 manual until the proposed update I package is promulgated. Until promulgation of the update package, the methods in the update package are not officially part of the SW-846 manual and thus do not carry the status of EPA-approved methods. In addition to the proposed Update, six finalized methods are included for immediate inclusion into the Third Edition of SW-846. Four methods, originally proposed October 1, 1984, will be finalized in a soon to be released rulemaking. They are, however, being submitted to subscribers for the first time in the update. These methods are 7211, 7381, 7461, and 7951. Two other methods were finalized in the 2nd Edition of SW-846. They were inadvertantly omitted from the 3rd Edition and are not being proposed as new. These methods are 7081 and 7761

  12. Consumer Behavior Research Methods

    DEFF Research Database (Denmark)

    Chrysochou, Polymeros

    2017-01-01

    This chapter starts by distinguishing consumer behavior research methods based on the type of data used, being either secondary or primary. Most consumer behavior research studies phenomena that require researchers to enter the field and collect data on their own, and therefore the chapter...... emphasizes the discussion of primary research methods. Based on the nature of the data primary research methods are further distinguished into qualitative and quantitative. The chapter describes the most important and popular qualitative and quantitative methods. It concludes with an overall evaluation...... of the methods and how to improve quality in consumer behavior research methods....

  13. Comparative study of the geostatistical ore reserve estimation method over the conventional methods

    International Nuclear Information System (INIS)

    Kim, Y.C.; Knudsen, H.P.

    1975-01-01

    Part I contains a comprehensive treatment of the comparative study of the geostatistical ore reserve estimation method over the conventional methods. The conventional methods chosen for comparison were: (a) the polygon method, (b) the inverse of the distance squared method, and (c) a method similar to (b) but allowing different weights in different directions. Briefly, the overall result from this comparative study is in favor of the use of geostatistics in most cases because the method has lived up to its theoretical claims. A good exposition on the theory of geostatistics, the adopted study procedures, conclusions and recommended future research are given in Part I. Part II of this report contains the results of the second and the third study objectives, which are to assess the potential benefits that can be derived by the introduction of the geostatistical method to the current state-of-the-art in uranium reserve estimation method and to be instrumental in generating the acceptance of the new method by practitioners through illustrative examples, assuming its superiority and practicality. These are given in the form of illustrative examples on the use of geostatistics and the accompanying computer program user's guide

  14. Qualitative methods textbooks

    OpenAIRE

    Barndt, William

    2003-01-01

    Over the past few years, the number of political science departments offering qualitative methods courses has grown substantially. The number of qualitative methods textbooks has kept pace, providing instructors with an overwhelming array of choices. But how to decide which text to choose from this exhortatory smorgasbord? The scholarship desperately needs evaluated. Yet the task is not entirely straightforward: qualitative methods textbooks reflect the diversity inherent in qualitative metho...

  15. Statistical error estimation of the Feynman-α method using the bootstrap method

    International Nuclear Information System (INIS)

    Endo, Tomohiro; Yamamoto, Akio; Yagi, Takahiro; Pyeon, Cheol Ho

    2016-01-01

    Applicability of the bootstrap method is investigated to estimate the statistical error of the Feynman-α method, which is one of the subcritical measurement techniques on the basis of reactor noise analysis. In the Feynman-α method, the statistical error can be simply estimated from multiple measurements of reactor noise, however it requires additional measurement time to repeat the multiple times of measurements. Using a resampling technique called 'bootstrap method' standard deviation and confidence interval of measurement results obtained by the Feynman-α method can be estimated as the statistical error, using only a single measurement of reactor noise. In order to validate our proposed technique, we carried out a passive measurement of reactor noise without any external source, i.e. with only inherent neutron source by spontaneous fission and (α,n) reactions in nuclear fuels at the Kyoto University Criticality Assembly. Through the actual measurement, it is confirmed that the bootstrap method is applicable to approximately estimate the statistical error of measurement results obtained by the Feynman-α method. (author)

  16. The use of the spectral method within the fast adaptive composite grid method

    Energy Technology Data Exchange (ETDEWEB)

    McKay, S.M.

    1994-12-31

    The use of efficient algorithms for the solution of partial differential equations has been sought for many years. The fast adaptive composite grid (FAC) method combines an efficient algorithm with high accuracy to obtain low cost solutions to partial differential equations. The FAC method achieves fast solution by combining solutions on different grids with varying discretizations and using multigrid like techniques to find fast solution. Recently, the continuous FAC (CFAC) method has been developed which utilizes an analytic solution within a subdomain to iterate to a solution of the problem. This has been shown to achieve excellent results when the analytic solution can be found. The CFAC method will be extended to allow solvers which construct a function for the solution, e.g., spectral and finite element methods. In this discussion, the spectral methods will be used to provide a fast, accurate solution to the partial differential equation. As spectral methods are more accurate than finite difference methods, the ensuing accuracy from this hybrid method outside of the subdomain will be investigated.

  17. Methods for measurement of electron emission yield under low energy electron-irradiation by collector method and Kelvin probe method

    Energy Technology Data Exchange (ETDEWEB)

    Tondu, Thomas; Belhaj, Mohamed; Inguimbert, Virginie [Onera, DESP, 2 Avenue Edouard Belin, 31400 Toulouse (France); Onera, DESP, 2 Avenue Edouard Belin, 31400 Toulouse, France and Fondation STAE, 4 allee Emile Monso, BP 84234-31432, Toulouse Cedex 4 (France); Onera, DESP, 2 Avenue Edouard Belin, 31400 Toulouse (France)

    2010-09-15

    Secondary electron emission yield of gold under electron impact at normal incidence below 50 eV was investigated by the classical collector method and by the Kelvin probe method. The authors show that biasing a collector to ensure secondary electron collection while keeping the target grounded can lead to primary electron beam perturbations. Thus reliable secondary electron emission yield at low primary electron energy cannot be obtained with a biased collector. The authors present two collector-free methods based on current measurement and on electron pulse surface potential buildup (Kelvin probe method). These methods are consistent, but at very low energy, measurements become sensitive to the earth magnetic field (below 10 eV). For gold, the authors can extrapolate total emission yield at 0 eV to 0.5, while a total electron emission yield of 1 is obtained at 40{+-}1 eV.

  18. Methods for measurement of electron emission yield under low energy electron-irradiation by collector method and Kelvin probe method

    International Nuclear Information System (INIS)

    Tondu, Thomas; Belhaj, Mohamed; Inguimbert, Virginie

    2010-01-01

    Secondary electron emission yield of gold under electron impact at normal incidence below 50 eV was investigated by the classical collector method and by the Kelvin probe method. The authors show that biasing a collector to ensure secondary electron collection while keeping the target grounded can lead to primary electron beam perturbations. Thus reliable secondary electron emission yield at low primary electron energy cannot be obtained with a biased collector. The authors present two collector-free methods based on current measurement and on electron pulse surface potential buildup (Kelvin probe method). These methods are consistent, but at very low energy, measurements become sensitive to the earth magnetic field (below 10 eV). For gold, the authors can extrapolate total emission yield at 0 eV to 0.5, while a total electron emission yield of 1 is obtained at 40±1 eV.

  19. Rossi Alpha Method

    International Nuclear Information System (INIS)

    Hansen, G.E.

    1985-01-01

    The Rossi Alpha Method has proved to be valuable for the determination of prompt neutron lifetimes in fissile assemblies having known reproduction numbers at or near delayed critical. This workshop report emphasizes the pioneering applications of the method by Dr. John D. Orndoff to fast-neutron critical assemblies at Los Alamos. The value of the method appears to disappear for subcritical systems where the Rossi-α is no longer an α-eigenvalue

  20. Semi top-down method combined with earth-bank, an effective method for basement construction.

    Science.gov (United States)

    Tuan, B. Q.; Tam, Ng M.

    2018-04-01

    Choosing an appropriate method of deep excavation not only plays a decisive role in technical success, but also in economics of the construction project. Presently, we mainly base on to key methods: “Bottom-up” and “Top-down” construction method. Right now, this paper presents an another method of construction that is “Semi Top-down method combining with earth-bank” in order to take the advantages and limit the weakness of the above methods. The Bottom-up method was improved by using the earth-bank to stabilize retaining walls instead of the bracing steel struts. The Top-down method was improved by using the open cut method for the half of the earthwork quantities.

  1. Stochastic optimization methods

    CERN Document Server

    Marti, Kurt

    2005-01-01

    Optimization problems arising in practice involve random parameters. For the computation of robust optimal solutions, i.e., optimal solutions being insensitive with respect to random parameter variations, deterministic substitute problems are needed. Based on the distribution of the random data, and using decision theoretical concepts, optimization problems under stochastic uncertainty are converted into deterministic substitute problems. Due to the occurring probabilities and expectations, approximative solution techniques must be applied. Deterministic and stochastic approximation methods and their analytical properties are provided: Taylor expansion, regression and response surface methods, probability inequalities, First Order Reliability Methods, convex approximation/deterministic descent directions/efficient points, stochastic approximation methods, differentiation of probability and mean value functions. Convergence results of the resulting iterative solution procedures are given.

  2. Methods of Software Verification

    Directory of Open Access Journals (Sweden)

    R. E. Gurin

    2015-01-01

    Full Text Available This article is devoted to the problem of software verification (SW. Methods of software verification designed to check the software for compliance with the stated requirements such as correctness, system security and system adaptability to small changes in the environment, portability and compatibility, etc. These are various methods both by the operation process and by the way of achieving result. The article describes the static and dynamic methods of software verification and paid attention to the method of symbolic execution. In its review of static analysis are discussed and described the deductive method, and methods for testing the model. A relevant issue of the pros and cons of a particular method is emphasized. The article considers classification of test techniques for each method. In this paper we present and analyze the characteristics and mechanisms of the static analysis of dependencies, as well as their views, which can reduce the number of false positives in situations where the current state of the program combines two or more states obtained both in different paths of execution and in working with multiple object values. Dependences connect various types of software objects: single variables, the elements of composite variables (structure fields, array elements, the size of the heap areas, the length of lines, the number of initialized array elements in the verification code using static methods. The article pays attention to the identification of dependencies within the framework of the abstract interpretation, as well as gives an overview and analysis of the inference tools.Methods of dynamic analysis such as testing, monitoring and profiling are presented and analyzed. Also some kinds of tools are considered which can be applied to the software when using the methods of dynamic analysis. Based on the work a conclusion is drawn, which describes the most relevant problems of analysis techniques, methods of their solutions and

  3. Winter Holts Oscillatory Method: A New Method of Resampling in Time Series.

    Directory of Open Access Journals (Sweden)

    Muhammad Imtiaz Subhani

    2016-12-01

    Full Text Available The core proposition behind this research is to create innovative methods of bootstrapping that can be applied in time series data. In order to find new methods of bootstrapping, various methods were reviewed; The data of automotive Sales, Market Shares and Net Exports of the top 10 countries, which includes China, Europe, United States of America (USA, Japan, Germany, South Korea, India, Mexico, Brazil, Spain and, Canada from 2002 to 2014 were collected through various sources which includes UN Comtrade, Index Mundi and World Bank. The findings of this paper confirmed that Bootstrapping for resampling through winter forecasting by Oscillation and Average methods give more robust results than the winter forecasting by any general methods.

  4. The discrete ordinate method in association with the finite-volume method in non-structured mesh; Methode des ordonnees discretes associee a la methode des volumes finis en maillage non structure

    Energy Technology Data Exchange (ETDEWEB)

    Le Dez, V; Lallemand, M [Ecole Nationale Superieure de Mecanique et d` Aerotechnique (ENSMA), 86 - Poitiers (France); Sakami, M; Charette, A [Quebec Univ., Chicoutimi, PQ (Canada). Dept. des Sciences Appliquees

    1997-12-31

    The description of an efficient method of radiant heat transfer field determination in a grey semi-transparent environment included in a 2-D polygonal cavity with surface boundaries that reflect the radiation in a purely diffusive manner is proposed, at the equilibrium and in radiation-conduction coupling situation. The technique uses simultaneously the finite-volume method in non-structured triangular mesh, the discrete ordinate method and the ray shooting method. The main mathematical developments and comparative results with the discrete ordinate method in orthogonal curvilinear coordinates are included. (J.S.) 10 refs.

  5. The discrete ordinate method in association with the finite-volume method in non-structured mesh; Methode des ordonnees discretes associee a la methode des volumes finis en maillage non structure

    Energy Technology Data Exchange (ETDEWEB)

    Le Dez, V.; Lallemand, M. [Ecole Nationale Superieure de Mecanique et d`Aerotechnique (ENSMA), 86 - Poitiers (France); Sakami, M.; Charette, A. [Quebec Univ., Chicoutimi, PQ (Canada). Dept. des Sciences Appliquees

    1996-12-31

    The description of an efficient method of radiant heat transfer field determination in a grey semi-transparent environment included in a 2-D polygonal cavity with surface boundaries that reflect the radiation in a purely diffusive manner is proposed, at the equilibrium and in radiation-conduction coupling situation. The technique uses simultaneously the finite-volume method in non-structured triangular mesh, the discrete ordinate method and the ray shooting method. The main mathematical developments and comparative results with the discrete ordinate method in orthogonal curvilinear coordinates are included. (J.S.) 10 refs.

  6. Development of 3-D FBR heterogeneous core calculation method based on characteristics method

    International Nuclear Information System (INIS)

    Takeda, Toshikazu; Maruyama, Manabu; Hamada, Yuzuru; Nishi, Hiroshi; Ishibashi, Junichi; Kitano, Akihiro

    2002-01-01

    A new 3-D transport calculation method taking into account the heterogeneity of fuel assemblies has been developed by combining the characteristics method and the nodal transport method. In the axial direction the nodal transport method is applied, and the characteristics method is applied to take into account the radial heterogeneity of fuel assemblies. The numerical calculations have been performed to verify 2-D radial calculations of FBR assemblies and partial core calculations. Results are compared with the reference Monte-Carlo calculations. A good agreement has been achieved. It is shown that the present method has an advantage in calculating reaction rates in a small region

  7. Comparison of Monte Carlo method and deterministic method for neutron transport calculation

    International Nuclear Information System (INIS)

    Mori, Takamasa; Nakagawa, Masayuki

    1987-01-01

    The report outlines major features of the Monte Carlo method by citing various applications of the method and techniques used for Monte Carlo codes. Major areas of its application include analysis of measurements on fast critical assemblies, nuclear fusion reactor neutronics analysis, criticality safety analysis, evaluation by VIM code, and calculation for shielding. Major techniques used for Monte Carlo codes include the random walk method, geometric expression method (combinatorial geometry, 1, 2, 4-th degree surface and lattice geometry), nuclear data expression, evaluation method (track length, collision, analog (absorption), surface crossing, point), and dispersion reduction (Russian roulette, splitting, exponential transform, importance sampling, corrected sampling). Major features of the Monte Carlo method are as follows: 1) neutron source distribution and systems of complex geometry can be simulated accurately, 2) physical quantities such as neutron flux in a place, on a surface or at a point can be evaluated, and 3) calculation requires less time. (Nogami, K.)

  8. Angular correlation methods

    International Nuclear Information System (INIS)

    Ferguson, A.J.

    1974-01-01

    An outline of the theory of angular correlations is presented, and the difference between the modern density matrix method and the traditional wave function method is stressed. Comments are offered on particular angular correlation theoretical techniques. A brief discussion is given of recent studies of gamma ray angular correlations of reaction products recoiling with high velocity into vacuum. Two methods for optimization to obtain the most accurate expansion coefficients of the correlation are discussed. (1 figure, 53 references) (U.S.)

  9. The Box Method

    DEFF Research Database (Denmark)

    Nielsen, Peter Vilhelm

    The velocity level in a room ventilated by jet ventilation is strongly influenced by the supply conditions. The momentum flow in the supply jets controls the air movement in the room and, therefore, it is very important that the inlet conditions and the numerical method can generate a satisfactor...... description of this momentum flow. The Box Method is a practical method for the description of an Air Terminal Device which will save grid points and ensure the right level of the momentum flow....

  10. Decentralized Quasi-Newton Methods

    Science.gov (United States)

    Eisen, Mark; Mokhtari, Aryan; Ribeiro, Alejandro

    2017-05-01

    We introduce the decentralized Broyden-Fletcher-Goldfarb-Shanno (D-BFGS) method as a variation of the BFGS quasi-Newton method for solving decentralized optimization problems. The D-BFGS method is of interest in problems that are not well conditioned, making first order decentralized methods ineffective, and in which second order information is not readily available, making second order decentralized methods impossible. D-BFGS is a fully distributed algorithm in which nodes approximate curvature information of themselves and their neighbors through the satisfaction of a secant condition. We additionally provide a formulation of the algorithm in asynchronous settings. Convergence of D-BFGS is established formally in both the synchronous and asynchronous settings and strong performance advantages relative to first order methods are shown numerically.

  11. Dissolution Methods Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — For a drug product that does not have a dissolution test method in the United States Pharmacopeia (USP), the FDA Dissolution Methods Database provides information on...

  12. The ICARE Method

    Science.gov (United States)

    Henke, Luke

    2010-01-01

    The ICARE method is a flexible, widely applicable method for systems engineers to solve problems and resolve issues in a complete and comprehensive manner. The method can be tailored by diverse users for direct application to their function (e.g. system integrators, design engineers, technical discipline leads, analysts, etc.). The clever acronym, ICARE, instills the attitude of accountability, safety, technical rigor and engagement in the problem resolution: Identify, Communicate, Assess, Report, Execute (ICARE). This method was developed through observation of Space Shuttle Propulsion Systems Engineering and Integration (PSE&I) office personnel approach in an attempt to succinctly describe the actions of an effective systems engineer. Additionally it evolved from an effort to make a broadly-defined checklist for a PSE&I worker to perform their responsibilities in an iterative and recursive manner. The National Aeronautics and Space Administration (NASA) Systems Engineering Handbook states, engineering of NASA systems requires a systematic and disciplined set of processes that are applied recursively and iteratively for the design, development, operation, maintenance, and closeout of systems throughout the life cycle of the programs and projects. ICARE is a method that can be applied within the boundaries and requirements of NASA s systems engineering set of processes to provide an elevated sense of duty and responsibility to crew and vehicle safety. The importance of a disciplined set of processes and a safety-conscious mindset increases with the complexity of the system. Moreover, the larger the system and the larger the workforce, the more important it is to encourage the usage of the ICARE method as widely as possible. According to the NASA Systems Engineering Handbook, elements of a system can include people, hardware, software, facilities, policies and documents; all things required to produce system-level results, qualities, properties, characteristics

  13. Ensemble Data Mining Methods

    Data.gov (United States)

    National Aeronautics and Space Administration — Ensemble Data Mining Methods, also known as Committee Methods or Model Combiners, are machine learning methods that leverage the power of multiple models to achieve...

  14. Simulation of Rossi-α method with analog Monte-Carlo method

    International Nuclear Information System (INIS)

    Lu Yuzhao; Xie Qilin; Song Lingli; Liu Hangang

    2012-01-01

    The analog Monte-Carlo code for simulating Rossi-α method based on Geant4 was developed. The prompt neutron decay constant α of six metal uranium configurations in Oak Ridge National Laboratory were calculated. α was also calculated by Burst-Neutron method and the result was consistent with the result of Rossi-α method. There is the difference between results of analog Monte-Carlo simulation and experiment, and the reasons for the difference is the gaps between uranium layers. The influence of gaps decrease as the sub-criticality deepens. The relative difference between results of analog Monte-Carlo simulation and experiment changes from 19% to 0.19%. (authors)

  15. Method Usage in Design : How methods function as mental tools for designers

    NARCIS (Netherlands)

    Daalhuizen, J.J.

    2014-01-01

    Methods are means to help designers achieve desired change as efficiently and effectively as possible. Methods can be used to do so in the context of learning - to help teach students how to design on a professional level. Methods can also be used in the context of performance - to help designers

  16. A highly accurate method for determination of dissolved oxygen: Gravimetric Winkler method

    International Nuclear Information System (INIS)

    Helm, Irja; Jalukse, Lauri; Leito, Ivo

    2012-01-01

    Highlights: ► Probably the most accurate method available for dissolved oxygen concentration measurement was developed. ► Careful analysis of uncertainty sources was carried out and the method was optimized for minimizing all uncertainty sources as far as practical. ► This development enables more accurate calibration of dissolved oxygen sensors for routine analysis than has been possible before. - Abstract: A high-accuracy Winkler titration method has been developed for determination of dissolved oxygen concentration. Careful analysis of uncertainty sources relevant to the Winkler method was carried out and the method was optimized for minimizing all uncertainty sources as far as practical. The most important improvements were: gravimetric measurement of all solutions, pre-titration to minimize the effect of iodine volatilization, accurate amperometric end point detection and careful accounting for dissolved oxygen in the reagents. As a result, the developed method is possibly the most accurate method of determination of dissolved oxygen available. Depending on measurement conditions and on the dissolved oxygen concentration the combined standard uncertainties of the method are in the range of 0.012–0.018 mg dm −3 corresponding to the k = 2 expanded uncertainty in the range of 0.023–0.035 mg dm −3 (0.27–0.38%, relative). This development enables more accurate calibration of electrochemical and optical dissolved oxygen sensors for routine analysis than has been possible before.

  17. Rubidium-strontium method

    International Nuclear Information System (INIS)

    Dubansky, A.

    1980-01-01

    The rubidium-strontium geological dating method is based on the determination of the Rb and Sr isotope ratio in rocks, mainly using mass spectrometry. The method is only practical for silicate minerals and rocks, potassium feldspars and slates. Also described is the rubidium-strontium isochrone method. This, however, requires a significant amount of experimental data and an analysis of large quantities of samples, often of the order of tons. The results are tabulated of rubidium-strontium dating of geological formations in the Czech Socialist Republic. (M.S.)

  18. An improved method for calculation of interface pressure force in PLIC-VOF methods

    International Nuclear Information System (INIS)

    Sefollahi, M.; Shirani, E.

    2004-08-01

    Conventional methods for the modeling of surface tension force in Piecewise Linear Interface Calculation-Volume of Fluid (PLIC-VOF) methods, such as Continuum Surface Force (CSF), Continuum Surface Stress (CSS) and also Meier's method, convert the surface tension force into a body force. Not only do they include the force in the interfacial cells but also in the neighboring cells. Thus they produce spurious currents. Also the pressure jump, due to the surface tension, is not calculated accurately in these methods. In this paper a more accurate method for the application of interface force in the computational modeling of free surfaces and interfaces which use PLIC-VOF methods is developed. This method is based on the evaluation of the surface tension force only in the interfacial cells and not the neighboring cells. Also the normal and the interface surface area needed for the calculation of the surface tension force is calculated more accurately. The present method is applied to a two-dimensional motionless drop of liquid and a bubble of gas as well as a non-circular two-dimensional drop, which oscillates due to the surface tension force, in an initially stagnant fluid with no gravity force. The results are compared with the results of the cases when CSF, CSS and Meier's methods are used. It is shown that the present method calculates pressure jump at the interface more accurately and produces less spurious currents comparing to CSS an CSF models. (author)

  19. Methods That Matter: Integrating Mixed Methods for More Effective Social Science Research

    Science.gov (United States)

    Hay, M. Cameron, Ed.

    2016-01-01

    To do research that really makes a difference--the authors of this book argue--social scientists need questions and methods that reflect the complexity of the world. Bringing together a consortium of voices across a variety of fields, "Methods that Matter" offers compelling and successful examples of mixed methods research that do just…

  20. Wielandt method applied to the diffusion equations discretized by finite element nodal methods

    International Nuclear Information System (INIS)

    Mugica R, A.; Valle G, E. del

    2003-01-01

    Nowadays the numerical methods of solution to the diffusion equation by means of algorithms and computer programs result so extensive due to the great number of routines and calculations that should carry out, this rebounds directly in the execution times of this programs, being obtained results in relatively long times. This work shows the application of an acceleration method of the convergence of the classic method of those powers that it reduces notably the number of necessary iterations for to obtain reliable results, what means that the compute times they see reduced in great measure. This method is known in the literature like Wielandt method and it has incorporated to a computer program that is based on the discretization of the neutron diffusion equations in plate geometry and stationary state by polynomial nodal methods. In this work the neutron diffusion equations are described for several energy groups and their discretization by means of those called physical nodal methods, being illustrated in particular the quadratic case. It is described a model problem widely described in the literature which is solved for the physical nodal grade schemes 1, 2, 3 and 4 in three different ways: to) with the classic method of the powers, b) method of the powers with the Wielandt acceleration and c) method of the powers with the Wielandt modified acceleration. The results for the model problem as well as for two additional problems known as benchmark problems are reported. Such acceleration method can also be implemented to problems of different geometry to the proposal in this work, besides being possible to extend their application to problems in 2 or 3 dimensions. (Author)

  1. Nanotube structures, methods of making nanotube structures, and methods of accessing intracellular space

    Science.gov (United States)

    VanDersarl, Jules J.; Xu, Alexander M.; Melosh, Nicholas A.; Tayebi, Noureddine

    2016-02-23

    In accordance with the purpose(s) of the present disclosure, as embodied and broadly described herein, embodiments of the present disclosure, in one aspect, relate to methods of making a structure including nanotubes, a structure including nanotubes, methods of delivering a fluid to a cell, methods of removing a fluid to a cell, methods of accessing intracellular space, and the like.

  2. Catalytic reforming methods

    Science.gov (United States)

    Tadd, Andrew R; Schwank, Johannes

    2013-05-14

    A catalytic reforming method is disclosed herein. The method includes sequentially supplying a plurality of feedstocks of variable compositions to a reformer. The method further includes adding a respective predetermined co-reactant to each of the plurality of feedstocks to obtain a substantially constant output from the reformer for the plurality of feedstocks. The respective predetermined co-reactant is based on a C/H/O atomic composition for a respective one of the plurality of feedstocks and a predetermined C/H/O atomic composition for the substantially constant output.

  3. FREEZING AND THAWING TIME PREDICTION METHODS OF FOODS II: NUMARICAL METHODS

    Directory of Open Access Journals (Sweden)

    Yahya TÜLEK

    1999-03-01

    Full Text Available Freezing is one of the excellent methods for the preservation of foods. If freezing and thawing processes and frozen storage method are carried out correctly, the original characteristics of the foods can remain almost unchanged over an extended periods of time. It is very important to determine the freezing and thawing time period of the foods, as they strongly influence the both quality of food material and process productivity and the economy. For developing a simple and effectively usable mathematical model, less amount of process parameters and physical properties should be enrolled in calculations. But it is a difficult to have all of these in one prediction method. For this reason, various freezing and thawing time prediction methods were proposed in literature and research studies have been going on.

  4. Divergence-Conforming Discontinuous Galerkin Methods and $C^0$ Interior Penalty Methods

    KAUST Repository

    Kanschat, Guido

    2014-01-01

    © 2014 Society for Industrial and Applied Mathematics. In this paper, we show that recently developed divergence-conforming methods for the Stokes problem have discrete stream functions. These stream functions in turn solve a continuous interior penalty problem for biharmonic equations. The equivalence is established for the most common methods in two dimensions based on interior penalty terms. Then, extensions of the concept to discontinuous Galerkin methods defined through lifting operators, for different weak formulations of the Stokes problem, and to three dimensions are discussed. Application of the equivalence result yields an optimal error estimate for the Stokes velocity without involving the pressure. Conversely, combined with a recent multigrid method for Stokes flow, we obtain a simple and uniform preconditioner for harmonic problems with simply supported and clamped boundary.

  5. Earthquake prediction by Kina Method

    International Nuclear Information System (INIS)

    Kianoosh, H.; Keypour, H.; Naderzadeh, A.; Motlagh, H.F.

    2005-01-01

    Earthquake prediction has been one of the earliest desires of the man. Scientists have worked hard to predict earthquakes for a long time. The results of these efforts can generally be divided into two methods of prediction: 1) Statistical Method, and 2) Empirical Method. In the first method, earthquakes are predicted using statistics and probabilities, while the second method utilizes variety of precursors for earthquake prediction. The latter method is time consuming and more costly. However, the result of neither method has fully satisfied the man up to now. In this paper a new method entitled 'Kiana Method' is introduced for earthquake prediction. This method offers more accurate results yet lower cost comparing to other conventional methods. In Kiana method the electrical and magnetic precursors are measured in an area. Then, the time and the magnitude of an earthquake in the future is calculated using electrical, and in particular, electrical capacitors formulas. In this method, by daily measurement of electrical resistance in an area we make clear that the area is capable of earthquake occurrence in the future or not. If the result shows a positive sign, then the occurrence time and the magnitude can be estimated by the measured quantities. This paper explains the procedure and details of this prediction method. (authors)

  6. Isotope methods in hydrology

    International Nuclear Information System (INIS)

    Moser, H.; Rauert, W.

    1980-01-01

    Of the investigation methods used in hydrology, tracer methods hold a special place as they are the only ones which give direct insight into the movement and distribution processes taking place in surface and ground waters. Besides the labelling of water with salts and dyes, as in the past, in recent years the use of isotopes in hydrology, in water research and use, in ground-water protection and in hydraulic engineering has increased. This by no means replaces proven methods of hydrological investigation but tends rather to complement and expand them through inter-disciplinary cooperation. The book offers a general introduction to the application of various isotope methods to specific hydrogeological and hydrological problems. The idea is to place the hydrogeologist and the hydrologist in the position to recognize which isotope method will help him solve his particular problem or indeed, make a solution possible at all. He should also be able to recognize what the prerequisites are and what work and expenditure the use of such methods involves. May the book contribute to promoting cooperation between hydrogeologists, hydrologists, hydraulic engineers and isotope specialists, and thus supplement proven methods of investigation in hydrological research and water utilization and protection wherever the use of isotope methods proves to be of advantage. (orig./HP) [de

  7. Storage and Disposal of Solid Radioactive Waste; Stockage et Evacuation des Dechets Radioactifs Solides; 0425 0420 0414 ; Almacenamiento y Evacuacion de Desechos Radiactivos Solidos

    Energy Technology Data Exchange (ETDEWEB)

    Pomarola, J. [Chef du Bureau Technique, Service de Controle des Radiations et de Genie Radioactif, Commissariat a l' Energie Atomique, Saclay (France)

    1960-07-01

    evacuacion definitiva: - en la superficie; - en el subsuelo; - en el mar. Un importante factor para elegir una u otra solucion lo constituyen las consideraciones de tipo economico. (author) [Russian] V nastojashhem dokumente rassmatrivajutsja reshenija otnositel'no okonchatel'nogo prednaznachenija tverdyh radioaktivnyh othodov. 1 - Prezhde vsego neobhodimo predusmotret' organizovannoe vremennoe zahoronenie. II - Okonchatel'noe zahoronenie : Vvidu aktivnosti i specifiki othodov, pri okonchatel'nom zahoronenii trebuetsja ustanovit': - Mesto i vid transportirovki kak vnutri, tak i vne jadernyh centrov. Vybor reshenija vytekaet iz vysheukazannyh soobrazhenij ; dalee posledovatel'no rassmatrivaetsja okonchatel'noe zahoronenie: - Na poverhnosti zemli - V zemle - V more Soobrazhenija jekonomicheskogo porjadka javljajutsja vazhnym faktorom v vybore reshenija. (author)

  8. Å ta spørsmål om form på alvor

    Directory of Open Access Journals (Sweden)

    Liv Mildrid Gjernes

    2017-01-01

    selvbiografiske elementer, referanser fra ulike estetiske praksiser og noe filosofisk teori som jeg mener kan belyse og inspirere. Essayet plasserer Åpen forms metode i en vitenskapsteoretisk sammenheng. Det inneholder også noe utdypende teori som samtidig belyser det estetiske som en allmenn kunnskapsform. 

  9. Single-Case Designs and Qualitative Methods: Applying a Mixed Methods Research Perspective

    Science.gov (United States)

    Hitchcock, John H.; Nastasi, Bonnie K.; Summerville, Meredith

    2010-01-01

    The purpose of this conceptual paper is to describe a design that mixes single-case (sometimes referred to as single-subject) and qualitative methods, hereafter referred to as a single-case mixed methods design (SCD-MM). Minimal attention has been given to the topic of applying qualitative methods to SCD work in the literature. These two…

  10. Radiochemistry methods in DOE Methods for Evaluating Environmental and Waste Management Samples: Addressing new challenges

    International Nuclear Information System (INIS)

    Fadeff, S.K.; Goheen, S.C.; Riley, R.G.

    1994-01-01

    Radiochemistry methods in Department of Energy Methods for Evaluating Environmental and Waste Management Samples (DOE Methods) add to the repertoire of other standard methods in support of U.S. Department of Energy environmental restoration and waste management (DOE/EM) radiochemical characterization activities. Current standard sources of radiochemistry methods are not always applicable for evaluating DOE/EM samples. Examples of current sources include those provided by the US Environmental Protection Agency, the American Society for Testing and Materials, Standard Methods for the Examination of Water and Wastewater, and Environmental Measurements Laboratory Procedures Manual (HASL-300). The applicability of these methods is generally limited to specific matrices (usually water), low-level radioactive samples, and a limited number of analytes. DOE Methods complements these current standard methods by addressing the complexities of EM characterization needs. The process for determining DOE/EM radiochemistry characterization needs is discussed. In this context of DOE/EM needs, the applicability of other sources of standard radiochemistry methods is defined, and gaps in methodology are identified. Current methods in DOE Methods and the EM characterization needs they address are discussed. Sources of new methods and the methods incorporation process are discussed. The means for individuals to participate in (1) identification of DOE/EM needs, (2) the methods incorporation process, and (3) submission of new methods are identified

  11. The Generalized Sturmian Method

    DEFF Research Database (Denmark)

    Avery, James Emil

    2011-01-01

    these ideas clearly so that they become more accessible. By bringing together these non-standard methods, the book intends to inspire graduate students, postdoctoral researchers and academics to think of novel approaches. Is there a method out there that we have not thought of yet? Can we design a new method...... generations of researchers were left to work out how to achieve this ambitious goal for molecular systems of ever-increasing size. This book focuses on non-mainstream methods to solve the molecular electronic Schrödinger equation. Each method is based on a set of core ideas and this volume aims to explain...

  12. Conformable variational iteration method

    Directory of Open Access Journals (Sweden)

    Omer Acan

    2017-02-01

    Full Text Available In this study, we introduce the conformable variational iteration method based on new defined fractional derivative called conformable fractional derivative. This new method is applied two fractional order ordinary differential equations. To see how the solutions of this method, linear homogeneous and non-linear non-homogeneous fractional ordinary differential equations are selected. Obtained results are compared the exact solutions and their graphics are plotted to demonstrate efficiency and accuracy of the method.

  13. A rapid method for soil cement design : Louisiana slope value method.

    Science.gov (United States)

    1964-03-01

    The current procedure used by the Louisiana Department of Highways for laboratory design of cement stabilized soil base and subbase courses is taken from standard AASHO test methods, patterned after Portland Cement Association criteria. These methods...

  14. Inventory of LCIA selection methods for assessing toxic releases. Methods and typology report part B

    DEFF Research Database (Denmark)

    Larsen, Henrik Fred; Birkved, Morten; Hauschild, Michael Zwicky

    method(s) in Work package 8 (WP8) of the OMNIITOX project. The selection methods and the other CRS methods are described in detail, a set of evaluation criteria are developed and the methods are evaluated against these criteria. This report (Deliverable 11B (D11B)) gives the results from task 7.1d, 7.1e......This report describes an inventory of Life Cycle Impact Assessment (LCIA) selection methods for assessing toxic releases. It consists of an inventory of current selection methods and other Chemical Ranking and Scoring (CRS) methods assessed to be relevant for the development of (a) new selection...... and 7.1f of WP 7 for selection methods. The other part of D11 (D11A) is reported in another report and deals with characterisation methods. A selection method is a method for prioritising chemical emissions to be included in an LCIA characterisation of toxic releases, i.e. calculating indicator scores...

  15. New mixed finite-element methods

    International Nuclear Information System (INIS)

    Franca, L.P.

    1987-01-01

    New finite-element methods are proposed for mixed variational formulations. The methods are constructed by adding to the classical Galerkin method various least-squares like terms. The additional terms involve integrals over element interiors, and include mesh-parameter dependent coefficients. The methods are designed to enhance stability. Consistency is achieved in the sense that exact solutions identically satisfy the variational equations.Applied to several problems, simple finite-element interpolations are rendered convergent, including convenient equal-order interpolations generally unstable within the Galerkin approach. The methods are subdivided into two classes according to the manner in which stability is attained: (1) circumventing Babuska-Brezzi condition methods; (2) satisfying Babuska-Brezzi condition methods. Convergence is established for each class of methods. Applications of the first class of methods to Stokes flow and compressible linear elasticity are presented. The second class of methods is applied to the Poisson, Timoshenko beam and incompressible elasticity problems. Numerical results demonstrate the good stability and accuracy of the methods, and confirm the error estimates

  16. Lesson learned - CGID based on the Method 1 and Method 2 for digital equipment

    International Nuclear Information System (INIS)

    Hwang, Wonil; Sohn, Kwang Young; Cho, Chang Hwan; Kim, Sung Jong

    2015-01-01

    The acceptance methods associated with commercial-grade dedication are the following: 1) Special tests and inspection (Method 1) 2) Commercial-grade surveys (Method 2) 3) Source verification (Method 3) 4) An acceptable item and supplier performance record (Method 4) Special tests and inspections, often referred to as Method 1, are performed by the dedicating entity after the item is received to verify selected critical characteristics. Conducting a commercial-grade survey of a supplier is often referred to as Method 2. Supplier audits to verify compliance with a nuclear QA program do not meet the intent of a commercial-grade survey. Source verification, often referred to as Method 3, entails verification of critical characteristics during manufacture and testing of the item being procured. The performance history (good or bad) of the item and supplier is a consideration when determining the use of the other acceptance methods and the rigor with which they are used on a case-by-case basis. Some digital equipment system has the delivery reference and its operating history for Nuclear Power Plant as far as surveyed. However it was found that there is difficulty in collecting this of supporting data sheet, so that supplier usually decide to conduct the CGID based on the Method-1 and Method-2 based on the initial qualification likely. It is conceived that the Method-4 might be a better approach for CGID(Commercial Grade Item Dedication) even if there are some difficulties in data package for justifying CGID from the vendor and operating organization. This paper present the lesson learned from the consulting for Method-1 and 2 for digital equipment dedication. Considering all the information above, there are a couple of issues to remind in order to perform the CGID for Method-2. In doing commercial grade survey based on Method 2, quality personnel as well as technical engineer shall be involved for integral dedication. Other than this, the review of critical

  17. Statistical methods

    CERN Document Server

    Szulc, Stefan

    1965-01-01

    Statistical Methods provides a discussion of the principles of the organization and technique of research, with emphasis on its application to the problems in social statistics. This book discusses branch statistics, which aims to develop practical ways of collecting and processing numerical data and to adapt general statistical methods to the objectives in a given field.Organized into five parts encompassing 22 chapters, this book begins with an overview of how to organize the collection of such information on individual units, primarily as accomplished by government agencies. This text then

  18. Sieve methods

    CERN Document Server

    Halberstam, Heine

    2011-01-01

    Derived from the techniques of analytic number theory, sieve theory employs methods from mathematical analysis to solve number-theoretical problems. This text by a noted pair of experts is regarded as the definitive work on the subject. It formulates the general sieve problem, explores the theoretical background, and illustrates significant applications.""For years to come, Sieve Methods will be vital to those seeking to work in the subject, and also to those seeking to make applications,"" noted prominent mathematician Hugh Montgomery in his review of this volume for the Bulletin of the Ameri

  19. Differential equation method

    International Nuclear Information System (INIS)

    Kotikov, A.V.

    1993-01-01

    A new method of massive Feynman diagrams calculation is presented. It provides a fairly simple procedure to obtain the result without the D-space integral calculation (for the dimensional regularization). Some diagrams are calculated as an illustration of this method capacities. (author). 7 refs

  20. Detection methods for irradiated food

    International Nuclear Information System (INIS)

    Stevenson, M.H.

    1993-01-01

    The plenary lecture gives a brief historical review of the development of methods for the detection of food irradiation and defines the demands on such methods. The methods described in detail are as follows: 1) Physical methods: As examples of luminescence methods, thermoluminescence and chermoluminescence are mentioned; ESR spectroscopy is discussed in detail by means of individual examples (crustaceans, frutis and vegetables, spieces and herbs, nuts). 2) Chemical methods: Examples given for these are methods that make use of alterations in lipids through radiation (formation of long-chain hydrocarbons, formation of 2-alkyl butanones), respectively radiation-induced alterations in the DNA. 3) Microbiological methods. An extensive bibliography is appended. (VHE) [de