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Sample records for multidimensional heteronuclear nmr

  1. Structural studies of the activation of the two component receiver domain NTRC by multidimensional heteronuclear NMR

    Energy Technology Data Exchange (ETDEWEB)

    Nohaile, Michael James [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    Multidimensional heteronuclear NMR spectroscopy was used to investigate the N-terminal domain of the transcriptional enhancer NTRC (NiTrogen Regulatory protein C). This domain belongs to the family of receiver domains of two-component regulatory systems involved in signal transduction. Phosphorylation of NTRC at D54 leads to an activated form of the molecule which stimulates transcription of genes involved in nitrogen regulation. Three and four dimensional NMR techniques were used to determine an intermediate resolution structure of the unphosphorylated, inactive form of the N-terminal domain of NTRC. The structure is comprised of five α-helices and a five-stranded β-sheet in a (β/α)5 topology. Analysis of the backbone dynamics of NTRC indicate that helix 4 and strand 5 are significantly more flexible than the rest of the secondary structure of the protein and that the loops making up the active site are flexible. The short lifetime of phospho-NTRC hampers the study of this form. However, conditions for determining the resonance assignments and, possibly, the three dimensional structure of phosphorylated NTRC have been obtained. Tentative assignments of the phosphorylated form indicate that the majority of the changes that NTRC experiences upon phosphorylation occur in helix 3, strand 4, helix 4, strand 5, and the loop between strand 5 and helix 5 (the 3445 face of NTRC) as well as near the site of phosphorylation. In order to examine a stable, activated form of the protein, constitutively active mutants of NTRC were investigated.

  2. Heteronuclear cross-polarization in multinuclear multidimensional NMR: Prospects for triple-resonance CP

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    Majumdar, A.; Zuiderweg, E.R.P. [Univ. of Michigan, Ann Arbor, MI (United States)

    1994-12-01

    Heteronuclear multiple-pulse-based Cross Polarization (HECP) between scalar coupled spins is gaining an important role in high-resolution multidimensional NMR of isotopically labeled biomolecules, especially in experiments involving net magnetization transfer. It has generally been observed that in these situations, the performance of HECP is superior to that of INEPT-based sequences. In particular, HECP-based three-dimensional HCCH spectroscopy is more efficient than the INEPT version of the same experiment. Differences in sensitivity have been intuitively attributed to relaxation effects and technical factors such as radiofrequency (rf) inhomogeneity We present theoretical analyses and computer simulations to probe the effects of these factors. Relaxation effects were treated phenomenologically; we found that relaxation differences are relatively small (up to 25%) between pulsed-free-precession (INEPT) and HECP-although always in favor of HECP. We explored the rf effects by employing a Gaussian distribution of rf amplitude over sample volume. We found that inhomogeneity effects significantly favor HECP over INEPT, especially under conditions of {open_quotes}matched {close_quotes} inhomogeneity in the two rf coils. The differences in favor of HECP indicate that an extension of HECP to triple resonance experiments (TRCP) in I -> S -> Q net transfers might yield better results relative to analogous INEPT-based net transfers. We theoretically analyze the possibilities of TRCP and find that transfer functions are critically dependent on the ratio J{sub IS}/J{sub SQ}. When J{sub IS} equals J{sub SQ}, we find that 100% transfer is possible for truly simultaneous TRCP and this transfer is obtained in a time 1.41 /J. The TRCP time requirement compares favorably with optimally concatenated INEPT-transfers, where net transfer I -> S -> Q is complete at 1.5 /J.

  3. Structural studies of bacterial transcriptional regulatory proteins by multidimensional heteronuclear NMR

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    Volkman, Brian Finley [Univ. of California, Berkeley, CA (United States)

    1995-02-01

    Nuclear magnetic resonance spectroscopy was used to elucidate detailed structural information for peptide and protein molecules. A small peptide was designed and synthesized, and its three-dimensional structure was calculated using distance information derived from two-dimensional NMR measurements. The peptide was used to induce antibodies in mice, and the cross-reactivity of the antibodies with a related protein was analyzed with enzyme-linked immunosorbent assays. Two proteins which are involved in regulation of transcription in bacteria were also studied. The ferric uptake regulation (Fur) protein is a metal-dependent repressor which controls iron uptake in bacteria. Two- and three-dimensional NMR techniques, coupled with uniform and selective isotope labeling allowed the nearly complete assignment of the resonances of the metal-binding domain of the Fur protein. NTRC is a transcriptional enhancer binding protein whose N-terminal domain is a "receiver domain" in the family of "two-component" regulatory systems. Phosphorylation of the N-terminal domain of NTRC activates the initiation of transcription of aeries encoding proteins involved in nitrogen regulation. Three- and four-dimensional NMR spectroscopy methods have been used to complete the resonance assignments and determine the solution structure of the N-terminal receiver domain of the NTRC protein. Comparison of the solution structure of the NTRC receiver domain with the crystal structures of the homologous protein CheY reveals a very similar fold, with the only significant difference being the position of helix 4 relative to the rest of the protein. The determination of the structure of the NTRC receiver domain is the first step toward understanding a mechanism of signal transduction which is common to many bacterial regulatory systems.

  4. Heteronuclear multidimensional NMR and homology modelling studies of the C-terminal nucleotide-binding domain of the human mitochondrial ABC transporter ABCB6

    Energy Technology Data Exchange (ETDEWEB)

    Kurashima-Ito, Kaori [RIKEN, Cellular and Molecular Biology Laboratory (Japan); Ikeya, Teppei [National Institute of Advanced Industrial Science and Technology (AIST), (Japan); Senbongi, Hiroshi [Mitochondrial Diseases Group, MRC Dunn Human NutritionUnit (United Kingdom); Tochio, Hidehito [International Graduate School of Arts and Sciences, Supramolecular Biology, Yokohama City University, Molecular Biophysics Laboratory (Japan); Mikawa, Tsutomu [RIKEN, Cellular and Molecular Biology Laboratory (Japan); Shibata, Takehiko [RIKEN, Shibata Distinguished Senior Scientist Laboratory (Japan); Ito, Yutaka [RIKEN, Cellular and Molecular Biology Laboratory (Japan)], E-mail: ito-yutaka@center.tmu.ac.jp

    2006-05-15

    Human ATP-binding cassette, sub-family B, member 6 (ABCB6) is a mitochondrial ABC transporter, and presumably contributes to iron homeostasis. Aimed at understanding the structural basis for the conformational changes accompanying the substrate-transportation cycle, we have studied the C-terminal nucleotide-binding domain of ABCB6 (ABCB6-C) in both the nucleotide-free and ADP-bound states by heteronuclear multidimensional NMR and homology modelling. A non-linear sampling scheme was utilised for indirectly acquired {sup 13}C and {sup 15}N dimensions of all 3D triple-resonance NMR experiments, in order to overcome the instability and the low solubility of ABCB6-C. The backbone resonances for approximately 25% of non-proline residues, which are mostly distributed around the functionally important loops and in the Helical domain, were not observed for nucleotide-free form of ABCB6-C. From the pH, temperature and magnetic field strength dependencies of the resonance intensities, we concluded that this incompleteness in the assignments is mainly due to the exchange between multiple conformations at an intermediate rate on the NMR timescale. These localised conformational dynamics remained in ADP-bound ABCB6-C except for the loops responsible for adenine base and {alpha}/{beta}-phosphate binding. These results revealed that the localised dynamic cooperativity, which was recently proposed for a prokaryotic ABC MJ1267, also exists in a higher eukaryotic ABC, and is presumably shared by all members of the ABC family. Since the Helical domain is the putative interface to the transmembrane domain, this cooperativity may explain the coupled functions between domains in the substrate-transportation cycle.

  5. Novel multi-dimensional heteronuclear NMR techniques for the study of 13C-O-acetylated oligosaccharides: Expanding the dimensions for carbohydrate structures

    Energy Technology Data Exchange (ETDEWEB)

    Jones, David N.M. [University of Colorado Health Sciences Center, Departments of Pharmacology (United States); Bendiak, Brad [University of Colorado Health Sciences Center, Departments of Cellular and Structural Biology (United States)

    1999-10-15

    Complex carbohydrates have critical roles in a wide variety of biological processes. An understanding of the molecular mechanisms that underlie these processes is essential in the development of novel oligosaccharide-based therapeutic strategies. Unfortunately, obtaining detailed structural information for larger oligosaccharides (>10 residues) can be exceedingly difficult, especially where the amount of sample available is limited. Here we demonstrate the application of {sup 13} C O-acetylation in combination with novel NMR experiments to obtain much of the information required to characterize the primary structure of oligosaccharides. (H)C{sub Me}COH-HEHAHA and H(C{sub Me})COH-HEHAHA experiments are presented that use heteronuclear Hartmann-Hahn transfer to correlate the acetyl groups with sugar ring protons in peracetylated oligosaccharides. The in-phase, pure absorption nature of the correlation peaks in these experiments allows measurement of both chemical shifts and, importantly, {sup 1}H-{sup 1}H coupling constants that are used to define the stereochemistry of the sugar ring. The (HC{sub Me})COH and (HC{sub Me})COH-RELAY experiments provide additional methods for obtaining chemical shift assignments for larger oligosaccharides to define the sites of glycosidic linkages from the patterns of acetylation.

  6. Heteronuclear three-dimensional NMR spectroscopy. Natural abundance 13C chemical shift editing of 1H-1H COSY spectra

    International Nuclear Information System (INIS)

    Fesik, S.W.; Gampe, R.T. Jr.; Zuiderweg, E.R.P.

    1989-01-01

    It has been demonstrated that heteronuclear 3D NMR spectroscopy can be effectively applied to small molecules with 13 C at natural abundance. A 78mM solution of the aminoglycoside, kanamycin A was used for this experiment. The heteronuclear 3D NMR spectroscopy is shown to be a useful method for resolving spectral overlap in all frequency domains. 10 refs., 2 figs

  7. 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

  8. 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.

  9. New strategy for stable-isotope-aided, multidimensional NMR spectroscopy of DNA oligomers

    Energy Technology Data Exchange (ETDEWEB)

    Ono, Okira; Tate, Shin-Ichi; Kainosho, Masatsune [Tokyo Metropolitan Univ., Tokyo (Japan)

    1994-12-01

    Nuclear Magnetic Resonance (NMR) is the most efficient method for determining the solution structures of biomolecules. By applying multidimensional heteronuclear NMR techniques to {sup 13}C/{sup 15}N-labeled proteins, we can determine the solution structures of proteins with molecular mass of 20 to 30kDa at an accuracy similar to that of x-ray crystallography. Improvements in NMR instrumentation and techniques as well as the development of protein engineering methods for labeling proteins have rapidly advanced multidimensional heteronuclear NMR of proteins. In contrast, multidimensional heteronuclear NMR studies of nucleic acids is less advanced because there were no efficient methods for preparing large amounts of labeled DNA/RNA oligomers. In this report, we focused on the chemical synthesis of DNA oligomers labeled at specific residue(s). RNA oligomers with specific labels, which are difficult to synthesize by the enzyme method, can be synthesized by the chemical method. The specific labels are useful for conformational analysis of larger molecules such as protein-nucleic acid complexes.

  10. Complete resonance assignment for the polypeptide backbone of interleukin 1β using three-dimensional heteronuclear NMR spectroscopy

    International Nuclear Information System (INIS)

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

    1990-01-01

    The complete sequence-specific assignment of the 15 N and 1 H backbone resonances of the NMR spectrum of recombinant human interleukin 1β has been obtained by using primarily 15 N- 1 H heteronuclear three-dimensional (3D) NMR techniques in combination with 15 N- 1 H heteronuclear and 1 H homonuclear two-dimensional NMR. The fingerprint region of the spectrum was analyzed by using a combination of 3D heteronuclear 1 H Hartmann-Hahn 15 N- 1 H multiple quantum coherence (3D HOHAHA-HMQC) and 3D heteronuclear 1 H nuclear Overhauser 15 N- 1 H multiple quantum coherence (3D NOESY-HMQC) spectroscopies. The authors show that the problems of amide NH and C α H chemical shift degeneracy that are prevalent for proteins of the size are readily overcome by using the 3D heteronuclear NMR technique. A doubling of some peaks in the spectrum was found to be due to N-terminal heterogeneity of the 15 N-labeled protein, corresponding to a mixture of wild-type and des-Ala-1-interleukin 1β. The complete list of 15 N and 1 H assignments is given for all the amide NH and C α H resonances of all non-proline residues, as well as the 1 H assignments for some of the amino acid side chains. This first example of the sequence-specific assignment of a protein using heteronuclear 3D NMR provides a basis for further conformational and dynamic studies of interleukin 1β

  11. Reaction monitoring using hyperpolarized NMR with scaling of heteronuclear couplings by optimal tracking

    Science.gov (United States)

    Zhang, Guannan; Schilling, Franz; Glaser, Steffen J.; Hilty, Christian

    2016-11-01

    Off-resonance decoupling using the method of Scaling of Heteronuclear Couplings by Optimal Tracking (SHOT) enables determination of heteronuclear correlations of chemical shifts in single scan NMR spectra. Through modulation of J-coupling evolution by shaped radio frequency pulses, off resonance decoupling using SHOT pulses causes a user-defined dependence of the observed J-splitting, such as the splitting of 13C peaks, on the chemical shift offset of coupled nuclei, such as 1H. Because a decoupling experiment requires only a single scan, this method is suitable for characterizing on-going chemical reactions using hyperpolarization by dissolution dynamic nuclear polarization (D-DNP). We demonstrate the calculation of [13C, 1H] chemical shift correlations of the carbanionic active sites from hyperpolarized styrene polymerized using sodium naphthalene as an initiator. While off resonance decoupling by SHOT pulses does not enhance the resolution in the same way as a 2D NMR spectrum would, the ability to obtain the correlations in single scans makes this method ideal for determination of chemical shifts in on-going reactions on the second time scale. In addition, we present a novel SHOT pulse that allows to scale J-splittings 50% larger than the respective J-coupling constant. This feature can be used to enhance the resolution of the indirectly detected chemical shift and reduce peak overlap, as demonstrated in a model reaction between p-anisaldehyde and isobutylamine. For both pulses, the accuracy is evaluated under changing signal-to-noise ratios (SNR) of the peaks from reactants and reaction products, with an overall standard deviation of chemical shift differences compared to reference spectra of 0.02 ppm when measured on a 400 MHz NMR spectrometer. Notably, the appearance of decoupling side-bands, which scale with peak intensity, appears to be of secondary importance.

  12. Highly efficient F-19 heteronuclear decoupling in solid-state NMR spectroscopy using supercycled refocused-CW irradiation

    DEFF Research Database (Denmark)

    Equbal, Asif; Basse, Kristoffer; Nielsen, Niels Christian

    2016-01-01

    We present heteronuclear F-19 refocused CW (rCW) decoupling pulse sequences for solid-state magic-angle- spinning NMR applications. The decoupling sequences have been designed specifically to ensure suppression of the pertinent C-13-F-19 dipolar coupling interactions while simultaneously suppress...

  13. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Gronenborn, A.M.; Clore, G.M. [National Institutes of Health, Bethesda, MD (United States)

    1994-12-01

    Complete understanding of a protein`s function and mechanism of action can only be achieved with a knowledge of its three-dimensional structure at atomic resolution. At present, there are two methods available for determining such structures. The first method, which has been established for many years, is x-ray diffraction of protein single crystals. The second method has blossomed only in the last 5 years and is based on the application of nuclear magnetic resonance (NMR) spectroscopy to proteins in solution. This review paper describes three- and four-dimensional NMR methods applied to protein structure determination and was adapted from Clore and Gronenborn. The review focuses on the underlying principals and practice of multidimensional NMR and the structural information obtained.

  14. PSYCHE CPMG-HSQMBC: An NMR Spectroscopic Method for Precise and Simple Measurement of Long-Range Heteronuclear Coupling Constants.

    Science.gov (United States)

    Timári, István; Szilágyi, László; Kövér, Katalin E

    2015-09-28

    Among the NMR spectroscopic parameters, long-range heteronuclear coupling constants convey invaluable information on torsion angles relevant to glycosidic linkages of carbohydrates. A broadband homonuclear decoupled PSYCHE CPMG-HSQMBC method for the precise and direct measurement of multiple-bond heteronuclear couplings is presented. The PSYCHE scheme built into the pulse sequence efficiently eliminates unwanted proton-proton splittings from the heteronuclear multiplets so that the desired heteronuclear couplings can be determined simply by measuring frequency differences between peak maxima of pure antiphase doublets. Moreover, PSYCHE CPMG-HSQMBC can provide significant improvement in sensitivity as compared to an earlier Zangger-Sterk-based method. Applications of the proposed pulse sequence are demonstrated for the extraction of (n)J((1)H,(77)Se) and (n)J((1)H,(13)C) values, respectively, in carbohydrates; further extensions can be envisioned in any J-based structural and conformational studies. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. NMR longitudinal relaxation enhancement in metal halides by heteronuclear polarization exchange during magic-angle spinning

    Energy Technology Data Exchange (ETDEWEB)

    Shmyreva, Anna A. [Center for Magnetic Resonance, St. Petersburg State University, St. Petersburg 198504 (Russian Federation); Safdari, Majid; Furó, István [Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm (Sweden); Dvinskikh, Sergey V., E-mail: sergeid@kth.se [Department of Chemistry, KTH Royal Institute of Technology, SE-10044 Stockholm (Sweden); Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg 199034 (Russian Federation)

    2016-06-14

    Orders of magnitude decrease of {sup 207}Pb and {sup 199}Hg NMR longitudinal relaxation times T{sub 1} upon magic-angle-spinning (MAS) are observed and systematically investigated in solid lead and mercury halides MeX{sub 2} (Me = Pb, Hg and X = Cl, Br, I). In lead(II) halides, the most dramatic decrease of T{sub 1} relative to that in a static sample is in PbI{sub 2}, while it is smaller but still significant in PbBr{sub 2}, and not detectable in PbCl{sub 2}. The effect is magnetic-field dependent but independent of the spinning speed in the range 200–15 000 Hz. The observed relaxation enhancement is explained by laboratory-frame heteronuclear polarization exchange due to crossing between energy levels of spin-1/2 metal nuclei and adjacent quadrupolar-spin halogen nuclei. The enhancement effect is also present in lead-containing organometal halide perovskites. Our results demonstrate that in affected samples, it is the relaxation data recorded under non-spinning conditions that characterize the local properties at the metal sites. A practical advantage of fast relaxation at slow MAS is that spectral shapes with orientational chemical shift anisotropy information well retained can be acquired within a shorter experimental time.

  16. 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

  17. Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D H2BC and clean HMBC

    DEFF Research Database (Denmark)

    Meier, Sebastian; Petersen, Bent O.; Duus, Jens Øllgaard

    2009-01-01

    carbohydrates whose structure has been determined by NMR, not least due to the enhanced resolution offered by the third dimension in 3D H2BC and the improved spectral quality due to artifact suppression in clean HMBC. Hence these new experiments set the scene to take advantage of the sensitivity boost achieved...... by the latest generation of cold probes for NMR structure determination of even larger and more complex carbohydrates in solution.......The new NMR experiments 3D H2BC and clean HMBC are explored for challenging applications to a complex carbohydrate at natural abundance of 13C. The 3D H2BC experiment is crucial for sequential assignment as it yields heteronuclear one- and two-bond together with COSY correlations for the 1H spins...

  18. Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhiyong [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel); Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, Fujian 361005 (China); Smith, Pieter E. S.; Frydman, Lucio, E-mail: lucio.frydman@weizmann.ac.il [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel)

    2014-11-21

    Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns.

  19. Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm

    International Nuclear Information System (INIS)

    Zhang, Zhiyong; Smith, Pieter E. S.; Frydman, Lucio

    2014-01-01

    Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns

  20. NMR of lignins

    Science.gov (United States)

    John Ralph; Larry L. Landucci

    2010-01-01

    This chapter will consider the basic aspects and findings of several forms of NMR spectroscopy, including separate discussions of proton, carbon, heteronuclear, and multidimensional NMR. Enhanced focus will be on 13C NMR, because of its qualitative and quantitative importance, followed by NMR’s contributions to our understanding of lignin...

  1. Timing and related artifacts in multidimensional NMR

    International Nuclear Information System (INIS)

    Marion, Dominique

    2012-01-01

    The information content of multidimensional NMR spectra is limited by the presence of several kinds of artifacts that originate from incorrect timing of evolution periods. The objective of this review is to provide tools for successful implementation of published pulse sequences, in which timing and pulse compensations are often implicit. We will analyze the constraints set by the use of Fourier transformation, the spin precession during rectangular or shaped pulses, the Bloch-Siegert effects due to pulse on other spins and the delay introduced by the filters for the acquisition dimension. A frequency dependent phase correction or an incorrect scaling of the first data point leads to baseline offsets or curvature due to the properties of the Fourier transform. Because any r.f. pulse has a finite length, chemical shift is always active during excitation, flip-back, inversion, and refocusing pulses. Rectangular or selective shaped pulses can be split into three periods: an ideal rotation surrounded by two chemical shift evolution periods, which should be subtracted from the adjacent delays to avoid linear phase correction. Bloch-Siegert effects originate from irradiation at frequencies near those observed in the spectrum and can lead to phase or frequency shifts. They can be minimized by simultaneous irradiation on both sides of the observed spins. In terms of timing, the very end of the pulse sequence the acquisition behaves differently since the data are filtered by either analog or digital means. This additional delay is filter and spectrometer specific and should be tuned to minimize the required phase correction. Combined together, all these adjustments lead to perfectly phased spectra with flat baseline and no peak shifts or distortion. (author)

  2. An improved synthesis of α-13C glycine and heteronuclear NMR studies of its incorporation into thioredoxin

    International Nuclear Information System (INIS)

    Wishart, D.S.; Sykes, B.D.; Richards, F.M.

    1992-01-01

    We present an improved method to easily prepare gram quantities of α- 13 C glycine beginning from K 13 CN. The four step synthesis involves the production of an N, N-diphenyl-cyanoformamidine intermediate through the coupling of cyanide to N, N-diphenylcarbodiimide. Subsequent reduction by LiAlH 4 and hydrolysis of the resulting amidine produces fully enriched α- 13 C labelled glycine with a 45-50% yield. This relatively fast and simple synthesis uses only commonly available compounds and requires no special equipment, making the process easy to perform in any well equipped biochemistry laboratory. We further demonstrate that the product may be used, without extensive purification, to specifically label bacterially expressed proteins (E. coli thioredoxin) through standard biosynthetic procedures. We also show that the 13 C glycine-labelled protein may be readily analyzed using commonly available heteronuclear NMR techniques. Complete assignments for all 9 glycines of native E. coli thoredoxin are presented. (Author)

  3. Adiabatic Low-Pass J Filters for Artifact Suppression in Heteronuclear NMR

    DEFF Research Database (Denmark)

    Meier, Sebastian; Benie, Andrew J; Duus, Jens Øllgaard

    2009-01-01

    NMR artifact purging: Modern NMR experiments depend on efficient coherence transfer pathways for their sensitivity and on suppression of undesired pathways leading to artifacts for their spectral clarity. A novel robust adiabatic element suppresses hard-to-get-at artifacts....

  4. Rapid prediction of multi-dimensional NMR data sets

    International Nuclear Information System (INIS)

    Gradmann, Sabine; Ader, Christian; Heinrich, Ines; Nand, Deepak; Dittmann, Marc; Cukkemane, Abhishek; Dijk, Marc van; Bonvin, Alexandre M. J. J.; Engelhard, Martin; Baldus, Marc

    2012-01-01

    We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such “in silico” data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAShttp://www.wenmr.eu/services/FANDAS).

  5. Rapid prediction of multi-dimensional NMR data sets

    Energy Technology Data Exchange (ETDEWEB)

    Gradmann, Sabine; Ader, Christian [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Heinrich, Ines [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Nand, Deepak [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Dittmann, Marc [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Cukkemane, Abhishek; Dijk, Marc van; Bonvin, Alexandre M. J. J. [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands); Engelhard, Martin [Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry (Germany); Baldus, Marc, E-mail: m.baldus@uu.nl [Utrecht University, Faculty of Science, Bijvoet Center for Biomolecular Research (Netherlands)

    2012-12-15

    We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such 'in silico' data sets during the various stages of the NMR data analysis. The input parameters can vary from (partial) NMR assignments directly obtained from experiments to values retrieved from in silico prediction programs. The resulting predicted data sets enable a rapid evaluation of sample labeling in light of spectral resolution and structural content, using standard NMR software such as Sparky. In addition, direct comparison to experimental data sets can be used to validate NMR assignments, distinguish different molecular components, refine structural models or other parameters derived from NMR data. The method is demonstrated in the context of solid-state NMR data obtained for the cyclic nucleotide binding domain of a bacterial cyclic nucleotide-gated channel and on membrane-embedded sensory rhodopsin II. FANDAS is freely available as web portal under WeNMR (http://www.wenmr.eu/services/FANDAShttp://www.wenmr.eu/services/FANDAS).

  6. NMR studies of isotopically labeled RNA

    Energy Technology Data Exchange (ETDEWEB)

    Pardi, A. [Univ. of Colorado, Boulder, CO (United States)

    1994-12-01

    In summary, the ability to generate NMR quantities of {sup 15}N and {sup 13}C-labeled RNAs has led to the development of heteronuclear multi-dimensional NMR techniques for simplifying the resonance assignment and structure determination of RNAs. These methods for synthesizing isotopically labeled RNAs are only several years old, and thus there are still relatively few applications of heteronuclear multi-dimensional NMR techniques to RNA. However, given the critical role that RNAs play in cellular function, one can expect to see an increasing number of NMR structural studies of biologically active RNAs.

  7. Broadband cross-polarization-based heteronuclear dipolar recoupling for structural and dynamic NMR studies of rigid and soft solids

    International Nuclear Information System (INIS)

    Kharkov, B. B.; Chizhik, V. I.; Dvinskikh, S. V.

    2016-01-01

    Dipolar recoupling is an essential part of current solid-state NMR methodology for probing atomic-resolution structure and dynamics in solids and soft matter. Recently described magic-echo amplitude- and phase-modulated cross-polarization heteronuclear recoupling strategy aims at efficient and robust recoupling in the entire range of coupling constants both in rigid and highly dynamic molecules. In the present study, the properties of this recoupling technique are investigated by theoretical analysis, spin-dynamics simulation, and experimentally. The resonance conditions and the efficiency of suppressing the rf field errors are examined and compared to those for other recoupling sequences based on similar principles. The experimental data obtained in a variety of rigid and soft solids illustrate the scope of the method and corroborate the results of analytical and numerical calculations. The technique benefits from the dipolar resolution over a wider range of coupling constants compared to that in other state-of-the-art methods and thus is advantageous in studies of complex solids with a broad range of dynamic processes and molecular mobility degrees

  8. Fast multi-dimensional NMR by minimal sampling

    Science.gov (United States)

    Kupče, Ēriks; Freeman, Ray

    2008-03-01

    A new scheme is proposed for very fast acquisition of three-dimensional NMR spectra based on minimal sampling, instead of the customary step-wise exploration of all of evolution space. The method relies on prior experiments to determine accurate values for the evolving frequencies and intensities from the two-dimensional 'first planes' recorded by setting t1 = 0 or t2 = 0. With this prior knowledge, the entire three-dimensional spectrum can be reconstructed by an additional measurement of the response at a single location (t1∗,t2∗) where t1∗ and t2∗ are fixed values of the evolution times. A key feature is the ability to resolve problems of overlap in the acquisition dimension. Applied to a small protein, agitoxin, the three-dimensional HNCO spectrum is obtained 35 times faster than systematic Cartesian sampling of the evolution domain. The extension to multi-dimensional spectroscopy is outlined.

  9. Hydrothermal liquefaction oil and hydrotreated product from pine feedstock characterized by heteronuclear two-dimensional NMR spectroscopy and FT-ICR mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Sudasinghe, Nilusha; Cort, John R.; Hallen, Richard T.; Olarte, Mariefel V.; Schmidt, Andrew J.; Schaub, Tanner

    2014-12-01

    Hydrothermal liquefaction (HTL) crude oil and hydrotreated product from pine tree farm waste (forest product residual, FPR) have been analyzed by direct infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) in both positive- and negative-ionization modes and high-resolution twodimensional heteronuclear 1H-13C NMR spectroscopy. FT-ICR MS resolves thousands of compounds in complex oils and provides unparalleled compositional details for individual molecules for identification of compound class (heteroatom content), type (number of rings plus double bonds to carbon or double bond equivalents (DBE) and carbon number (degree of alkylation). Heteronuclear 1H-13C NMR spectroscopy provides one-bond and multiple-bond correlations between pairs of 1H and 13C chemical shifts that are characteristic of different organic functional groups. Taken together this information provides a picture of the chemical composition of these oils. Pyrolysis crude oil product from pine wood was characterized for comparison. Generally, pyrolysis oil is comprised of a more diverse distribution of heteroatom classes with higher oxygen number relative to HTL oil as shown by both positive- and negative-ion ESI FT-ICR MS. A total of 300 N1, 594 O1 and 267 O2 compounds were observed as products of hydrotreatment. The relative abundance of N1O1, N1O2, N1O3, N2, N2O1, N2O2 and O3 compounds are reduced to different degrees after hydrotreatment and other higher heteroatom containing species (O4-O10, N1O4, N1O5 and N2O3) are completely removed by hydrotreatment.

  10. Development of uniformly stable isotope labeling system in higher plants for hetero-nuclear NMR experiments in vitro and in vivo

    International Nuclear Information System (INIS)

    Kikuchi, J.

    2005-01-01

    Full text: Novel methods for measurement of living systems are making new breakthroughs in life science. In the era of the metabolome (analysis of all measurable metabolites), a MS-based approach is considered to be the major technology, whereas a NMR-based method is recognized as minor technology due to its low sensitivity. Therefore, my laboratory is currently focusing to develop novel methodologies for an NMR-based metabolomics. This will be achieved by uniform stable isotope labeling of higher plants allowing application of multi-dimensional NMR experiments used in protein structure determination. Using these novel methods, I will analyze the dynamic molecular networks inside tissues. Especially, use of stable isotope labeling methods has enormous advantage for discrimination of incorporated or de novo synthesized compounds. Furthermore, potentiality of in vivo-NMR metabolomics will be discussed in the conference. (author)

  11. 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

  12. Analytical solution to the coupled evolution of multidimensional NMR data

    International Nuclear Information System (INIS)

    Mueller, Geoffrey A.

    2009-01-01

    A substantial time savings in the collection of multidimensional NMR data can be achieved by coupling the evolution of nuclei in the indirect dimensions. In order to save time, the sampling of the indirect dimensions is inherently incomplete. Therefore, many algorithms and samplings schemes have been developed aimed at separating the coevolved frequencies into analyzable data with limited artifacts. This paper extends the use of circulant matrices to describe coupled evolution with convolutions. By understanding the data in terms of convolutions, there is an exact solution to the inversion problem of extracting the orthogonal vectors from the coupled dimensions. Previously, this inversion problem has been solved using peak coordinates extracted from spectra. In contrast, the method described here uses spectra directly. This solution suggests a simple sampling scheme of collecting N orthogonal spectra, and N + 1 projections at specific projection angles, however, the theory developed can be extended generally to arbitrary projection angles. The circulant matrix methodology is demonstrated for simulated and real data. Further, an algorithm for separating overlapped signals in the detected dimension is presented. The algorithm involves the forward calculation of the coupled spectra from the orthogonal spectra, followed by back calculation of the orthogonal spectra from the coupled spectra, thus permitting rigorous cross-validation. This algorithm is shown to be robust in that erroneous solutions give rise to large artifacts

  13. Avoiding bias effects in NMR experiments for heteronuclear dipole-dipole coupling determinations: principles and application to organic semiconductor materials.

    Science.gov (United States)

    Kurz, Ricardo; Cobo, Marcio Fernando; de Azevedo, Eduardo Ribeiro; Sommer, Michael; Wicklein, André; Thelakkat, Mukundan; Hempel, Günter; Saalwächter, Kay

    2013-09-16

    Carbon-proton dipole-dipole couplings between bonded atoms represent a popular probe of molecular dynamics in soft materials or biomolecules. Their site-resolved determination, for example, by using the popular DIPSHIFT experiment, can be challenged by spectral overlap with nonbonded carbon atoms. The problem can be solved by using very short cross-polarization (CP) contact times, however, the measured modulation curves then deviate strongly from the theoretically predicted shape, which is caused by the dependence of the CP efficiency on the orientation of the CH vector, leading to an anisotropic magnetization distribution even for isotropic samples. Herein, we present a detailed demonstration and explanation of this problem, as well as providing a solution. We combine DIPSHIFT experiments with the rotor-directed exchange of orientations (RODEO) method, and modifications of it, to redistribute the magnetization and obtain undistorted modulation curves. Our strategy is general in that it can also be applied to other types of experiments for heteronuclear dipole-dipole coupling determinations that rely on dipolar polarization transfer. It is demonstrated with perylene-bisimide-based organic semiconductor materials, as an example, in which measurements of dynamic order parameters reveal correlations of the molecular dynamics with the phase structure and functional properties. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Adiabatic fast passage application in solid state NMR study of cross relaxation and molecular dynamics in heteronuclear systems.

    Science.gov (United States)

    Baranowski, M; Woźniak-Braszak, A; Jurga, K

    2016-01-01

    The paper presents the benefits of using fast adiabatic passage for the study of molecular dynamics in the solid state heteronuclear systems in the laboratory frame. A homemade pulse spectrometer operating at the frequency of 30.2MHz and 28.411MHz for protons and fluorines, respectively, has been enhanced with microcontroller direct digital synthesizer DDS controller [1-4]. This work briefly describes how to construct a low-cost and easy-to-assemble adiabatic extension set for homemade and commercial spectrometers based on recently very popular Arduino shields. The described set was designed for fast adiabatic generation. Timing and synchronization problems are discussed. The cross-relaxation experiments with different initial states of the two spin systems have been performed. Contrary to our previous work [5] where the steady-state NOE experiments were conducted now proton spins (1)H are polarized in the magnetic field B0 while fluorine spins (19)F are perturbed by selective saturation for a short time and then the system is allowed to evolve for a period in the absence of a saturating field. The adiabatic passage application leads to a reversal of magnetization of fluorine spins and increases the amplitude of the signal. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Isotope labeling for NMR studies of macromolecular structure and interactions

    International Nuclear Information System (INIS)

    Wright, P.E.

    1994-01-01

    Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform 13 C, 15 N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific 13 C and 15 N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions

  16. Isotope labeling for NMR studies of macromolecular structure and interactions

    Energy Technology Data Exchange (ETDEWEB)

    Wright, P.E. [Scripps Research Institute, La Jolla, CA (United States)

    1994-12-01

    Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

  17. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Guangjin, E-mail: hou@udel.edu, E-mail: tpolenov@udel.edu; Lu, Xingyu, E-mail: luxingyu@udel.edu, E-mail: lexvega@comcast.net; Vega, Alexander J., E-mail: luxingyu@udel.edu, E-mail: lexvega@comcast.net; Polenova, Tatyana, E-mail: hou@udel.edu, E-mail: tpolenov@udel.edu [Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261 (United States)

    2014-09-14

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear {sup 1}H-X (X = {sup 13}C, {sup 15}N, {sup 31}P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the {sup 1}H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the {sup 1}H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from {sup 1}H chemical shift anisotropy, while keeping the {sup 1}H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [{sup 15}N]-N-acetyl-valine and [U-{sup 13}C,{sup 15}N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate {sup 1}H-{sup 15}N dipolar couplings in the context of 3D experiments is presented on U-{sup 13}C,{sup 15}N-enriched dynein light chain protein LC8.

  18. Na/Ca Intermixing around Silicate and Phosphate Groups in Bioactive Phosphosilicate Glasses Revealed by Heteronuclear Solid-State NMR and Molecular Dynamics Simulations.

    Science.gov (United States)

    Mathew, Renny; Stevensson, Baltzar; Edén, Mattias

    2015-04-30

    We characterize the intermixing of network-modifying Na(+)/Ca(2+) ions around the silicate (QSi(n)) and phosphate (QP(n)) tetrahedra in a series of 16 Na2O–CaO–SiO2–P2O5 glasses, whose P content and silicate network connectivity were varied independently. The set includes both bioactive and bioinactive compositions and also encompasses two soda-lime-silicate members devoid of P, as well as two CaO–SiO2 glasses and one Na2O–SiO2–P2O5 glass. The various Si/P↔Na/Ca contacts were probed by molecular dynamics (MD) simulations together with heteronuclear magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) experimentation utilizing (23)Na{(31)P} and (23)Na{(29)Si} REDOR, as well as (31)P{ (23)Na} and (29)Si{(23)Na} REAPDOR. We introduce an approach for quantifying the extent of Na(+)/Ca(2+) ordering around a given QP(n) or QSi(n) group, encoded by the preference factor 0⩽ PM ⩽ 1 conveying the relative weights of a random cation intermixing (PM = 0) and complete preference/ordering (PM = 1) for one of the species M, which represents either Na(+) or Ca(2+). The MD-derived preference factors reveal phosphate and silicate species surrounded by Na(+)/Ca(2+) ions intermixed nearly randomly (PM ≲ 0.15), except for the QSi(4) and QSi(1) groups, which manifest more significant cation ordering with preference for Na+ and Ca2+, respectively. The overall weak preferences are essentially independent of the Si and P contents of the glass, whereas PM primarily correlates with the total amount of network modifiers: as the latter is increased, the Na/Ca distribution around the {QP(0), QSi(1), QSi(2)} groups with preference for Ca2(+ )tend to randomize (i.e., PCa decreases), while the PNa-values grow slightly for the {QP(1), QSi(3), QSi(4)} species already preferring coordination of Na. The set of experimental preference factors {PCa} for the orthophosphate (QP(0)) groups extracted from (31)P{(23)Na} REAPDOR NMR-derived M2(P–Na) dipolar second moments agrees

  19. Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

    KAUST Repository

    Cannistraci, Carlo Vittorio

    2015-01-26

    Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet\\'s performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.

  20. Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

    KAUST Repository

    Cannistraci, Carlo Vittorio; Abbas, Ahmed; Gao, Xin

    2015-01-01

    Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet's performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis.

  1. Heteronuclear Micro-Helmholtz Coil Facilitates µm-Range Spatial and Sub-Hz Spectral Resolution NMR of nL-Volume Samples on Customisable Microfluidic Chips.

    Directory of Open Access Journals (Sweden)

    Nils Spengler

    Full Text Available We present a completely revised generation of a modular micro-NMR detector, featuring an active sample volume of ∼ 100 nL, and an improvement of 87% in probe efficiency. The detector is capable of rapidly screening different samples using exchangeable, application-specific, MEMS-fabricated, microfluidic sample containers. In contrast to our previous design, the sample holder chips can be simply sealed with adhesive tape, with excellent adhesion due to the smooth surfaces surrounding the fluidic ports, and so withstand pressures of ∼2.5 bar, while simultaneously enabling high spectral resolution up to 0.62 Hz for H2O, due to its optimised geometry. We have additionally reworked the coil design and fabrication processes, replacing liquid photoresists by dry film stock, whose final thickness does not depend on accurate volume dispensing or precise levelling during curing. We further introduced mechanical alignment structures to avoid time-intensive optical alignment of the chip stacks during assembly, while we exchanged the laser-cut, PMMA spacers by diced glass spacers, which are not susceptible to melting during cutting. Doing so led to an overall simplification of the entire fabrication chain, while simultaneously increasing the yield, due to an improved uniformity of thickness of the individual layers, and in addition, due to more accurate vertical positioning of the wirebonded coils, now delimited by a post base plateau. We demonstrate the capability of the design by acquiring a 1H spectrum of ∼ 11 nmol sucrose dissolved in D2O, where we achieved a linewidth of 1.25 Hz for the TSP reference peak. Chemical shift imaging experiments were further recorded from voxel volumes of only ∼ 1.5 nL, which corresponded to amounts of just 1.5 nmol per voxel for a 1 M concentration. To extend the micro-detector to other nuclei of interest, we have implemented a trap circuit, enabling heteronuclear spectroscopy, demonstrated by two 1H/13C 2D HSQC

  2. Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

    Science.gov (United States)

    Helmus, Jonathan J; Jaroniec, Christopher P

    2013-04-01

    Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

  3. Nmrglue: an open source Python package for the analysis of multidimensional NMR data

    Energy Technology Data Exchange (ETDEWEB)

    Helmus, Jonathan J., E-mail: jjhelmus@gmail.com [Argonne National Laboratory, Environmental Science Division (United States); Jaroniec, Christopher P., E-mail: jaroniec@chemistry.ohio-state.edu [Ohio State University, Department of Chemistry and Biochemistry (United States)

    2013-04-15

    Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.comhttp://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

  4. Nmrglue: an open source Python package for the analysis of multidimensional NMR data

    International Nuclear Information System (INIS)

    Helmus, Jonathan J.; Jaroniec, Christopher P.

    2013-01-01

    Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.comhttp://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

  5. Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy

    International Nuclear Information System (INIS)

    Hanrahan, Michael P.; Fought, Ellie L.; Windus, Theresa L.; Wheeler, Lance M.; Anderson, Nicholas C.

    2017-01-01

    The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1 H– 29 Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1 H– 29 Si HETCOR and dipolar 2D 1 H– 1 H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Instead the 2D NMR spectra illustrate that there is large distribution of 1 H and 29 Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1 H– 29 Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surface hydrides. Varying the 29 Si evolution time in refocused INEPT experiments and fitting the oscillation of the NMR signals allows for the relative populations of the different surface hydrides to be estimated. This analysis confirms that monohydride species are the predominant surface species on the as-synthesized Si NCs. A reduction in the populations of the di- and trihydrides is observed upon functionalization with alkyl groups, consistent with our previous hypothesis that the trihydride, or silyl (*SiH 3 ), group is primarily responsible for initiating surface functionalization reactions. Density functional theory (DFT) calculations were used to obtain quantum chemical structural models of the Si NC surface and reproduce the observed 1 H and 29 Si chemical shifts. Furthermore, the approaches outlined here will be useful to obtain a more detailed picture of surface structures for Si NCs and other hydride-passivated nanomaterials.

  6. A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field.

    Science.gov (United States)

    Lu, George J; Son, Woo Sung; Opella, Stanley J

    2011-04-01

    A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly ¹⁵N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly ¹⁵N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods.

    Science.gov (United States)

    Lesot, Philippe; Kazimierczuk, Krzysztof; Trébosc, Julien; Amoureux, Jean-Paul; Lafon, Olivier

    2015-11-01

    Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years. Copyright © 2015 John Wiley & Sons, Ltd.

  8. Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

    Energy Technology Data Exchange (ETDEWEB)

    Bingol, Kerem; Brüschweiler, Rafael

    2017-02-01

    Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexity of these tasks.

  9. Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR.

    Science.gov (United States)

    Mobli, Mehdi; Hoch, Jeffrey C

    2014-11-01

    Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Robust refocusing of 13C magnetization in multidimensional NMR experiments by adiabatic fast passage pulses

    International Nuclear Information System (INIS)

    Zweckstetter, Markus; Holak, Tad A.

    1999-01-01

    We show that adiabatic fast passage (AFP) pulses are robust refocusing elements of transverse 13 C magnetization in multidimensional NMR experiments. A pair of identical AFP pulses can refocus selected parts or a complete 13 C chemical shift range in 13 C spectra. In the constant time 13 C- 1 H HSQC, replacement of attenuated rectangular pulses by selective AFP pulses results in a sensitivity enhancement of up to a factor of 1.8. In the 3D CBCA(CO)NH the signal-to-noise ratio is increased by a factor of up to 1.6

  11. Application of random coherence order selection in gradient-enhanced multidimensional NMR

    International Nuclear Information System (INIS)

    Bostock, Mark J.; Nietlispach, Daniel

    2016-01-01

    Development of multidimensional NMR is essential to many applications, for example in high resolution structural studies of biomolecules. Multidimensional techniques enable separation of NMR signals over several dimensions, improving signal resolution, whilst also allowing identification of new connectivities. However, these advantages come at a significant cost. The Fourier transform theorem requires acquisition of a grid of regularly spaced points to satisfy the Nyquist criterion, while frequency discrimination and acquisition of a pure phase spectrum require acquisition of both quadrature components for each time point in every indirect (non-acquisition) dimension, adding a factor of 2 N -1 to the number of free- induction decays which must be acquired, where N is the number of dimensions. Compressed sensing (CS) ℓ 1 -norm minimisation in combination with non-uniform sampling (NUS) has been shown to be extremely successful in overcoming the Nyquist criterion. Previously, maximum entropy reconstruction has also been used to overcome the limitation of frequency discrimination, processing data acquired with only one quadrature component at a given time interval, known as random phase detection (RPD), allowing a factor of two reduction in the number of points for each indirect dimension (Maciejewski et al. 2011 PNAS 108 16640). However, whilst this approach can be easily applied in situations where the quadrature components are acquired as amplitude modulated data, the same principle is not easily extended to phase modulated (P-/N-type) experiments where data is acquired in the form exp (iωt) or exp (-iωt), and which make up many of the multidimensional experiments used in modern NMR. Here we demonstrate a modification of the CS ℓ 1 -norm approach to allow random coherence order selection (RCS) for phase modulated experiments; we generalise the nomenclature for RCS and RPD as random quadrature detection (RQD). With this method, the power of RQD can be extended

  12. The covariance of the differences between experimental and theoretical chemical shifts as an aid for assigning two-dimensional heteronuclear correlation solid-state NMR spectra

    Czech Academy of Sciences Publication Activity Database

    Czernek, Jiří; Brus, Jiří

    2014-01-01

    Roč. 608, 21 July (2014), s. 334-339 ISSN 0009-2614 R&D Projects: GA ČR(CZ) GA14-03636S Institutional support: RVO:61389013 Keywords : NMR * DFT * covariance Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.897, year: 2014

  13. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  14. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK

    International Nuclear Information System (INIS)

    Würz, Julia M.; Güntert, Peter

    2017-01-01

    The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity. The performance of CYPICK was evaluated for a variety of spectra from different proteins by systematic comparison with peak lists obtained by other, manual or automated, peak picking methods, as well as by analyzing the results of automated chemical shift assignment and structure calculation based on input peak lists from CYPICK. The results show that CYPICK yielded peak lists that compare in most cases favorably to those obtained by other automated peak pickers with respect to the criteria of finding a maximal number of real signals, a minimal number of artifact peaks, and maximal correctness of the chemical shift assignments and the three-dimensional structure obtained by fully automated assignment and structure calculation.

  15. Peak picking multidimensional NMR spectra with the contour geometry based algorithm CYPICK

    Energy Technology Data Exchange (ETDEWEB)

    Würz, Julia M.; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany)

    2017-01-15

    The automated identification of signals in multidimensional NMR spectra is a challenging task, complicated by signal overlap, noise, and spectral artifacts, for which no universally accepted method is available. Here, we present a new peak picking algorithm, CYPICK, that follows, as far as possible, the manual approach taken by a spectroscopist who analyzes peak patterns in contour plots of the spectrum, but is fully automated. Human visual inspection is replaced by the evaluation of geometric criteria applied to contour lines, such as local extremality, approximate circularity (after appropriate scaling of the spectrum axes), and convexity. The performance of CYPICK was evaluated for a variety of spectra from different proteins by systematic comparison with peak lists obtained by other, manual or automated, peak picking methods, as well as by analyzing the results of automated chemical shift assignment and structure calculation based on input peak lists from CYPICK. The results show that CYPICK yielded peak lists that compare in most cases favorably to those obtained by other automated peak pickers with respect to the criteria of finding a maximal number of real signals, a minimal number of artifact peaks, and maximal correctness of the chemical shift assignments and the three-dimensional structure obtained by fully automated assignment and structure calculation.

  16. Heteronuclear 2D (1H-13C) MAS NMR Resolves the Electronic Structure of Coordinated Histidines in Light-Harvesting Complex II: Assessment of Charge Transfer and Electronic Delocalization Effect

    International Nuclear Information System (INIS)

    Matysik, Joerg; Boer, Ido de; Gast, Peter; Gorkom, Hans J. van; Groot, Huub J.M. de

    2004-01-01

    In a recent MAS NMR study, two types of histidine residues in the light-harvesting complex II (LH2) of Rhodopseudomonas acidophila were resolved: Type 1 (neutral) and Type 2 (positively charged) (Alia et al. J. Am. Chem. Soc.). The isotropic 13 C shifts of histidines coordinating to B850 BChl a are similar to fully positively charged histidine, while the 15 N shift anisotropy shows a predominantly neutral character. In addition the possibility that the ring currents are quenched by overlap in the superstructure of the complete ring of 18 B850 molecules in the LH2 complex could not be excluded. In the present work, by using two-dimensional heteronuclear ( 1 H- 13 C) dipolar correlation spectroscopy with phase-modulated Lee-Goldburg homonuclear 1 H decoupling applied during the t 1 period, a clear and unambiguous assignment of the protons of histidine interacting with the magnesium of a BChl a molecule is obtained and a significant ring current effect from B850 on the coordinating histidine is resolved. Using the ring current shift on 1 H, we refine the 13 C chemical shift assignment of the coordinating histidine and clearly distinguish the electronic structure of coordinating histidines from that of fully positively charged histidine. The DFT calculations corroborate that the coordinating histidines carry ∼0.2 electronic equivalent of positive charge in LH2. In addition, the data indicate that the ground state electronic structures of individual BChl a/His complexes is largely independent of supermolecular π interactions in the assembly of 18 B850 ring in LH2

  17. (13)C heteronuclear NMR studies of the interaction of cultured neurons and astrocytes and aluminum blockade of the preferential release of citrate from astrocytes.

    Science.gov (United States)

    Meshitsuka, Shunsuke; Aremu, David A

    2008-02-01

    Citrate has been identified as a major tricarboxylic acid (TCA) cycle constituent preferentially released by astrocytes. We undertook the present study to examine further the nature of metabolic compartmentation in central nervous system tissues using (13)C-labeled glucose and to provide new information on the influence of aluminum on the metabolic interaction between neurons and astrocytes. Metabolites released into the culture medium from astrocytes and neuron-astrocyte coculture, as well as the perchloric acid extracts of the cells were analyzed using 2D (1)H and (13)C NMR spectroscopy. Astrocytes released citrate into the culture medium and the released citrate was consumed by neurons in coculture. Citrate release by astrocytes was blocked in the presence of aluminum, with progressive accumulation of citrate within the cells. We propose citrate supply is a more efficient energy source than lactate for neurons to produce ATP, especially in the hypoglycemic state on account of it being a direct component of the TCA cycle. Astrocytes may be the cellular compartment for aluminum accumulation as a citrate complex in the brain.

  18. Dante-Z sequence as selective impulsion in high field mono and multidimensional NMR. Application to the study of proteins, peptides and their interactions

    International Nuclear Information System (INIS)

    Roumestand, C.; Toma, F.

    1992-01-01

    DANTE-Z is a simple and efficient way for NMR spectral selection. We present here different applications of DANTE-Z in high-resolution NMR of peptides and proteins. We have been using proton selective excitation by DANTE-Z to perform 1D-correlated (homo- or heteronuclear) experiments corresponding to one line of either 2D or 3D experiments. Following the same scheme, we could also edit planes of 3D experiments by concatenating 1D-correlated experiments with conventional 2D experiments. In the heteronuclear case (i.e. 1 H, 31 P), we could also edit planes of a 4D experiment by the simultaneous selection of 1 H and the X nucleus. Owing to the favourable excitation profile of DANTE-Z, we used it successfully for topological excitations (spectral width from 150 Hz up to 1500 Hz) in 'semi-soft'-2D experiments and 'soft'-2D experiment. These applications are illustrated by the results obtained at 600 MHz on a protein and a phosphonamide peptide

  19. Heteronuclear proton assisted recoupling

    Science.gov (United States)

    De Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Eddy, Matt; Megy, Simon; Böckmann, Anja; Griffin, Robert G.

    2011-03-01

    We describe a theoretical framework for understanding the heteronuclear version of the third spin assisted recoupling polarization transfer mechanism and demonstrate its potential for detecting long-distance intramolecular and intermolecular 15N-13C contacts in biomolecular systems. The pulse sequence, proton assisted insensitive nuclei cross polarization (PAIN-CP) relies on a cross term between 1H-15N and 1H-13C dipolar couplings to mediate zero- and/or double-quantum 15N-13C recoupling. In particular, using average Hamiltonian theory we derive effective Hamiltonians for PAIN-CP and show that the transfer is mediated by trilinear terms of the form N±C∓Hz (ZQ) or N±C±Hz (DQ) depending on the rf field strengths employed. We use analytical and numerical simulations to explain the structure of the PAIN-CP optimization maps and to delineate the appropriate matching conditions. We also detail the dependence of the PAIN-CP polarization transfer with respect to local molecular geometry and explain the observed reduction in dipolar truncation. In addition, we demonstrate the utility of PAIN-CP in structural studies with 15N-13C spectra of two uniformly 13C,15N labeled model microcrystalline proteins—GB1, a 56 amino acid peptide, and Crh, a 85 amino acid domain swapped dimer (MW = 2 × 10.4 kDa). The spectra acquired at high magic angle spinning frequencies (ωr/2π > 20 kHz) and magnetic fields (ω0H/2π = 700-900 MHz) using moderate rf fields, yield multiple long-distance intramonomer and intermonomer 15N-13C contacts. We use these distance restraints, in combination with the available x-ray structure as a homology model, to perform a calculation of the monomer subunit of the Crh protein.

  20. Heteronuclear Long-Range Correlation

    DEFF Research Database (Denmark)

    Sørensen, Ole W.

    The lecture will cover heteronuclear long-range correlation techniques like HMBC, H2BC, and HAT HMBC with the emphasis on determining the number of covalent bonds between two spins being correlated. H2BC and HMBC spectra are quite complementary as a peak can be strong in one of the two spectra...

  1. Chemical shift-dependent apparent scalar couplings: An alternative concept of chemical shift monitoring in multi-dimensional NMR experiments

    International Nuclear Information System (INIS)

    Kwiatkowski, Witek; Riek, Roland

    2003-01-01

    The paper presents an alternative technique for chemical shift monitoring in a multi-dimensional NMR experiment. The monitored chemical shift is coded in the line-shape of a cross-peak through an apparent residual scalar coupling active during an established evolution period or acquisition. The size of the apparent scalar coupling is manipulated with an off-resonance radio-frequency pulse in order to correlate the size of the coupling with the position of the additional chemical shift. The strength of this concept is that chemical shift information is added without an additional evolution period and accompanying polarization transfer periods. This concept was incorporated into the three-dimensional triple-resonance experiment HNCA, adding the information of 1 H α chemical shifts. The experiment is called HNCA coded HA, since the chemical shift of 1 H α is coded in the line-shape of the cross-peak along the 13 C α dimension

  2. Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR

    International Nuclear Information System (INIS)

    Eddy, Matthew T.; Su, Yongchao; Silvers, Robert; Andreas, Loren; Clark, Lindsay; Wagner, Gerhard; Pintacuda, Guido; Emsley, Lyndon; Griffin, Robert G.

    2015-01-01

    The human voltage dependent anion channel 1 (VDAC) is a 32 kDa β-barrel integral membrane protein that controls the transport of ions across the outer mitochondrial membrane. Despite the determination of VDAC solution and diffraction structures, a structural basis for the mechanism of its function is not yet fully understood. Biophysical studies suggest VDAC requires a lipid bilayer to achieve full function, motivating the need for atomic resolution structural information of VDAC in a membrane environment. Here we report an essential step toward that goal: extensive assignments of backbone and side chain resonances for VDAC in DMPC lipid bilayers via magic angle spinning nuclear magnetic resonance (MAS NMR). VDAC reconstituted into DMPC lipid bilayers spontaneously forms two-dimensional lipid crystals, showing remarkable spectral resolution (0.5–0.3 ppm for 13 C line widths and <0.5 ppm 15 N line widths at 750 MHz). In addition to the benefits of working in a lipid bilayer, several distinct advantages are observed with the lipid crystalline preparation. First, the strong signals and sharp line widths facilitated extensive NMR resonance assignments for an integral membrane β-barrel protein in lipid bilayers by MAS NMR. Second, a large number of residues in loop regions were readily observed and assigned, which can be challenging in detergent-solubilized membrane proteins where loop regions are often not detected due to line broadening from conformational exchange. Third, complete backbone and side chain chemical shift assignments could be obtained for the first 25 residues, which comprise the functionally important N-terminus. The reported assignments allow us to compare predicted torsion angles for VDAC prepared in DMPC 2D lipid crystals, DMPC liposomes, and LDAO-solubilized samples to address the possible effects of the membrane mimetic environment on the conformation of the protein. Concluding, we discuss the strengths and weaknesses of the reported

  3. NMR

    International Nuclear Information System (INIS)

    Kneeland, J.B.; Lee, B.C.P.; Whalen, J.P.; Knowles, R.J.R.; Cahill, P.T.

    1984-01-01

    Although still quite new, NMR imaging has already emerged as a safe, noninvasive, painless, and effective diagnostic modality requiring no ionizing radiation. Also, NMR appears already to have established itself as the method of choice for the examination of the brain spinal cord (excluding herniated disks). Another area in which NMR excels is in the examination of the pelvis. The use of surface coils offers the promise of visualizing structures with resolution unobtainable by any other means. In addition, NMR, with its superb visualization of vascular structures and potential ability to measure flow, may soon revolutionize the diagnosis of cardiovascular disease. Finally, NMR, through biochemically and physiologically based T/sub 1/ and T/sub 2/ indices or through spectroscopy, may provide a means of monitoring therapeutic response so as to permit tailoring of treatment to the individual patient. In short, NMR is today probably at the same stage as the x-ray was in Roentgen's day

  4. Selective {sup 2}H and {sup 13}C labeling in NMR analysis of solution protein structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    LeMaster, D.M. [Northwestern Univ., Evanston, IL (United States)

    1994-12-01

    Preparation of samples bearing combined isotope enrichment patterns has played a central role in the recent advances in NMR analysis of proteins in solution. In particular, uniform {sup 13}C, {sup 15}N enrichment has made it possible to apply heteronuclear multidimensional correlation experiments for the mainchain assignments of proteins larger than 30 KDa. In contrast, selective labeling approaches can offer advantages in terms of the directedness of the information provided, such as chirality and residue type assignments, as well as through enhancements in resolution and sensitivity that result from editing the spectral complexity, the relaxation pathways and the scalar coupling networks. In addition, the combination of selective {sup 13}C and {sup 2}H enrichment can greatly facilitate the determination of heteronuclear relaxation behavior.

  5. Heteronuclear 2D NMR studies on an engineered insulin monomer: Assignments and characterization of the receptor-binding surface by selective 2H and 13C labeling with application to protein design

    International Nuclear Information System (INIS)

    Weiss, M.A.; Hua, Qingxin; Lynch, C.S.; Shoelson, S.E.; Frank, B.H.

    1991-01-01

    Insulin provides an important model for the application of genetic engineering to rational protein design and has been well characterized in the crystal state. However, self-association of insulin in solution has precluded complementary 2D NMR study under physiological conditions. The authors demonstrate here that such limitations may be circumvented by the use of a monomeric analogue that contains three amino acid substitutions on the protein surface (HisB10 → Asp, ProB28 → Lys, and LysB29 → Pro); this analogue (designated DKP-insulin) retains native receptor-binding potency. Comparative 1 H NMR studies of native human insulin and a series of three related analogues-(i) the singly substituted analogue [HisB10→Asp], (ii) the doubly substituted analogue [ProB28→Lys; LysB29→Pro], and (iii) DKP-insulin-demonstrate progressive reduction in concentration-dependent line-broadening in accord with the results of analytical ultracentrifugation. Extensive nonlocal interactions are observed in the NOESY spectrum of DKP-insulin, indicating that this analogue adopts a compact and stably folded structure as a monomer in overall accord with crystal models. Site-specific 2 H and 13 C isotopic labels are introduced by semisynthesis as probes for the structure and dynamics of the receptor-binding surface. These studies confirm and extend under physiological conditions the results of a previous 2D NMR analysis of native insulin in 20% acetic acid. Implications for the role of protein flexibility in receptor recognition are discussed with application to the design of novel insulin analogues

  6. 1H, 13C and 13N chemical shifts and 1H-15N and 13C-15N heteronuclear spin-spin coupling constants n the NMR spectra of 5-substituted furfural oximes

    International Nuclear Information System (INIS)

    Popelis, Yu.Yu.; Liepin'sh, E.E.; Lukevits, E.Ya.

    1986-01-01

    The 1 H, 13 C, and 15 N NMR spectra of 15 N-enriched 5-substituted furfural oximes were investigated. It was shown that the chemical shifts of the ring atoms and the oxime group correlate satisfactorily with the F and R substituent constants, whereas their sensitivity to the effect of the substituents is lower than in monosubstituted furan derivatives. The constants of spin-spin coupling between the ring protons and the oxime group were determined. An analysis of the 1 H- 1 H spin-spin coupling constants (SSCC) on the basis of their stereospecificity indicates that the E isomers have primarily an s-trans conformation in polar dimethyl sulfoxide, whereas the Z isomers, on the other hand, have an s-cis conformation. The signs of the direct and geminal 13 C- 15 N SSCC were determined for 5-trimethylsilylfurfural oxime

  7. TG/DTG, FT-ICR Mass Spectrometry, and NMR Spectroscopy Study of Heavy Fuel Oil

    KAUST Repository

    Elbaz, Ayman M.; Abdul Jameel, Abdul Gani; Hourani, Nadim; Emwas, Abdul-Hamid M.; Sarathy, Mani; Roberts, William L.

    2015-01-01

    infusion atmospheric pressure chemical ionization Fourier transform ion cyclotron resonance mass spectrometry (APCI-FTICR MS), high resolution 1H nuclear magnetic resonance (NMR), 13C NMR, and two-dimensional heteronuclear multiple bond correlation (HMBC

  8. On the Analytical Superiority of 1D NMR for Fingerprinting the Higher Order Structure of Protein Therapeutics Compared to Multidimensional NMR Methods.

    Science.gov (United States)

    Poppe, Leszek; Jordan, John B; Rogers, Gary; Schnier, Paul D

    2015-06-02

    An important aspect in the analytical characterization of protein therapeutics is the comprehensive characterization of higher order structure (HOS). Nuclear magnetic resonance (NMR) is arguably the most sensitive method for fingerprinting HOS of a protein in solution. Traditionally, (1)H-(15)N or (1)H-(13)C correlation spectra are used as a "structural fingerprint" of HOS. Here, we demonstrate that protein fingerprint by line shape enhancement (PROFILE), a 1D (1)H NMR spectroscopy fingerprinting approach, is superior to traditional two-dimensional methods using monoclonal antibody samples and a heavily glycosylated protein therapeutic (Epoetin Alfa). PROFILE generates a high resolution structural fingerprint of a therapeutic protein in a fraction of the time required for a 2D NMR experiment. The cross-correlation analysis of PROFILE spectra allows one to distinguish contributions from HOS vs protein heterogeneity, which is difficult to accomplish by 2D NMR. We demonstrate that the major analytical limitation of two-dimensional methods is poor selectivity, which renders these approaches problematic for the purpose of fingerprinting large biological macromolecules.

  9. Heteronuclear long-range correlation, what’s new and how far can it take us?

    DEFF Research Database (Denmark)

    Sørensen, Ole W.

    : A novel experiment for small-molecule and biomolecular NMR at natural isotopic abundance. Sebastian Meier, Andrew J. Benie, Jens Ø. Duus and Ole W. Sørensen, Journal of Magnetic Resonance, in press, doi:10.1016/j.jmr.2009.06.017 Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D...... H2BC and clean HMBC. Sebastian Meier, Bent O. Petersen, Jens Ø. Duus, Ole W. Sørensen. Carbohydrate Research, in press, doi:10.1016/j.carres.2009.08.013...

  10. Collisional properties of weakly bound heteronuclear dimers

    NARCIS (Netherlands)

    Marcelis, B.; Kokkelmans, S.J.J.M.F.; Shlyapnikov, G.V.; Petrov, D.S.

    2008-01-01

    We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional stability due to an effective dimer-dimer repulsion originating

  11. Application of heteronuclear couplings to conformational analysis of oligonucleotides

    International Nuclear Information System (INIS)

    Zhu, G.; Live, D.; Bax, A.

    1994-01-01

    The value of vicinal coupling constants extracted from NMR spectra in deducing torsion angles for conformational analysis is well recognized. Due to the abundance of protons, their couplings have been mostly widely used. In many instances, couplings between protons and other nuclei may be a valuable complement to proton-proton couplings or, in some instances, may be the only coupling available to characterize the torsion angle about a bond. Recently, heteronuclear couplings have been used to great benefit in studies of isotopically enriched proteins, and this general approach has been extended to peptides at natural abundance. The possibility of using this approach to study oligonucleotides is also attractive but has not as yet been widely exploited. With the development of strategies for labeling such molecules, particularly RNAs, this may become an important component in conformational analysis. For DNA, labeling is less accessible, but sufficient quantities of unlabeled material are readily available for measuring these couplings at natural abundance. We chose several DNA systems to explore the usefulness of heteronuclear couplings in addressing the sugar conformation and the glycosidic torsion angle. Intensities of cross peaks in long-range HMQC experiments can be related to the couplings. Crosspeaks involving H1' and C1' atoms have been emphasized because of the superior shift dispersion at these positions between sugar protons and carbon atoms. Results will be shown for the self-complementary Dickerson duplex dodecamer sequence d(CGCGAATTCGCG) and for d(GGTCGG), which dimerizes to form a G-tetrad structure incorporating both syn and anti base orientations. The couplings provide a clear discrimination between presence of C3'-endo and C2'-endo conformations of the sugars and syn and anti bases arrangements

  12. Application of heteronuclear couplings to conformational analysis of oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, G. [Univ. of Maryland, College Park, MD (United States); Live, D. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Bax, A. [NIDDK National Institutes of Health, Bethesda, MD (United States)

    1994-12-01

    The value of vicinal coupling constants extracted from NMR spectra in deducing torsion angles for conformational analysis is well recognized. Due to the abundance of protons, their couplings have been mostly widely used. In many instances, couplings between protons and other nuclei may be a valuable complement to proton-proton couplings or, in some instances, may be the only coupling available to characterize the torsion angle about a bond. Recently, heteronuclear couplings have been used to great benefit in studies of isotopically enriched proteins, and this general approach has been extended to peptides at natural abundance. The possibility of using this approach to study oligonucleotides is also attractive but has not as yet been widely exploited. With the development of strategies for labeling such molecules, particularly RNAs, this may become an important component in conformational analysis. For DNA, labeling is less accessible, but sufficient quantities of unlabeled material are readily available for measuring these couplings at natural abundance. We chose several DNA systems to explore the usefulness of heteronuclear couplings in addressing the sugar conformation and the glycosidic torsion angle. Intensities of cross peaks in long-range HMQC experiments can be related to the couplings. Crosspeaks involving H1{prime} and C1{prime} atoms have been emphasized because of the superior shift dispersion at these positions between sugar protons and carbon atoms. Results will be shown for the self-complementary Dickerson duplex dodecamer sequence d(CGCGAATTCGCG) and for d(GGTCGG), which dimerizes to form a G-tetrad structure incorporating both syn and anti base orientations. The couplings provide a clear discrimination between presence of C3{prime}-endo and C2{prime}-endo conformations of the sugars and syn and anti bases arrangements.

  13. 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

  14. Triple-resonance multidimensional NMR study of calmodulin complexed with the binding domain of skeletal muscle myosin light-chain kinase: Indication of a conformational change in the central helix

    International Nuclear Information System (INIS)

    Ikura, Mitsuhiko; Kay, L.E.; Bax, A.; Krinks, M.

    1991-01-01

    Heteronuclear 3D and 4D NMR experiments have been used to obtain 1 H, 13 C, and 15 N backbone chemical shift assignments in Ca 2+ -loaded clamodulin complexed with a 26-residue synthetic peptide (M13) corresponding to the calmodulin-bionding domain (residues 577-602) of rabbit skeletal muscle muosin light-chain kinase. Comparison of the chemical shift values with those observed in peptide-free calmodulin shows that binding of M13 peptide induces substantial chemical shift changes that are not localized in one particular region of the protein. The largest changes are found in the first helix of the Ca 2+ -binding site 1 (E11-E14), the N-terminal portion of the central helix (M72-D78), and the second helix of the Ca 2+ -binding site 4 (F141-M145). Analysis of backbone NOE connectivities indicates a change from α-helical to an extended conformation for residues 75-77 upon complexation with M13. Upon complexation with M13, a significant decrease in the amide exchange rate is observed for residues T110, L112, G113, and E114 at the end of the second helix of site 3

  15. An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates

    International Nuclear Information System (INIS)

    Gal, Maayan; Kern, Thomas; Schanda, Paul; Frydman, Lucio; Brutscher, Bernhard

    2009-01-01

    Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1 H- 15 N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds

  16. Heteronuclear relaxation in time-dependent spin systems: 15N-T1ρ dispersion during adiabatic fast passage

    International Nuclear Information System (INIS)

    Konrat, Robert; Tollinger, Martin

    1999-01-01

    A novel NMR experiment comprising adiabatic fast passage techniques for the measurement of heteronuclear self-relaxation rates in fully 15N-enriched proteins is described. Heteronuclear self-relaxation is monitored by performing adiabatic fast passage (AFP) experiments at variable adiabaticity (e.g., variation of RF spin-lock field intensity). The experiment encompasses gradient- selection and sensitivity-enhancement. It is shown that transverse relaxation rates derived with this method are in good agreement with the ones measured by the classical Carr-Purcell-Meiboom-Gill (CPMG) sequences. An application of this method to the study of the carboxyl-terminal LIM domain of quail cysteine and glycine-rich protein qCRP2(LIM2) is presented

  17. Multidimensional spectrometer

    Science.gov (United States)

    Zanni, Martin Thomas; Damrauer, Niels H.

    2010-07-20

    A multidimensional spectrometer for the infrared, visible, and ultraviolet regions of the electromagnetic spectrum, and a method for making multidimensional spectroscopic measurements in the infrared, visible, and ultraviolet regions of the electromagnetic spectrum. The multidimensional spectrometer facilitates measurements of inter- and intra-molecular interactions.

  18. PASA - A Program for Automated Protein NMR Backbone Signal Assignment by Pattern-Filtering Approach

    International Nuclear Information System (INIS)

    Xu Yizhuang; Wang Xiaoxia; Yang Jun; Vaynberg, Julia; Qin Jun

    2006-01-01

    We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13 C α and/or 13 C β chemical shift matching. The pattern filter employs one or multiple constraints such as 13 C α /C β chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-based structural analyses, genomics, and proteomics

  19. Two dimensional solid state NMR

    International Nuclear Information System (INIS)

    Kentgens, A.P.M.

    1987-01-01

    This thesis illustrates, by discussing some existing and newly developed 2D solid state experiments, that two-dimensional NMR of solids is a useful and important extension of NMR techniques. Chapter 1 gives an overview of spin interactions and averaging techniques important in solid state NMR. As 2D NMR is already an established technique in solutions, only the basics of two dimensional NMR are presented in chapter 2, with an emphasis on the aspects important for solid spectra. The following chapters discuss the theoretical background and applications of specific 2D solid state experiments. An application of 2D-J resolved NMR, analogous to J-resolved spectroscopy in solutions, to natural rubber is given in chapter 3. In chapter 4 the anisotropic chemical shift is mapped out against the heteronuclear dipolar interaction to obtain information about the orientation of the shielding tensor in poly-(oxymethylene). Chapter 5 concentrates on the study of super-slow molecular motions in polymers using a variant of the 2D exchange experiment developed by us. Finally chapter 6 discusses a new experiment, 2D nutation NMR, which makes it possible to study the quadrupole interaction of half-integer spins. 230 refs.; 48 figs.; 8 tabs

  20. Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers

    International Nuclear Information System (INIS)

    Mote, Kaustubh R.; Gopinath, T.; Traaseth, Nathaniel J.; Kitchen, Jason; Gor’kov, Peter L.; Brey, William W.; Veglia, Gianluigi

    2011-01-01

    Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring 1 H- 15 N dipolar couplings (DC) and 15 N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles’ heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([ 1 H, 15 N]-SE-PISEMA-PDSD). The incorporation of 2D 15 N/ 15 N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the 15 N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers.

  1. Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers.

    Science.gov (United States)

    Mote, Kaustubh R; Gopinath, T; Traaseth, Nathaniel J; Kitchen, Jason; Gor'kov, Peter L; Brey, William W; Veglia, Gianluigi

    2011-11-01

    Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([(1)H,(15)N]-SE-PISEMA-PDSD). The incorporation of 2D (15)N/(15)N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the (15)N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers. © Springer Science+Business Media B.V. 2011

  2. Quantum theory of NMR adiabatic pulses and their applications

    International Nuclear Information System (INIS)

    Ke, Y.

    1993-01-01

    Recently explosive developments of in vivo NMR spectroscopy (NMRS) and imaging (NMRI) in biological and medical sciences have resulted in the establishment of NMR as one of the most advanced major technique in life sciences. These developments have created huge demands for a variety of NMR adiabatic pulses with play a very important role in NMR experiments in vivo. In order to develop new NMR adiabatic pulses, a rigorous systematical quantum theory for this kind of pulses is greatly needed. Providing such a theory is one of the important goals of this dissertation. Quantum density matrix theory and product operator method have been used throughout this dissertation. Another goal, which is the major goal of this thesis research, is to use the quantum theory as a guide to develop new NMR adiabatic pulses and their applications. To fill this goal, a technique to construct a new type of adiabatic pulses, narrow band selective adiabatic pulses, has been invented, which is described through the example of constructing an adiabatic DANTE inversion pulse. This new adiabatic pulse is the first narrow band selective adiabatic pulses: Adiabatic homonuclear and heteronuclear spectral editing sequences. Unique to the first pulse sequence is a B 1 -field filter which is built by using two non-refocusing adiabatic full passage pulses to refocus the wanted signal and dephase unwanted signals. This extra filter greatly enhance the editing efficiency. Unlike commonly used heteronuclear spectral editing sequences which depend on the polarization transfer or spectral subtraction by phase cycling techniques, the second pulse sequences accomplishes the editing of heteronuclear J-coupled signals based on the fact that this sequence is transparent to the uncoupled spins and is equivalent a 90 degrees excitation pulse to the heteronuclear J-coupled spins. Experimental results have confirmed the ability of spectral editing with these two new sequences

  3. Fundamentals of Protein NMR Spectroscopy

    CERN Document Server

    Rule, Gordon S

    2006-01-01

    NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data pr...

  4. Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins.

    Science.gov (United States)

    Traaseth, Nathaniel J; Chao, Fa-An; Masterson, Larry R; Mangia, Silvia; Garwood, Michael; Michaeli, Shalom; Seelig, Burckhard; Veglia, Gianluigi

    2012-06-01

    NMR relaxation methods probe biomolecular motions over a wide range of timescales. In particular, the rotating frame spin-lock R(1ρ) and Carr-Purcell-Meiboom-Gill (CPMG) R(2) experiments are commonly used to characterize μs to ms dynamics, which play a critical role in enzyme folding and catalysis. In an effort to complement these approaches, we introduced the Heteronuclear Adiabatic Relaxation Dispersion (HARD) method, where dispersion in rotating frame relaxation rate constants (longitudinal R(1ρ) and transverse R(2ρ)) is created by modulating the shape and duration of adiabatic full passage (AFP) pulses. Previously, we showed the ability of the HARD method to detect chemical exchange dynamics in the fast exchange regime (k(ex)∼10(4)-10(5) s(-1)). In this article, we show the sensitivity of the HARD method to slower exchange processes by measuring R(1ρ) and R(2ρ) relaxation rates for two soluble proteins (ubiquitin and 10C RNA ligase). One advantage of the HARD method is its nominal dependence on the applied radio frequency field, which can be leveraged to modulate the dispersion in the relaxation rate constants. In addition, we also include product operator simulations to define the dynamic range of adiabatic R(1ρ) and R(2ρ) that is valid under all exchange regimes. We conclude from both experimental observations and simulations that this method is complementary to CPMG-based and rotating frame spin-lock R(1ρ) experiments to probe conformational exchange dynamics for biomolecules. Finally, this approach is germane to several NMR-active nuclei, where relaxation rates are frequency-offset independent. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. 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.

  6. Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples

    Energy Technology Data Exchange (ETDEWEB)

    Gopinath, T. [University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics (United States); Mote, Kaustubh R. [University of Minnesota, Department of Chemistry (United States); Veglia, Gianluigi, E-mail: vegli001@umn.edu [University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics (United States)

    2015-05-15

    We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living {sup 15}N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through {sup 15}N–{sup 15}N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish {sup 15}N–{sup 15}N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI–HETCOR and 3D PISEMAI–HETCOR-mixing experiments.

  7. Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples.

    Science.gov (United States)

    Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi

    2015-05-01

    We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.

  8. Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples

    International Nuclear Information System (INIS)

    Gopinath, T.; Mote, Kaustubh R.; Veglia, Gianluigi

    2015-01-01

    We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living 15 N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through 15 N– 15 N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish 15 N– 15 N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI–HETCOR and 3D PISEMAI–HETCOR-mixing experiments

  9. Structural study of pyrones by NMR

    International Nuclear Information System (INIS)

    Mandarino, D.G.

    1985-01-01

    Extracts of two species of Aniba, designed Aniba-SA (light petroleum extract) and Aniba-SB (benzene extract), afforded by chromatographic fraccionation some compounds. The isolated compounds were identified using spectrometric data and C 13 -NMR coupled and decompled spectra of pyrones were registered. Measurement of the heteronuclear residual coupling by irradiation proton frequency off-resonance was used for distinguish C-5, C-7 and C-8 carbons of the pyrones SB-1, SB-3, SB-4 and SB-5. (M.J.C.) [pt

  10. Selected topics from recent NMR studies of organolithium compounds

    Directory of Open Access Journals (Sweden)

    Günther Harald

    1999-01-01

    Full Text Available After a short introduction to NMR spectroscopy of alkali and alkaline earth metals the review concentrates on NMR investigations of organolithium compounds. The isotopic fingerprint method, which rests on deuterium-induced isotope shifts for 6Li resonances, is introduced and exemplified with applications from the aggregation behavior of cyclopropyllithium systems and mixed aggregate formation between methyllithium and lithium salts. In the following chapter, one- and two-dimensional pulse experiments, both for homo- and for heteronuclear spin systems are discussed. Finally, the structural aspects associated with benzyllithium are outlined and the formation of polylithium systems by lithium reduction of biphenylenes is described.

  11. MODELO MULTIDIMENSIONAL

    Directory of Open Access Journals (Sweden)

    Alexis Cedeño Trujillo

    2006-04-01

    Full Text Available

    Data Warehousing, es una tecnología para el almacenamiento de grandes volúmenes de datos en una amplia perspectiva de tiempo para el soporte a la toma de decisiones. Debido a su orientación analítica, impone un procesamiento distinto al de los sistemas operacionales y requiere de un diseño de base de datos más cercano a la visión de los usuarios finales, permitiendo que sea más fácil la recuperación de información y la navegación. Este diseño de base de datos se conoce como modelo multidimensional, este artículo, abordará sus características principales.

  12. Detailed {sup 1}H and {sup 13}C NMR spectral data assignment for two dihydrobenzofuran neolignans

    Energy Technology Data Exchange (ETDEWEB)

    Medeiros, Talita C.T.; Dias, Herbert J.; Crotti, Antônio E.M., E-mail: millercrotti@ffclrp.usp.br [Universidade de São Paulo (USP), Ribeirão Preto, SP (Brazil). Faculdade de Filosofia, Ciências e Letras. Departamento de Química

    2016-07-01

    In this work we present a complete proton ({sup 1}H) and carbon 13 ({sup 13}C) nuclear magnetic resonance (NMR) spectral analysis of two synthetic dihydrofuran neolignans (±)-trans-dehydrodicoumarate dimethyl ester and (±)-trans-dehydrodiferulate dimethyl ester. Unequivocal assignments were achieved by 1 H NMR, proton decoupled {sup 13}C ({sup 13}C{"1H}) NMR spectra, gradient-selected correlation spectroscopy (gCOSY), J-resolved, gradient-selected heteronuclear multiple quantum coherence (gHMQC), gradient-selected heteronuclear multiple bond coherence (gHMBC) and nuclear Overhauser effect spectroscopy (NOESY) experiments. All hydrogen coupling constants were measured, clarifying all the hydrogen signals multiplicities. Computational methods were also used to simulate the {sup 1}H and {sup 13}C chemical shifts and showed good agreement with the trans configuration of the substituents at C{sub 7} and C{sub 8}. (author)

  13. Detailed 1H and 13C NMR spectral data assignment for two dihydrobenzofuran neolignans

    International Nuclear Information System (INIS)

    Medeiros, Talita C.T.; Dias, Herbert J.; Crotti, Antônio E.M.

    2016-01-01

    In this work we present a complete proton ( 1 H) and carbon 13 ( 13 C) nuclear magnetic resonance (NMR) spectral analysis of two synthetic dihydrofuran neolignans (±)-trans-dehydrodicoumarate dimethyl ester and (±)-trans-dehydrodiferulate dimethyl ester. Unequivocal assignments were achieved by 1 H NMR, proton decoupled 13 C ( 13 C{ 1 H}) NMR spectra, gradient-selected correlation spectroscopy (gCOSY), J-resolved, gradient-selected heteronuclear multiple quantum coherence (gHMQC), gradient-selected heteronuclear multiple bond coherence (gHMBC) and nuclear Overhauser effect spectroscopy (NOESY) experiments. All hydrogen coupling constants were measured, clarifying all the hydrogen signals multiplicities. Computational methods were also used to simulate the 1 H and 13 C chemical shifts and showed good agreement with the trans configuration of the substituents at C 7 and C 8 . (author)

  14. Synthesis and investigation of new heteronuclear [Zn-La] coordination compounds based on unsaturated lanthanum complex with N,N'-tetraethyl-N''-trichloacetylphosphortriamide

    International Nuclear Information System (INIS)

    Amyirkhanov, O.V.; Sliva, T.Yu.; Moroz, O.V.; Trush, Je.A.; Frits'kij, Yi.O.

    2011-01-01

    New heteronuclear [Zn-La] coordination compounds, perspective luminescent materials, with general formulas [Zn(Ve)La(X) 2 (Ac)] ({Zn-La;Ve;X}) and [Zn(Vp)La(X) 2 (Ac)] ({Zn-La;Vp;X}) have been synthesized HX=CCl 3 C(O)NHP(O)[N(C 2 H 5 ) 2 ] 2 - N,N'-tetraethyl-N''-trichloracetylphosphortriamide, H 2 Ve and H 2 Vp are products of the condensation of 1,2-diaminoethane and 1,3-diaminopropane with o-vanillin, respectively). The composition of [Zn-La] complexes has been determined, and the coordination mode of a phosphorylated ligand has been suggested by element analysis, IR- and 1 H, 31 P NMR-spectroscopy.

  15. Immobilization of (dd)heteronuclear hexacyanoferrates(II) in a gelatin matrix

    International Nuclear Information System (INIS)

    Mikhajlov, O.V.

    2008-01-01

    Data pertinent to potentiality of preparing salts of (dd)heteronuclear hexacyanoferrates(II) with(M 1 ) II and (M 2 ) II (M 1 , M 2 = Mn, Co, Ni, Cu, Zn, Cd) as a result of contact between M 1 2 [Fe(CN) 6 ] immobilized in a gelatin matrix and aqueous solutions of metal chlorides have been systematized and summarized. The decisive role of the gelatin matrix, performing the function of an organizing system in formation of (dd)heteronuclear hexacyanoferrates(II) of metals, has been pointed out [ru

  16. Multidimensional Heat Conduction

    DEFF Research Database (Denmark)

    Rode, Carsten

    1998-01-01

    Analytical theory of multidimensional heat conduction. General heat conduction equation in three dimensions. Steay state, analytical solutions. The Laplace equation. Method of separation of variables. Principle of superposition. Shape factors. Transient, multidimensional heat conduction....

  17. Two-dimensional NMR spectroscopy. Applications for chemists and biochemists

    International Nuclear Information System (INIS)

    Croasmun, W.R.; Carlson, R.M.K.

    1987-01-01

    Two-dimensional nuclear magnetic resonance spectroscopy (2-D NMR) has become a very powerful class of experiments (in the hands of an adept scientist) with broad adaptability to new situations. It is the product of a happy marriage between modern pulse FT-NMR technology, with its large memory and high-speed computers, and the physicists and chemists who love to manipulate spin systems. Basic 2-D experiments are now a standard capability of modern NMR spectrometers, and this timely book intends to make 2-D NMR users of those who are familiar with normal 1-D NMR. The 2-D NMR goal is correlation of the lines of the observed NMR spectrum with other properties of the system. This book deals with applications to high-resolution spectrum analysis, utilizing either coupling between the NMR-active nuclei or chemical exchange to perform the correlation. The coupling can be scalar (through bonds) or direct through space (within 5 A). The coupling may be homonuclear (between like nuclei) or heteronuclear

  18. 2D 1H -13C Heteronuclear Shift Correlation Of 2a - Hydroxy Aiantolactone From Pulicaria Undulata C.A. Mey

    Directory of Open Access Journals (Sweden)

    A. Rustaiyan

    1992-07-01

    Full Text Available We have reported recently the isolation and characterization of several sesquiterpene lactones from Pulicaria undulata (1."nThe lactones were isolated from an Et20 - Petrol (1:3 fraction by different chromatographic techniques including HPLC (RP 8, MeOH - H2O, 13:7."nIn this way three eudesmanolides 1 - 3, a guaianolide 4, a nor -guaianolide 5, as well as the pseudoguaianolide 6 and the xanthanolide 7 were isolated. One of the eudesmanolides (2a - hydroxy aiantolactone, 1, was present as the main component."nSuch lactones being known as biologically active substances, we have decided to describe for the first time a detailed interpretation of proton, 1H -NMR, 13C - NMR and 2D lH -13C - heteronuclear shift correlation spectra of 2a - hydroxy aiantolactone. The stereochemistry of C - 2 , C - 7 and C - 8 was determined by the NOESY experiments, H - 7 and H - 8 are in the a configuration and H - 2 is in the b configuration.

  19. Pumping vortex into a Bose-Einstein condensate of heteronuclear molecules

    International Nuclear Information System (INIS)

    Xu, Z F; Wang, R Q; You, L

    2009-01-01

    Heteronuclear molecules have attracted wide attention due to their permanent electric dipole moments. Analogous to atoms with magnetic dipoles, the existence of nonzero electric dipoles significantly enhances the possibilities and mechanisms for the control and design of quantum degenerate molecule systems with electric (E) fields. This work proposes a vortex creation mechanism inside a condensate of heteronuclear molecules through the adiabatic flipping of the axial bias of an analogous E-field Ioffe-Pritchard trap (IPT), extending the original protocol of Isoshima et al (2000 Phys. Rev. A 61 063610) for an atomic spinor condensate inside a magnetic (B)-field IPT. We provide both analytic proof and numerical simulations to illustrate the high fidelity operation of this vortex pump protocol. We hope our work provides stimulating experimental possibilities for active investigations in quantum degenerate molecule systems.

  20. Structural characterization by NMR of the natively unfolded extracellular domain of beta-dystroglycan: toward the identification of the binding epitope for alpha-dystroglycan.

    Science.gov (United States)

    Bozzi, Manuela; Bianchi, Marzia; Sciandra, Francesca; Paci, Maurizio; Giardina, Bruno; Brancaccio, Andrea; Cicero, Daniel O

    2003-11-25

    Dystroglycan (DG) is an adhesion molecule playing a crucial role for tissue stability during both early embriogenesis and adulthood and is composed by two tightly interacting subunits: alpha-DG, membrane-associated and highly glycosylated, and the transmembrane beta-DG. Recently, by solid-phase binding assays and NMR experiments, we have shown that the C-terminal domain of alpha-DG interacts with a recombinant extracellular fragment of beta-DG (positions 654-750) independently from glycosylation and that the linear binding epitope is located between residues 550 and 565 of alpha-DG. In order to elucidate which moieties of beta-DG are specifically involved in the complex with alpha-DG, the ectodomain has been recombinantly expressed and purified in a labeled ((13)C,(15)N) form and studied by multidimensional NMR. Although it represents a natively unfolded protein domain, we obtained an almost complete backbone assignment. Chemical shift index, (1)H-(15)N heteronuclear single-quantum coherence and nuclear Overhauser effect (HSQC-NOESY) spectra and (3)J(HN,H)(alpha) coupling constant values confirm that this protein is highly disordered, but (1)H-(15)N steady-state NOE experiments indicate that the protein presents two regions of different mobility. The first one, between residues 659 and 722, is characterized by a limited degree of mobility, whereas the C-terminal portion, containing about 30 amino acids, is highly flexible. The binding of beta-DG(654-750) to the C-terminal region of the alpha subunit, alpha-DG(485-620), has been investigated, showing that the region of beta-DG(654-750) between residues 691 and 719 is involved in the interaction.

  1. Long-range dispersion interactions. I. Formalism for two heteronuclear atoms

    International Nuclear Information System (INIS)

    Zhang, J.-Y.; Mitroy, J.

    2007-01-01

    A general procedure for systematically evaluating the long-range dispersion interaction between two heteronuclear atoms in arbitrary states is outlined. The C 6 dispersion parameter can always be written in terms of sum rules involving oscillator strengths only and formulas for a number of symmetry cases are given. The dispersion coefficients for excited alkali-metal atoms interacting with the ground-state H and He are tabulated

  2. NMR 1H,13C, 15N backbone and 13C side chain resonance assignment of the G12C mutant of human K-Ras bound to GDP.

    Science.gov (United States)

    Sharma, Alok K; Lee, Seung-Joo; Rigby, Alan C; Townson, Sharon A

    2018-05-02

    K-Ras is a key driver of oncogenesis, accounting for approximately 80% of Ras-driven human cancers. The small GTPase cycles between an inactive, GDP-bound and an active, GTP-bound state, regulated by guanine nucleotide exchange factors and GTPase activating proteins, respectively. Activated K-Ras regulates cell proliferation, differentiation and survival by signaling through several effector pathways, including Raf-MAPK. Oncogenic mutations that impair the GTPase activity of K-Ras result in a hyperactivated state, leading to uncontrolled cellular proliferation and tumorogenesis. A cysteine mutation at glycine 12 is commonly found in K-Ras associated cancers, and has become a recent focus for therapeutic intervention. We report here 1 H N, 15 N, and 13 C resonance assignments for the 19.3 kDa (aa 1-169) human K-Ras protein harboring an oncogenic G12C mutation in the GDP-bound form (K-RAS G12C-GDP ), using heteronuclear, multidimensional NMR spectroscopy. Backbone 1 H- 15 N correlations have been assigned for all non-proline residues, except for the first methionine residue.

  3. NMR imaging

    International Nuclear Information System (INIS)

    Andrew, E.R.

    1983-01-01

    Since hydrogen is the most abundant element in all living organisms, proton NMR lends itself well as a method of investigation in biology and medicine. NMR imaging has some special advantages as a diagnostic tool: no ionizing radiation is used, it is noninvasive; it provides a safer means of imaging than the use of x-rays, gamma rays, positrons, or heavy ions. In contrast with ultrasound, the radiation penetrates the bony structures without attenuation. In additional to morphological information, NMR imaging provides additional diagnostic insights through relaxation parameters, which are not available from other imaging methods. In the decade since the first primitive NMR images were obtained, the quality of images now obtained approaches those from CT x-ray scanners. Prototype instruments are being constructed for clinical evaluation and the first whole-body scanners are beginning to appear on the market at costs comparable to CT scanners. Primary differences in equipment for conventional NMR and NMR imaging are the much larger aperture magnets that are required for the examination of human subjects and the addition of coils to generate field gradients and facilities for manipulating the gradients. Early results from clinical trials in many parts of the world are encouraging, and in a few years, the usefuleness of this modality of medical imaging to the medical profession in diagnosis and treatment of disease will be defined. 10 figures

  4. SQL and Multidimensional Data

    Directory of Open Access Journals (Sweden)

    Mihaela MUNTEAN

    2006-01-01

    Full Text Available Using SQL you can manipulate multidimensional data and extract that data into a relational table. There are many PL/SQL packages that you can use directly in SQL*Plus or indirectly in Analytic Workspace Manager and OLAP Worksheet. In this article I discussed about some methods that you can use for manipulating and extracting multidimensional data.

  5. Multidimensional high harmonic spectroscopy

    International Nuclear Information System (INIS)

    Bruner, Barry D; Soifer, Hadas; Shafir, Dror; Dudovich, Nirit; Serbinenko, Valeria; Smirnova, Olga

    2015-01-01

    High harmonic generation (HHG) has opened up a new frontier in ultrafast science where attosecond time resolution and Angstrom spatial resolution are accessible in a single measurement. However, reconstructing the dynamics under study is limited by the multiple degrees of freedom involved in strong field interactions. In this paper we describe a new class of measurement schemes for resolving attosecond dynamics, integrating perturbative nonlinear optics with strong-field physics. These approaches serve as a basis for multidimensional high harmonic spectroscopy. Specifically, we show that multidimensional high harmonic spectroscopy can measure tunnel ionization dynamics with high precision, and resolves the interference between multiple ionization channels. In addition, we show how multidimensional HHG can function as a type of lock-in amplifier measurement. Similar to multi-dimensional approaches in nonlinear optical spectroscopy that have resolved correlated femtosecond dynamics, multi-dimensional high harmonic spectroscopy reveals the underlying complex dynamics behind attosecond scale phenomena. (paper)

  6. 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.

  7. Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.

    Science.gov (United States)

    Didenko, Tatiana; Proudfoot, Andrew; Dutta, Samit Kumar; Serrano, Pedro; Wüthrich, Kurt

    2015-08-24

    High-resolution structure determination of small proteins in solution is one of the big assets of NMR spectroscopy in structural biology. Improvements in the efficiency of NMR structure determination by advances in NMR experiments and automation of data handling therefore attracts continued interest. Here, non-uniform sampling (NUS) of 3D heteronuclear-resolved [(1)H,(1)H]-NOESY data yielded two- to three-fold savings of instrument time for structure determinations of soluble proteins. With the 152-residue protein NP_372339.1 from Staphylococcus aureus and the 71-residue protein NP_346341.1 from Streptococcus pneumonia we show that high-quality structures can be obtained with NUS NMR data, which are equally well amenable to robust automated analysis as the corresponding uniformly sampled data. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Compact NMR

    Energy Technology Data Exchange (ETDEWEB)

    Bluemich, Bernhard; Haber-Pohlmeier, Sabina; Zia, Wasif [RWTH Aachen Univ. (Germany). Inst. fuer Technische und Makromolekulare Chemie (ITMC)

    2014-06-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is the most popular method for chemists to analyze molecular structures, while Magnetic Resonance Imaging (MRI) is a non-invasive diagnostic tool for medical doctors that provides high-contrast images of biological tissue. In both applications, the sample (or patient) is positioned inside a large, superconducting magnet to magnetize the atomic nuclei. Interrogating radio-frequency pulses result in frequency spectra that provide the chemist with molecular information, the medical doctor with anatomic images, and materials scientist with NMR relaxation parameters. Recent advances in magnet technology have led to a variety of small permanent magnets to allow compact and low-cost instruments. The goal of this book is to provide an introduction to the practical use of compact NMR at a level nearly as basic as the operation of a smart phone.

  9. Quantum atom-heteronuclear molecule dark state: Role of population imbalance

    International Nuclear Information System (INIS)

    Jing Hui; Cui Shuai

    2010-01-01

    Recently, the finite-number effect of initial atoms in coherent atom-molecule conversion was investigated by Zhao et al. [Phys. Rev. Lett. 101, 010401 (2008)]. Here, by extending to the atom-heteronuclear molecule dark state, we find that the initial populations imbalance of the atoms plays a significant role in quantum conversion rate and adiabatic fidelity. In particular, even for the finite total number of imbalanced two-species atoms, the mean-field conversion rate, contrary to the general belief, still can be remarkably close to the exact quantum results.

  10. The direct measurement of the heteronuclear chemical shifts relative to tetramethylsilane

    International Nuclear Information System (INIS)

    Moritz, A.G.

    1988-12-01

    The measurement of heteronuclear chemical shifts using absolute frequencies of the heteronucleus and the 1 H resonance of tetramethylsilane has been examined. This method avoids the problems associated with external standards and gives results which can be obtained quickly and with high precision. The method has a number of advantages in the accurate measurement of chemical shifts, as for example 31 P in chemical warfare agents and related chemicals and allows multinuclear data to be obtained without dynamic range or potential interference problems. 15 refs., 4 tabs

  11. Phase behaviour of heteronuclear dimers in three-dimensional systems-a Monte Carlo study

    International Nuclear Information System (INIS)

    Rzysko, W; Binder, K

    2008-01-01

    Monte Carlo simulation in the grand canonical ensemble, the histogram reweighting technique and finite size scaling are used to study the phase behaviour of dimers in three-dimensional systems. A single molecule is composed of two segments A and B, and the bond between them cannot be broken. The phase diagrams have been estimated for a set of model systems. Different structures formed by heteronuclear dimers have been found. The results show a great variety of vapour-liquid coexistence behaviour depending on the strength of the interactions between segments

  12. NMR imaging

    International Nuclear Information System (INIS)

    Ouchi, Toshihiro; Steiner, R.E.

    1984-01-01

    Three epidermoid and two dermoid tumours, pathologically proven, were examined by NMR and CT scans. Although most brain tumours have a low signal with a long T 1 , a dermoid cyst and one of the two components of the other dermoid tumour had a high signal and therefore a short T 1 . All three epidermoid tumours had a low signal and a long T 1 . Because of the high level contrast between some of the tumours and cerebrospinal fluid, NMR is helpful to detect the lesion. Neither of the liquid fluid levels in the tumour cysts or floating fat in the subarachnoid space was recognized in one patients, but the fine leakage of the content from the epidermoid cyst into the lateral ventricle was detected on a saturation recovery 1000 image in one case. (author)

  13. Multinuclear NMR resonance assignments and the secondary structure of Escherichia coli thioesterase/protease I: A member of a new subclass of lipolytic enzymes

    International Nuclear Information System (INIS)

    Lin Tahsien; Chen Chinpan; Huang Rongfong; Lee Yalin; Shaw Jeifu; Huang Taihuang

    1998-01-01

    Escherichia coli thioesterase/protease I is a 183 amino acid protein with a molecular mass of 20500. This protein belongs to a new subclass of lipolytic enzymes of the serine protease superfamily, but with a new GDSLS consensus motif, of which no structure has yet been determined. The protein forms a tetramer at pH values above 6.5 and exists as a monomer at lower pH values. Both monomer and tetramer are catalytically active. From analysis of a set of heteronuclear multidimensional NMR spectra with uniform and specific amino acid labeled protein samples, we have obtained near-complete resonance assignments of the backbone 1 H, 13 C and 15 N nuclei (BMRB databank accession number 4060). The secondary structure of E. coli thioesterase/protease I was further deduced from the consensus chemical shift indices, backbone short- and medium-range NOEs, and amide proton exchange rates. The protein was found to consist of four β-strands and seven α-helices, arranged in alternate order. The four β-strands were shown to form a parallel β-sheet. The topological arrangement of the β-strands of -1x, +2x, +1x appears to resemble that of the core region of the αβ hydrolase superfamily, typically found in common lipases and esterases. However, substantial differences, such as the number of β-strands and the location of the catalytic triad residues, make it difficult to give a definitive classification of the structure of E. coli thioesterase/protease I at present

  14. Applied multidimensional systems theory

    CERN Document Server

    Bose, Nirmal K

    2017-01-01

    Revised and updated, this concise new edition of the pioneering book on multidimensional signal processing is ideal for a new generation of students. Multidimensional systems or m-D systems are the necessary mathematical background for modern digital image processing with applications in biomedicine, X-ray technology and satellite communications. Serving as a firm basis for graduate engineering students and researchers seeking applications in mathematical theories, this edition eschews detailed mathematical theory not useful to students. Presentation of the theory has been revised to make it more readable for students, and introduce some new topics that are emerging as multidimensional DSP topics in the interdisciplinary fields of image processing. New topics include Groebner bases, wavelets, and filter banks.

  15. Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways

    Science.gov (United States)

    Chikayama, Eisuke; Suto, Michitaka; Nishihara, Takashi; Shinozaki, Kazuo; Hirayama, Takashi; Kikuchi, Jun

    2008-01-01

    Background Metabolic phenotyping has become an important ‘bird's-eye-view’ technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of ‘top-down’ chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. Methodology/Principal Findings The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 1H and 13C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each 13C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient 13C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. Conclusions/Significance Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of 13C atoms of

  16. Effect of ecosystem type and fire on chemistry of WEOM as measured by LDI-TOF-MS and NMR.

    Science.gov (United States)

    Crecelius, Anna C; Vitz, Jürgen; Näthe, Kerstin; Meyer, Stefanie; Michalzik, Beate; Schubert, Ulrich S

    2017-01-01

    Soil organic matter (SOM) and its water-soluble components play an important role in terrestrial carbon cycling and associated ecosystem functions. Chemically, they are complex mixtures of organic compounds derived from decomposing plant material, microbial residues, as well as root exudates, and soil biota. To test the effect of the ecosystem type (forest and grassland) and fires events on the chemistry of dissolved organic matter (DOM), we applied a combination of laser-desorption/ionization time-of-flight mass spectrometry (LDI-TOF-MS) and 2D ( 1 H and 13 C) nuclear magnetic resonance (NMR) spectroscopy to water-extractable organic matter (WEOM) from a range of top soil samples. The aim was to assess the suitability of LDI-TOF-MS for the rapid characterization of WEOM. Therefore, we evaluated the effects of sample (pH and dilution) conditions and use of positive or negative reflector mode to identify the conditions under which LDI-TOF-MS best distinguished between WEOM from different sources. Thirty-six samples were measured with both analytical techniques and their chemical patterns were statistically evaluated to distinguish firstly the effect of the type of ecosystem (forest versus grassland) on WEOM characteristics, and secondly the impact of fire on the chemical composition of WEOM. The nonmetric multidimensional scaling (NMDS) analysis of the most suitable experimental LDI-TOF-MS conditions showed a clear separation between the type of vegetation and fire-induced changes, mostly reflecting the presence of poly(ethylene glycol) in grassland soils. Discrimination among WEOM from different vegetation types was preserved in the fire treated samples. The calculation of the relative abundance of certain functional structures in the WEOM samples revealed a common composition of forest and grassland WEOM, with polysaccharides and proteins making up to 60%. The compositional impact of forest fire on WEOM was more pronounced compared to the one of grassland, leading

  17. Multi-dimensional imaging

    CERN Document Server

    Javidi, Bahram; Andres, Pedro

    2014-01-01

    Provides a broad overview of advanced multidimensional imaging systems with contributions from leading researchers in the field Multi-dimensional Imaging takes the reader from the introductory concepts through to the latest applications of these techniques. Split into 3 parts covering 3D image capture, processing, visualization and display, using 1) a Multi-View Approach and 2.) a Holographic Approach, followed by a 3rd part addressing other 3D systems approaches, applications and signal processing for advanced 3D imaging. This book describes recent developments, as well as the prospects and

  18. Synthesis and magnetic properties of heteronuclear 3d-4f compound

    International Nuclear Information System (INIS)

    Cristovao, B.; Ferenc, W.

    2007-01-01

    A novel heteronuclear 3d-4f compound having formula NdCu 3 L 3 ·13H 2 O (where H 3 L = Schiff base derived from 5-bromosalicylaldehyde and glycylglycine and L 3 = C 11 H 8 N 2 O 4 Br) was obtained. It was characterized by elemental and thermal analyses and magnetic measurements. The Cu(II)-Nd(III) compound is stable up to 323 K. During dehydration process the water molecules are lost in two stages. The magnetic susceptibility data for this complex change with temperature according to the Curie-Weiss law with Θ = -35 K. The magnetic moment values decrease from 5.00μ B at 303 K to 4.38μB at 76 K. (author)

  19. Interaction-induced decay of a heteronuclear two-atom system

    Science.gov (United States)

    Xu, Peng; Yang, Jiaheng; Liu, Min; He, Xiaodong; Zeng, Yong; Wang, Kunpeng; Wang, Jin; Papoular, D. J.; Shlyapnikov, G. V.; Zhan, Mingsheng

    2015-01-01

    Two-atom systems in small traps are of fundamental interest for understanding the role of interactions in degenerate cold gases and for the creation of quantum gates in quantum information processing with single-atom traps. One of the key quantities is the inelastic relaxation (decay) time when one of the atoms or both are in a higher hyperfine state. Here we measure this quantity in a heteronuclear system of 87Rb and 85Rb in a micro optical trap and demonstrate experimentally and theoretically the presence of both fast and slow relaxation processes, depending on the choice of the initial hyperfine states. This experimental method allows us to single out a particular relaxation process thus provides an extremely clean platform for collisional physics studies. Our results have also implications for engineering of quantum states via controlled collisions and creation of two-qubit quantum gates. PMID:26199051

  20. Symbolic Multidimensional Scaling

    NARCIS (Netherlands)

    P.J.F. Groenen (Patrick); Y. Terada

    2015-01-01

    markdownabstract__Abstract__ Multidimensional scaling (MDS) is a technique that visualizes dissimilarities between pairs of objects as distances between points in a low dimensional space. In symbolic MDS, a dissimilarity is not just a value but can represent an interval or even a histogram. Here,

  1. Pulsed zero field NMR of solids and liquid crystals

    International Nuclear Information System (INIS)

    Thayer, A.M.

    1987-02-01

    This work describes the development and applications to solids and liquid crystals of zero field nuclear magnetic resonance (NMR) experiments with pulsed dc magnetic fields. Zero field NMR experiments are one approach for obtaining high resolution spectra of amorphous and polycrystalline materials which normally (in high field) display broad featureless spectra. The behavior of the spin system can be coherently manipulated and probed in zero field with dc magnetic field pulses which are employed in a similar manner to radiofrequency pulses in high field NMR experiments. Nematic phases of liquid crystalline systems are studied in order to observe the effects of the removal of an applied magnetic field on sample alignment and molecular order parameters. In nematic phases with positive and negative magnetic susceptibility anisotropies, a comparison between the forms of the spin interactions in high and low fields is made. High resolution zero field NMR spectra of unaligned smectic samples are also obtained and reflect the symmetry of the liquid crystalline environment. These experiments are a sensitive measure of the motionally induced asymmetry in biaxial phases. Homonuclear and heteronuclear solute spin systems are compared in the nematic and smectic phases. Nonaxially symmetric dipolar couplings are reported for several systems. The effects of residual fields in the presence of a non-zero asymmetry parameter are discussed theoretically and presented experimentally. Computer programs for simulations of these and other experimental results are also reported. 179 refs., 75 figs

  2. NMR spectroscopy

    International Nuclear Information System (INIS)

    Gruenert, J.

    1989-01-01

    The book reviews the applications of NMR-spectroscopy in medicine and biology. The first chapter of about 40 pages summarizes the history of development and explains the chemical and physical fundamentals of this new and non-invasive method in an easily comprehensible manner. The other chapters summarize diagnostic results obtained with this method in organs and tissues, so that the reader will find a systematic overview of the available findings obtained in the various organ systems. It must be noted, however, that ongoing research work and new insight quite naturally will necessitate corrections to be done, as is the case here with some biochemical interpretations which would need adjustment to latest research results. NMR-spectroscopy is able to measure very fine energy differences on the molecular level, and thus offers insight into metabolic processes, with the advantage that there is no need of applying ionizing radiation in order to qualitatively or quantitatively analyse the metabolic processes in the various organ systems. (orig./DG) With 40 figs., 4 tabs [de

  3. Numeric invariants from multidimensional persistence

    Energy Technology Data Exchange (ETDEWEB)

    Skryzalin, Jacek [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Carlsson, Gunnar [Stanford Univ., Stanford, CA (United States)

    2017-05-19

    In this paper, we analyze the space of multidimensional persistence modules from the perspectives of algebraic geometry. We first build a moduli space of a certain subclass of easily analyzed multidimensional persistence modules, which we construct specifically to capture much of the information which can be gained by using multidimensional persistence over one-dimensional persistence. We argue that the global sections of this space provide interesting numeric invariants when evaluated against our subclass of multidimensional persistence modules. Lastly, we extend these global sections to the space of all multidimensional persistence modules and discuss how the resulting numeric invariants might be used to study data.

  4. HN-NCA heteronuclear TOCSY-NH experiment for {sup 1}H{sup N} and {sup 15}N sequential correlations in ({sup 13}C, {sup 15}N) labelled intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Wiedemann, Christoph; Goradia, Nishit; Häfner, Sabine [Leibniz Institute for Age Research, Fritz Lipmann Institute, Research Group Biomolecular NMR Spectroscopy (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Görlach, Matthias; Ohlenschläger, Oliver; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Leibniz Institute for Age Research, Fritz Lipmann Institute, Research Group Biomolecular NMR Spectroscopy (Germany)

    2015-10-15

    A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue ‘i’ with that of residues ‘i−1’ and ‘i+1’ in ({sup 13}C, {sup 15}N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploits the favourable relaxation properties of IDPs and the presence of {sup 1}J{sub CαN} and {sup 2}J{sub CαN} couplings to transfer the {sup 15}N{sub x} magnetisation from amino acid residue ‘i’ to adjacent residues via the application of a band-selective {sup 15}N–{sup 13}C{sup α} heteronuclear cross-polarisation sequence of ∼100 ms duration. Employing non-uniform sampling in the indirect dimensions, the efficacy of the approach has been demonstrated by the acquisition of 3D HNN chemical shift correlation spectra of α-synuclein. The experimental performance of the RF pulse sequence has been compared with that of the conventional INEPT-based HN(CA)NH pulse scheme. As the availability of data from both the HCCNH and HNN experiments will make it possible to use the information extracted from one experiment to simplify the analysis of the data of the other and lead to a robust approach for unambiguous backbone and side-chain resonance assignments, a time-saving strategy for the simultaneous collection of HCCNH and HNN data is also described.

  5. Multidimensional nonlinear descriptive analysis

    CERN Document Server

    Nishisato, Shizuhiko

    2006-01-01

    Quantification of categorical, or non-numerical, data is a problem that scientists face across a wide range of disciplines. Exploring data analysis in various areas of research, such as the social sciences and biology, Multidimensional Nonlinear Descriptive Analysis presents methods for analyzing categorical data that are not necessarily sampled randomly from a normal population and often involve nonlinear relations. This reference not only provides an overview of multidimensional nonlinear descriptive analysis (MUNDA) of discrete data, it also offers new results in a variety of fields. The first part of the book covers conceptual and technical preliminaries needed to understand the data analysis in subsequent chapters. The next two parts contain applications of MUNDA to diverse data types, with each chapter devoted to one type of categorical data, a brief historical comment, and basic skills peculiar to the data types. The final part examines several problems and then concludes with suggestions for futu...

  6. The multidimensional nucleon structure

    Directory of Open Access Journals (Sweden)

    Pasquini Barbara

    2016-01-01

    Full Text Available We discuss different kinds of parton distributions, which allow one to obtain a multidimensional picture of the internal structure of the nucleon. We use the concept of generalized transverse momentum dependent parton distributions and Wigner distributions, which combine the features of transverse-momentum dependent parton distributions and generalized parton distributions. We show examples of these functions within a phenomenological quark model, with focus on the role of the spin-spin and spin-orbit correlations of quarks.

  7. Two dimensional NMR of liquids and oriented molecules

    International Nuclear Information System (INIS)

    Gochin, M.

    1987-02-01

    Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of 13 C and 1 H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface

  8. Two dimensional NMR of liquids and oriented molecules

    Energy Technology Data Exchange (ETDEWEB)

    Gochin, M.

    1987-02-01

    Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of /sup 13/C and /sup 1/H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface.

  9. NMR and the surgery of tumours at the craniocervical junction

    International Nuclear Information System (INIS)

    Ahyai, A.; Matsumara, A.; Rittmeyer, K.

    1987-01-01

    The diagnosis of tumors in the posterior fossa and at the craniocervical junction has always been problematic. In this region of the brain a clear visualization of the exact extent and relations of a space-occupying lesion is indispensable in assessing whether it is operable. Even though a tumor with its perifocal edema can be detected by CT, NMR opens new perspectives for the neurosurgeon. The authors present these cases in 3 groups. Group 1 comprises patients for whom NMR results contra-indicated operation. Group II consists of patients who would probably not have been operated on prior to the use of NMR. Group III includes patients who would probably not have been operated on prior to the use of NMR (e.g arachnoid cysts, Dandy-Walker malformations, etc); the excellent multi-dimensional imaging by NMR rendered the advisability of operation questionable, so that improved diagnostics may have spared the patients unnecessary operations

  10. 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

  11. Recent Pulse Sequences for Heteronuclear Long-Range Correlation and More

    DEFF Research Database (Denmark)

    Sørensen, Ole W.

    This talk will give an overview of the key elements and principles of experiments listed on http://www.crc.dk/nmr/, from where also pulse programs in Bruker and Varian format can be downloaded.......This talk will give an overview of the key elements and principles of experiments listed on http://www.crc.dk/nmr/, from where also pulse programs in Bruker and Varian format can be downloaded....

  12. Atom-dimer scattering in a heteronuclear mixture with a finite intraspecies scattering length

    Science.gov (United States)

    Gao, Chao; Zhang, Peng

    2018-04-01

    We study the three-body problem of two ultracold identical bosonic atoms (denoted by B ) and one extra atom (denoted by X ), where the scattering length aB X between each bosonic atom and atom X is resonantly large and positive. We calculate the scattering length aad between one bosonic atom and the shallow dimer formed by the other bosonic atom and atom X , and investigate the effect induced by the interaction between the two bosonic atoms. We find that even if this interaction is weak (i.e., the corresponding scattering length aB B is of the same order of the van der Waals length rvdW or even smaller), it can still induce a significant effect for the atom-dimer scattering length aad. Explicitly, an atom-dimer scattering resonance can always occur when the value of aB B varies in the region with | aB B|≲ rvdW . As a result, both the sign and the absolute value of aad, as well as the behavior of the aad-aB X function, depends sensitively on the exact value of aB B. Our results show that, for a good quantitative theory, the intraspecies interaction is required to be taken into account for this heteronuclear system, even if this interaction is weak.

  13. Observation of Resonant Effects in Ultracold Collisions between Heteronuclear Feshbach Molecules

    Science.gov (United States)

    Ye, Xin; Wang, Fudong; Zhu, Bing; Guo, Mingyang; Lu, Bo; Wang, Dajun

    2016-05-01

    Magnetic field dependent dimer-dimer collisional losses are studied with ultracold 23 Na87 Rb Feshbach molecules. By ramping the magnetic field across the 347.8 G inter-species Feshbach resonance and removing residual atoms with a magnetic field gradient, ~ 8000 pure NaRb Feshbach molecules with a temperature below 1 μK are produced. By holding the pure molecule sample in a crossed optical dipole trap and measuring the time-dependent loss curves under different magnetic fields near the Feshbach resonance, the dimer-dimer loss rates with respect to the atomic scattering length a are mapped out. We observe a resonant feature at around a = 600a0 and a rising tail at above a = 1600a0 . This behavior resembles previous theoretical works on homonuclear Feshbach molecule, where resonant effects between dimer-dimer collisions tied to tetramer bound states were predicted. Our work shows the possibility of exploring four-body physics within a heteronuclear system. We are supported by Hong Kong RGC General Research Fund no. CUHK403813.

  14. Adsorption of asymmetric rigid rods or heteronuclear diatomic moleculeson homogeneous surfaces

    Science.gov (United States)

    Engl, W.; Courbin, L.; Panizza, P.

    2004-10-01

    We treat the adsorption on homogeneous surfaces of asymmetric rigid rods (like for instance heteronuclear diatomic molecules). We show that the n→0 vector spin formalism is well suited to describe such a problem. We establish an isomorphism between the coupling constants of the magnetic Hamiltonian and the adsorption parameters of the rigid rods. By solving this Hamiltonian within a mean-field approximation, we obtain analytical expressions for the densities of the different rod’s configurations, both isotherm and isobar adsorptions curves. The most probable configurations of the molecules (normal or parallel to the surface) which depends on temperature and energy parameters are summarized in a diagram. We derive that the variation of Qv , the heat of adsorption at constant volume, with the temperature is a direct signature of the adsorbed molecules configuration change. We show that this formalism can be generalized to more complicated problems such as for instance the adsorption of symmetric and asymmetric rigid rods mixtures in the presence or not of interactions.

  15. Multidimensional Models of Information Need

    OpenAIRE

    Yun-jie (Calvin) Xu; Kai Huang (Joseph) Tan

    2009-01-01

    User studies in information science have recognised relevance as a multidimensional construct. An implication of multidimensional relevance is that a user's information need should be modeled by multiple data structures to represent different relevance dimensions. While the extant literature has attempted to model multiple dimensions of a user's information need, the fundamental assumption that a multidimensional model is better than a uni-dimensional model has not been addressed. This study ...

  16. Determination of relative configurations and conformations of oxindole alkaloids from Uncaria guianensis by NMR; Determinacao por RMN das configuracoes relativas e conformacoes de alcaloides oxindolicos isolados de Uncaria guianensis

    Energy Technology Data Exchange (ETDEWEB)

    Carbonezi, Carlos Alberto; Hamerski, Lidilhone; Flausino Junior, Otavio Aparecido; Furlan, Maysa; Bolzani, Vanderlan da Silva [UNESP, Araraquara, SP (Brazil). Inst. de Quimica]. E-mail: bolzaniv@iq.unesp.br; Young, Maria Claudia Marx [Instituto de Botanica, Sao Paulo, SP (Brazil). Secao de Fisiologia e Bioquimica de Plantas

    2004-12-01

    Phytochemical studies with leaves of Uncaria guianensis resulted in the isolation of the oxindole alkaloids isomitraphylline (1), 3-isoajmalicine (2) mitraphylline (3), and isomitraphylinic acid (4). Structural assignments of these alkaloids, including relative configurations and conformations, were performed through spectral data and physical properties. 1D and 2D homonuclear and heteronuclear NMR spectroscopy was a valuable tool for the establishment of the relative stereochemistry of those compounds. (author)

  17. Purification and Characterization of Recombinant N-Terminally Pyroglutamate-Modified Amyloid-β Variants and Structural Analysis by Solution NMR Spectroscopy.

    Directory of Open Access Journals (Sweden)

    Christina Dammers

    Full Text Available Alzheimer's disease (AD is the leading cause of dementia in the elderly and is characterized by memory loss and cognitive decline. Pathological hallmark of AD brains are intracellular neurofibrillary tangles and extracellular amyloid plaques. The major component of these plaques is the highly heterogeneous amyloid-β (Aβ peptide, varying in length and modification. In recent years pyroglutamate-modified amyloid-β (pEAβ peptides have increasingly moved into the focus since they have been described to be the predominant species of all N-terminally truncated Aβ. Compared to unmodified Aβ, pEAβ is known to show increased hydrophobicity, higher toxicity, faster aggregation and β-sheet stabilization and is more resistant to degradation. Nuclear magnetic resonance (NMR spectroscopy is a particularly powerful method to investigate the conformations of pEAβ isoforms in solution and to study peptide/ligand interactions for drug development. However, biophysical characterization of pEAβ and comparison to its non-modified variant has so far been seriously hampered by the lack of highly pure recombinant and isotope-enriched protein. Here we present, to our knowledge, for the first time a reproducible protocol for the production of pEAβ from a recombinant precursor expressed in E. coli in natural isotope abundance as well as in uniformly [U-15N]- or [U-13C, 15N]-labeled form, with yields of up to 15 mg/l E. coli culture broth. The chemical state of the purified protein was evaluated by RP-HPLC and formation of pyroglutamate was verified by mass spectroscopy. The recombinant pyroglutamate-modified Aβ peptides showed characteristic sigmoidal aggregation kinetics as monitored by thioflavin-T assays. The quality and quantity of produced pEAβ40 and pEAβ42 allowed us to perform heteronuclear multidimensional NMR spectroscopy in solution and to sequence-specifically assign the backbone resonances under near-physiological conditions. Our results suggest

  18. Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

    Science.gov (United States)

    Kupka, Teobald; Wieczorek, Piotr P.

    2016-01-01

    In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.

  19. Multidimensional sexual perfectionism.

    Science.gov (United States)

    Stoeber, Joachim; Harvey, Laura N; Almeida, Isabel; Lyons, Emma

    2013-11-01

    Perfectionism is a multidimensional personality characteristic that can affect all areas of life. This article presents the first systematic investigation of multidimensional perfectionism in the domain of sexuality exploring the unique relationships that different forms of sexual perfectionism show with positive and negative aspects of sexuality. A sample of 272 university students (52 male, 220 female) completed measures of four forms of sexual perfectionism: self-oriented, partner-oriented, partner-prescribed, and socially prescribed. In addition, they completed measures of sexual esteem, sexual self-efficacy, sexual optimism, sex life satisfaction (capturing positive aspects of sexuality) and sexual problem self-blame, sexual anxiety, sexual depression, and negative sexual perfectionism cognitions during sex (capturing negative aspects). Results showed unique patterns of relationships for the four forms of sexual perfectionism, suggesting that partner-prescribed and socially prescribed sexual perfectionism are maladaptive forms of sexual perfectionism associated with negative aspects of sexuality whereas self-oriented and partner-oriented sexual perfectionism emerged as ambivalent forms associated with positive and negative aspects.

  20. Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets

    International Nuclear Information System (INIS)

    Bellstedt, Peter; Seiboth, Thomas; Häfner, Sabine; Kutscha, Henriette; Ramachandran, Ramadurai; Görlach, Matthias

    2013-01-01

    NMR-based structure determination of a protein requires the assignment of resonances as indispensable first step. Even though heteronuclear through-bond correlation methods are available for that purpose, challenging situations arise in cases where the protein in question only yields samples of limited concentration and/or stability. Here we present a strategy based upon specific individual unlabeling of all 20 standard amino acids to complement standard NMR experiments and to achieve unambiguous backbone assignments for the fast precipitating 23 kDa catalytic domain of human aprataxin of which only incomplete standard NMR data sets could be obtained. Together with the validation of this approach utilizing the protein GB1 as a model, a comprehensive insight into metabolic interconversion ('scrambling”) of NH and CO groups in a standard Escherichia coli expression host is provided

  1. Targeted natural product isolation guided by HPLC-SPE-NMR: Constituents of Hubertia species

    DEFF Research Database (Denmark)

    Sprogoe, K.; Staek, D.; Jager, A.K.

    2007-01-01

    -hydroxyphenyl)acetyl]quinic acid (3), was performed. Finally, targeted isolation of 1 was achieved by SPE fractionation and preparative HPLC, followed by evaluation of its antioxidant and antimicrobial activity. In contrast to chlorogenic acid and 3,5-di-O-caffeoylquinic acid, which act as antioxidants...... full or partial identification of all major extract constituents and demonstrated the presence of unusual quinic acid derivatives containing the (1-hydroxy-4-oxocyclohexa-2,5-dienyl)acetyl residue that exhibit strongly coupled ABXY patterns, the parameters of which were obtained by spin simulations....... Using homo- and heteronuclear 2D NMR data acquired in the HPLC-SPE-NMR mode, complete structure determination of three new natural products, i.e., 3,5-di-O-caffeoyl-4-O-[(1-hydroxy-4-oxocyclohexa-2,5-dienyl)acetyl]quini c acid (1), its 2-hydroxy derivative (2), and 3,5-di-O-caffeoyl-4-O-[(4...

  2. Resolution Improvement in Multidimensional Nuclear Magnetic Resonance Spectroscopy of Proteins

    International Nuclear Information System (INIS)

    Duma, L.

    2004-01-01

    The work presented in this thesis is concerned with both liquid-state and solid-state nuclear magnetic resonance (NMR) spectroscopy. Most of this work is devoted to the investigation by solid-state NMR of C 13 -enriched compounds with the principal aim of presenting techniques devised for further improving the spectral resolution in multidimensional NMR of microcrystalline proteins. In fully C 13 -labelled compounds, the J-coupling induces a broadening of the carbon lineshapes. We show that spin-state-selective technique called IPAP can be successfully combined with standard polarisation transfer schemes in order to remove the J-broadening in multidimensional solid-state NMR correlation experiments of fully C 13 -enriched proteins. We present subsequently two techniques tailored for liquid-state NMR spectroscopy. The carbon directly detected techniques provide chemical shift information for all backbone hetero-nuclei. They are very attracting for the study of large bio-molecular systems or for the investigation of paramagnetic proteins. In the last part of this thesis, we study the spin-echo J-modulation for homonuclear two-spin 1/2 systems. Under magic-angle spinning, the theory of J-induced spin-echo modulation allows to derive a set of modulation regimes which give a spin-echo modulation exactly equal to the J-coupling. We show that the chemical-shift anisotropy and the dipolar interaction tend to stabilize the spin-echo J-modulation. The theoretical conclusions are supported by numerical simulations and experimental results obtained for three representative samples containing C 13 spin pairs. (author)

  3. [Intraoperative multidimensional visualization].

    Science.gov (United States)

    Sperling, J; Kauffels, A; Grade, M; Alves, F; Kühn, P; Ghadimi, B M

    2016-12-01

    Modern intraoperative techniques of visualization are increasingly being applied in general and visceral surgery. The combination of diverse techniques provides the possibility of multidimensional intraoperative visualization of specific anatomical structures. Thus, it is possible to differentiate between normal tissue and tumor tissue and therefore exactly define tumor margins. The aim of intraoperative visualization of tissue that is to be resected and tissue that should be spared is to lead to a rational balance between oncological and functional results. Moreover, these techniques help to analyze the physiology and integrity of tissues. Using these methods surgeons are able to analyze tissue perfusion and oxygenation. However, to date it is not clear to what extent these imaging techniques are relevant in the clinical routine. The present manuscript reviews the relevant modern visualization techniques focusing on intraoperative computed tomography and magnetic resonance imaging as well as augmented reality, fluorescence imaging and optoacoustic imaging.

  4. Multidimensional HAM-conditions

    DEFF Research Database (Denmark)

    Hansen, Ernst Jan de Place

    Heat, Air and Moisture (HAM) conditions, experimental data are needed. Tests were performed in the large climate simulator at SBi involving full-scale wall elements. The elements were exposed for steady-state conditions, and temperature cycles simulating April and September climate in Denmark....... The effect on the moisture and temperature conditions of the addition of a vapour barrier and an outer cladding on timber frame walls was studied. The report contains comprehensive appendices documenting the full-scale tests. The tests were performed as a part of the project 'Model for Multidimensional Heat......, Air and Moisture Conditions in Building Envelope Components' carried out as a co-project between DTU Byg and SBi....

  5. 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.

  6. Multidimensional Databases and Data Warehousing

    CERN Document Server

    Jensen, Christian

    2010-01-01

    The present book's subject is multidimensional data models and data modeling concepts as they are applied in real data warehouses. The book aims to present the most important concepts within this subject in a precise and understandable manner. The book's coverage of fundamental concepts includes data cubes and their elements, such as dimensions, facts, and measures and their representation in a relational setting; it includes architecture-related concepts; and it includes the querying of multidimensional databases.The book also covers advanced multidimensional concepts that are considered to b

  7. Prediction of peak overlap in NMR spectra

    International Nuclear Information System (INIS)

    Hefke, Frederik; Schmucki, Roland; Güntert, Peter

    2013-01-01

    Peak overlap is one of the major factors complicating the analysis of biomolecular NMR spectra. We present a general method for predicting the extent of peak overlap in multidimensional NMR spectra and its validation using both, experimental data sets and Monte Carlo simulation. The method is based on knowledge of the magnetization transfer pathways of the NMR experiments and chemical shift statistics from the Biological Magnetic Resonance Data Bank. Assuming a normal distribution with characteristic mean value and standard deviation for the chemical shift of each observable atom, an analytic expression was derived for the expected overlap probability of the cross peaks. The analytical approach was verified to agree with the average peak overlap in a large number of individual peak lists simulated using the same chemical shift statistics. The method was applied to eight proteins, including an intrinsically disordered one, for which the prediction results could be compared with the actual overlap based on the experimentally measured chemical shifts. The extent of overlap predicted using only statistical chemical shift information was in good agreement with the overlap that was observed when the measured shifts were used in the virtual spectrum, except for the intrinsically disordered protein. Since the spectral complexity of a protein NMR spectrum is a crucial factor for protein structure determination, analytical overlap prediction can be used to identify potentially difficult proteins before conducting NMR experiments. Overlap predictions can be tailored to particular classes of proteins by preparing statistics from corresponding protein databases. The method is also suitable for optimizing recording parameters and labeling schemes for NMR experiments and improving the reliability of automated spectra analysis and protein structure determination.

  8. Structure of multidimensional patterns

    International Nuclear Information System (INIS)

    Smith, S.P.

    1982-01-01

    The problem of describing the structure of multidimensional data is important in exploratory data analysis, statistical pattern recognition, and image processing. A data set is viewed as a collection of points embedded in a high dimensional space. The primary goal of this research is to determine if the data have any clustering structure; such a structure implies the presence of class information (categories) in the data. A statistical hypothesis is used in the decision making. To this end, data with no structure are defined as data following the uniform distribution over some compact convex set in K-dimensional space, called the sampling window. This thesis defines two new tests for uniformity along with various sampling window estimators. The first test is a volume-based test which captures density changes in the data. The second test compares a uniformly distributed sample to the data by using the minimal spanning tree (MST) of the polled samples. Sampling window estimators are provided for simple sampling windows and use the convex hull of the data as a general sampling window estimator. For both of the tests for uniformity, theoretical results are provided on their size, and study their size and power against clustered alternatives is studied. Simulation is also used to study the efficacy of the sampling window estimators

  9. Indirectly detected chemical shift correlation NMR spectroscopy in solids under fast magic angle spinning

    Energy Technology Data Exchange (ETDEWEB)

    Mao, Kanmi [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    The development of fast magic angle spinning (MAS) opened up an opportunity for the indirect detection of insensitive low-γ nuclei (e.g., 13C and 15N) via the sensitive high-{gamma} nuclei (e.g., 1H and 19F) in solid-state NMR, with advanced sensitivity and resolution. In this thesis, new methodology utilizing fast MAS is presented, including through-bond indirectly detected heteronuclear correlation (HETCOR) spectroscopy, which is assisted by multiple RF pulse sequences for 1H-1H homonuclear decoupling. Also presented is a simple new strategy for optimization of 1H-1H homonuclear decoupling. As applications, various classes of materials, such as catalytic nanoscale materials, biomolecules, and organic complexes, are studied by combining indirect detection and other one-dimensional (1D) and two-dimensional (2D) NMR techniques. Indirectly detected through-bond HETCOR spectroscopy utilizing refocused INEPT (INEPTR) mixing was developed under fast MAS (Chapter 2). The time performance of this approach in 1H detected 2D 1H{l_brace}13C{r_brace} spectra was significantly improved, by a factor of almost 10, compared to the traditional 13C detected experiments, as demonstrated by measuring naturally abundant organic-inorganic mesoporous hybrid materials. The through-bond scheme was demonstrated as a new analytical tool, which provides complementary structural information in solid-state systems in addition to through-space correlation. To further benefit the sensitivity of the INEPT transfer in rigid solids, the combined rotation and multiple-pulse spectroscopy (CRAMPS) was implemented for homonuclear 1H decoupling under fast MAS (Chapter 3). Several decoupling schemes (PMLG5m$\\bar{x}$, PMLG5mm$\\bar{x}$x and SAM3) were analyzed to maximize the performance of through-bond transfer based

  10. NMR-CT scanner

    International Nuclear Information System (INIS)

    Kose, Katsumi; Sato, Kozo; Sugimoto, Hiroshi; Sato, Masataka.

    1983-01-01

    A brief explanation is made on the imaging methods for a practical diagnostic NMR-CT scanner : A whole-body NMR-CT scanner utilizing a resistive magnet has been developed by Toshiba in cooperation with the Institute for Solid State Physics, the University of Tokyo. Typical NMR-CT images of volunteers and patients obtained in the clinical experiments using this device are presented. Detailed specifications are also shown about the practical NMR-CTs which are to be put on the market after obtaining the government approval. (author)

  11. S3 HMBC hetero: Spin-State-Selective HMBC for accurate measurement of long-range heteronuclear coupling constants

    DEFF Research Database (Denmark)

    Hoeck, Casper; Gotfredsen, Charlotte Held; Sørensen, Ole W.

    2017-01-01

    A novel method, Spin-State-Selective (S3) HMBC hetero, for accurate measurement of heteronuclear coupling constants is introduced. The method extends the S3 HMBC technique for measurement of homonuclear coupling constants by appending a pulse sequence element that interchanges the polarization...

  12. NMR imaging and pharmaceutical sciences

    International Nuclear Information System (INIS)

    Beall, P.T.; Good, W.R.

    1986-01-01

    Described is the technique of NMR-imaging in diagnostic medicine. Proton and phosphorus NMR in diagnosis of abnormal tissue pathology. Discussed is the value of NMR to the pharmaceutical sciences. NMR may play an important role in monitoring the response of tissues to drugs, determining the localization of drugs, performing real time pharmacokinetics and testing the use of NMR contrast pharmaceuticals

  13. Fragment based drug discovery: practical implementation based on ¹⁹F NMR spectroscopy.

    Science.gov (United States)

    Jordan, John B; Poppe, Leszek; Xia, Xiaoyang; Cheng, Alan C; Sun, Yax; Michelsen, Klaus; Eastwood, Heather; Schnier, Paul D; Nixey, Thomas; Zhong, Wenge

    2012-01-26

    Fragment based drug discovery (FBDD) is a widely used tool for discovering novel therapeutics. NMR is a powerful means for implementing FBDD, and several approaches have been proposed utilizing (1)H-(15)N heteronuclear single quantum coherence (HSQC) as well as one-dimensional (1)H and (19)F NMR to screen compound mixtures against a target of interest. While proton-based NMR methods of fragment screening (FBS) have been well documented and are widely used, the use of (19)F detection in FBS has been only recently introduced (Vulpetti et al. J. Am. Chem. Soc.2009, 131 (36), 12949-12959) with the aim of targeting "fluorophilic" sites in proteins. Here, we demonstrate a more general use of (19)F NMR-based fragment screening in several areas: as a key tool for rapid and sensitive detection of fragment hits, as a method for the rapid development of structure-activity relationship (SAR) on the hit-to-lead path using in-house libraries and/or commercially available compounds, and as a quick and efficient means of assessing target druggability.

  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. Photochemical deposition of NiCoO x thin films from Ni/Co heteronuclear triketonate complexes

    International Nuclear Information System (INIS)

    Buono-Core, G.E.; Tejos, M.; Cabello, G.; Guzman, N.; Hill, R.H.

    2006-01-01

    UV light irradiation of thin films of a polyketonate Ni/Co heteronuclear complex, NiCo(DBA) 2 [DBA, dibenzoylacetone)], spin coated on Si(1 0 0) substrates produced NiCoO x mixed oxides as amorphous films. On annealing at 600 deg. C under air, the mixed oxide film decomposed to NiO and CoO as indicated by XRD measurements. The morphology of the as-deposited films was examined by AFM analysis showing a smooth surface with low rms roughness values. The ratio of Ni/Co (1.08) present in the film reflects the stoichiometry in the starting compound within the experimental error, as shown by XPS analysis. The large amount of carbon (20.8%) detected on the surface of the film may be due to the presence of phenyl rings in the precursor complex

  16. Performance of new 400-MHz HTS power-driven magnet NMR technology on typical pharmaceutical API, cinacalcet HCl.

    Science.gov (United States)

    Silva Elipe, Maria Victoria; Donovan, Neil; Krull, Robert; Pooke, Donald; Colson, Kimberly L

    2018-04-17

    After years towards higher field strength magnets, nuclear magnetic resonance (NMR) technology in commercial instruments in the past decade has expanded at low and high magnetic fields to take advantage of new opportunities. At lower field strengths, permanent magnets are well established, whereas for midrange and high field, developments utilize superconducting magnets cooled with cryogenic liquids. Recently, the desire to locate NMR spectrometers in nontypical NMR laboratories has created interest in the development of cryogen-free magnets. These magnets require no cryogenic maintenance, eliminating routine filling and large cryogen dewars in the facility. Risks of spontaneous quenches and safety concerns when working with cryogenic liquids are eliminated. The highest field commercially available cryogen-free NMR magnet previously reported was at 4.7 T in 2013. Here we tested a prototype cryogen-free 9.4-T power-driven high-temperature-superconducting (HTS) magnet mated to commercial NMR spectrometer electronics. We chose cinacalcet HCl, a typical active pharmaceutical ingredient, to evaluate its performance towards structure elucidation. Satisfactory standard 1D and 2D homonuclear and heteronuclear NMR results were obtained and compared with those from a standard 9.4-T cryogenically cooled superconducting NMR instrument. The results were similar between both systems with minor differences. Further comparison with different shims and probes in the HTS magnet system confirmed that the magnet homogeneity profile could be matched with commercially available NMR equipment for optimal results. We conclude that HTS magnet technology works well providing results comparable with those of standard instruments, leading us to investigate additional applications for this magnet technology outside a traditional NMR facility. Copyright © 2018 John Wiley & Sons, Ltd.

  17. Lectures on pulsed NMR

    International Nuclear Information System (INIS)

    Pines, A.

    1988-08-01

    These lectures discuss some recent developments in pulsed NMR, emphasizing fundamental principles with selected illustrative applications. Major topics covered include multiple-quantum spectroscopy, spin decoupling, the interaction of spins with a quantized field, adiabatic rapid passage, spin temperature and statistics of cross-polarization, coherent averaging, and zero field NMR. 32 refs., 56 figs

  18. Lectures on pulsed NMR

    International Nuclear Information System (INIS)

    Pines, A.

    1986-09-01

    These lectures discuss some recent developments in pulsed NMR, emphasizing fundamental principles with selected illustrative applications. Major topics covered include multiple-quantum spectroscopy, spin decoupling, the interaction of spins with a quantized field, adiabatic rapid passage, spin temperature and statistics of cross-polarization, coherent averaging, and zero field NMR. 55 figs

  19. Contributions to multidimensional quadrature formulas

    International Nuclear Information System (INIS)

    Guenther, C.

    1976-11-01

    The general objective of this paper is to construct multidimensional quadrature formulas similar to the Gaussian Quadrature Formulas in one dimension. The correspondence between these formulas and orthogonal and nonnegative polynomials is established. One part of the paper considers the construction of multidimensional quadrature formulas using only methods of algebraic geometry, on the other part it is tried to obtain results on quadrature formulas with real nodes and, if possible, with positive weights. The results include the existence of quadrature formulas, information on the number resp. on the maximum possible number of points in the formulas for given polynomial degree N and the construction of formulas. (orig.) [de

  20. Multi-Dimensional Path Queries

    DEFF Research Database (Denmark)

    Bækgaard, Lars

    1998-01-01

    to create nested path structures. We present an SQL-like query language that is based on path expressions and we show how to use it to express multi-dimensional path queries that are suited for advanced data analysis in decision support environments like data warehousing environments......We present the path-relationship model that supports multi-dimensional data modeling and querying. A path-relationship database is composed of sets of paths and sets of relationships. A path is a sequence of related elements (atoms, paths, and sets of paths). A relationship is a binary path...

  1. Multidimensional real analysis I differentiation

    CERN Document Server

    Duistermaat, J J; van Braam Houckgeest, J P

    2004-01-01

    Part one of the authors' comprehensive and innovative work on multidimensional real analysis. This book is based on extensive teaching experience at Utrecht University and gives a thorough account of differential analysis in multidimensional Euclidean space. It is an ideal preparation for students who wish to go on to more advanced study. The notation is carefully organized and all proofs are clean, complete and rigorous. The authors have taken care to pay proper attention to all aspects of the theory. In many respects this book presents an original treatment of the subject and it contains man

  2. High Field In Vivo 13C Magnetic Resonance Spectroscopy of Brain by Random Radiofrequency Heteronuclear Decoupling and Data Sampling

    Science.gov (United States)

    Li, Ningzhi; Li, Shizhe; Shen, Jun

    2017-06-01

    In vivo 13C magnetic resonance spectroscopy (MRS) is a unique and effective tool for studying dynamic human brain metabolism and the cycling of neurotransmitters. One of the major technical challenges for in vivo 13C-MRS is the high radio frequency (RF) power necessary for heteronuclear decoupling. In the common practice of in vivo 13C-MRS, alkanyl carbons are detected in the spectra range of 10-65ppm. The amplitude of decoupling pulses has to be significantly greater than the large one-bond 1H-13C scalar coupling (1JCH=125-145 Hz). Two main proton decoupling methods have been developed: broadband stochastic decoupling and coherent composite or adiabatic pulse decoupling (e.g., WALTZ); the latter is widely used because of its efficiency and superb performance under inhomogeneous B1 field. Because the RF power required for proton decoupling increases quadratically with field strength, in vivo 13C-MRS using coherent decoupling is often limited to low magnetic fields (protons via weak long-range 1H-13C scalar couplings, which can be decoupled using low RF power broadband stochastic decoupling. Recently, the carboxylic/amide 13C-MRS technique using low power random RF heteronuclear decoupling was safely applied to human brain studies at 7T. Here, we review the two major decoupling methods and the carboxylic/amide 13C-MRS with low power decoupling strategy. Further decreases in RF power deposition by frequency-domain windowing and time-domain random under-sampling are also discussed. Low RF power decoupling opens the possibility of performing in vivo 13C experiments of human brain at very high magnetic fields (such as 11.7T), where signal-to-noise ratio as well as spatial and temporal spectral resolution are more favorable than lower fields.

  3. Iterative algorithm of discrete Fourier transform for processing randomly sampled NMR data sets

    International Nuclear Information System (INIS)

    Stanek, Jan; Kozminski, Wiktor

    2010-01-01

    Spectra obtained by application of multidimensional Fourier Transformation (MFT) to sparsely sampled nD NMR signals are usually corrupted due to missing data. In the present paper this phenomenon is investigated on simulations and experiments. An effective iterative algorithm for artifact suppression for sparse on-grid NMR data sets is discussed in detail. It includes automated peak recognition based on statistical methods. The results enable one to study NMR spectra of high dynamic range of peak intensities preserving benefits of random sampling, namely the superior resolution in indirectly measured dimensions. Experimental examples include 3D 15 N- and 13 C-edited NOESY-HSQC spectra of human ubiquitin.

  4. Temperature-induced transitions in disordered proteins probed by NMR spectroscopy

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin; Kragelund, Birthe Brandt

    2012-01-01

    Intrinsically disordered proteins are abundant in nature and perform many important physiological functions. Multidimensional NMR spectroscopy has been crucial for the understanding of the conformational properties of disordered proteins and is increasingly used to probe their conformational...... ensembles. Compared to folded proteins, disordered proteins are more malleable and more easily perturbed by environmental factors. Accordingly, the experimental conditions and especially the temperature modify the structural and functional properties of disordered proteins. NMR spectroscopy allows analysis...... of temperature-induced structural changes at residue resolution using secondary chemical shift analysis, paramagnetic relaxation enhancement, and residual dipolar couplings. This chapter discusses practical aspects of NMR studies of temperature-induced structural changes in disordered proteins....

  5. A Multidimensional Software Engineering Course

    Science.gov (United States)

    Barzilay, O.; Hazzan, O.; Yehudai, A.

    2009-01-01

    Software engineering (SE) is a multidimensional field that involves activities in various areas and disciplines, such as computer science, project management, and system engineering. Though modern SE curricula include designated courses that address these various subjects, an advanced summary course that synthesizes them is still missing. Such a…

  6. Multidimensional Databases and Data Warehousing

    DEFF Research Database (Denmark)

    Jensen, Christian S.; Pedersen, Torben Bach; Thomsen, Christian

    The present book's subject is multidimensional data models and data modeling concepts as they are applied in real data warehouses. The book aims to present the most important concepts within this subject in a precise and understandable manner. The book's coverage of fundamental concepts includes...

  7. Recycling Behavior: A Multidimensional Approach

    Science.gov (United States)

    Meneses, Gonzalo Diaz; Palacio, Asuncion Beerli

    2005-01-01

    This work centers on the study of consumer recycling roles to examine the sociodemographic and psychographic profile of the distribution of recycling tasks and roles within the household. With this aim in mind, an empirical work was carried out, the results of which suggest that recycling behavior is multidimensional and comprises the undertaking…

  8. Sine-squared shifted pulses for recoupling interactions in solid-state NMR

    Science.gov (United States)

    Jain, Mukul G.; Rajalakshmi, G.; Equbal, Asif; Mote, Kaustubh R.; Agarwal, Vipin; Madhu, P. K.

    2017-06-01

    Rotational-Echo DOuble-Resonance (REDOR) is a versatile experiment for measuring internuclear distance between two heteronuclear spins in solid-state NMR. At slow to intermediate magic-angle spinning (MAS) frequencies, the measurement of distances between strongly coupled spins is challenging due to rapid dephasing of magnetisation. This problem can be remedied by employing the pulse-shifted version of REDOR known as Shifted-REDOR (S-REDOR) that scales down the recoupled dipolar coupling. In this study, we propose a new variant of the REDOR sequence where the positions of the π pulses are determined by a sine-squared function. This new variant has scaling properties similar to S-REDOR. We use theory, numerical simulations, and experiments to compare the dipolar recoupling efficiencies and the experimental robustness of the three REDOR schemes. The proposed variant has advantages in terms of radiofrequency field requirements at fast MAS frequencies.

  9. Discrete decoding based ultrafast multidimensional nuclear magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Wei, Zhiliang; Lin, Liangjie; Ye, Qimiao; Li, Jing; Cai, Shuhui; Chen, Zhong

    2015-01-01

    The three-dimensional (3D) nuclear magnetic resonance (NMR) spectroscopy constitutes an important and powerful tool in analyzing chemical and biological systems. However, the abundant 3D information arrives at the expense of long acquisition times lasting hours or even days. Therefore, there has been a continuous interest in developing techniques to accelerate recordings of 3D NMR spectra, among which the ultrafast spatiotemporal encoding technique supplies impressive acquisition speed by compressing a multidimensional spectrum in a single scan. However, it tends to suffer from tradeoffs among spectral widths in different dimensions, which deteriorates in cases of NMR spectroscopy with more dimensions. In this study, the discrete decoding is proposed to liberate the ultrafast technique from tradeoffs among spectral widths in different dimensions by focusing decoding on signal-bearing sites. For verifying its feasibility and effectiveness, we utilized the method to generate two different types of 3D spectra. The proposed method is also applicable to cases with more than three dimensions, which, based on the experimental results, may widen applications of the ultrafast technique

  10. Discrete decoding based ultrafast multidimensional nuclear magnetic resonance spectroscopy

    Science.gov (United States)

    Wei, Zhiliang; Lin, Liangjie; Ye, Qimiao; Li, Jing; Cai, Shuhui; Chen, Zhong

    2015-07-01

    The three-dimensional (3D) nuclear magnetic resonance (NMR) spectroscopy constitutes an important and powerful tool in analyzing chemical and biological systems. However, the abundant 3D information arrives at the expense of long acquisition times lasting hours or even days. Therefore, there has been a continuous interest in developing techniques to accelerate recordings of 3D NMR spectra, among which the ultrafast spatiotemporal encoding technique supplies impressive acquisition speed by compressing a multidimensional spectrum in a single scan. However, it tends to suffer from tradeoffs among spectral widths in different dimensions, which deteriorates in cases of NMR spectroscopy with more dimensions. In this study, the discrete decoding is proposed to liberate the ultrafast technique from tradeoffs among spectral widths in different dimensions by focusing decoding on signal-bearing sites. For verifying its feasibility and effectiveness, we utilized the method to generate two different types of 3D spectra. The proposed method is also applicable to cases with more than three dimensions, which, based on the experimental results, may widen applications of the ultrafast technique.

  11. Functional studies using NMR

    International Nuclear Information System (INIS)

    McCready, V.R.; Leach, M.O.; Sutton; Ell, P.

    1986-01-01

    The object of this book is to discuss and evaluate an area of Nuclear Magnetic Resonance which to date has been less emphasized than it might be, namely the use of NMR for functional studies. The book commences with a discussion of the areas in which the NMR techniques might be needed due to deficiencies in other techniques. The physics of NMR especially relating to functional measurement are then explained. Technical factors in producing functional images are discussed and the use of paramagnetic substances for carrying out flow studies are detailed. Particular attention is paid to specific studies in the various organs. The book ends with a survey of imaging in each organ and the relation of NMR images to other techniques such as ultrasound, nuclear medicine and X-rays

  12. Functional studies using NMR

    International Nuclear Information System (INIS)

    McCready, V.R.; Leach, M.; Ell, P.J.

    1987-01-01

    This volume is based on a series of lectures delivered at a one-day teaching symposium on functional and metabolic aspects of NMR measurements held at the Middlesex Hospital Medical School on 1st September 1985 as a part of the European Nuclear Medicine Society Congress. Currently the major emphasis in medical NMR in vivo is on its potential to image and display abnormalities in conventional radiological images, providing increased contrast between normal and abnormal tissue, improved definition of vasculature, and possibly an increased potential for differential diagnosis. Although these areas are undeniably of major importance, it is probable that NMR will continue to complement conventional measurement methods. The major potential benefits to be derived from in vivo NMR measurements are likely to arise from its use as an instrument for functional and metabolic studies in both clinical research and in the everyday management of patients. It is to this area that this volume is directed

  13. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    Unknown

    2005-01-03

    Jan 3, 2005 ... covering all the systems, so far discovered.5,7,8,12. With the increasing ... Structural investigations on proteins by NMR are, currently ... rapid analysis of unfolded proteins. ...... and hence help in design of drugs against them.

  14. Multi-dimensional Fuzzy Euler Approximation

    Directory of Open Access Journals (Sweden)

    Yangyang Hao

    2017-05-01

    Full Text Available Multi-dimensional Fuzzy differential equations driven by multi-dimen-sional Liu process, have been intensively applied in many fields. However, we can not obtain the analytic solution of every multi-dimensional fuzzy differential equation. Then, it is necessary for us to discuss the numerical results in most situations. This paper focuses on the numerical method of multi-dimensional fuzzy differential equations. The multi-dimensional fuzzy Taylor expansion is given, based on this expansion, a numerical method which is designed for giving the solution of multi-dimensional fuzzy differential equation via multi-dimensional Euler method will be presented, and its local convergence also will be discussed.

  15. Theory of NMR probe design

    International Nuclear Information System (INIS)

    Schnall, M.D.

    1988-01-01

    The NMR probe is the intrinsic part of the NMR system which allows transmission of a stimulus to a sample and the reception of a resulting signal from a sample. NMR probes are used in both imaging and spectroscopy. Optimal probe design is important to the production of adequate signal/moise. It is important for anyone using NMR techniques to understand how NMR probes work and how to optimize probe design

  16. Executive Information Systems' Multidimensional Models

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Executive Information Systems are design to improve the quality of strategic level of management in organization through a new type of technology and several techniques for extracting, transforming, processing, integrating and presenting data in such a way that the organizational knowledge filters can easily associate with this data and turn it into information for the organization. These technologies are known as Business Intelligence Tools. But in order to build analytic reports for Executive Information Systems (EIS in an organization we need to design a multidimensional model based on the business model from the organization. This paper presents some multidimensional models that can be used in EIS development and propose a new model that is suitable for strategic business requests.

  17. Solution NMR study of the yeast cytochrome c peroxidase: cytochrome c interaction

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, Alexander N., E-mail: ovolkov@vub.ac.be; Nuland, Nico A. J. van [Vrije Universiteit Brussel, Jean Jeener NMR Centre, Structural Biology Brussels (Belgium)

    2013-07-15

    Here we present a solution NMR study of the complex between yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP), a paradigm for understanding the biological electron transfer. Performed for the first time, the CcP-observed heteronuclear NMR experiments were used to probe the Cc binding in solution. Combining the Cc- and CcP-detected experiments, the binding interface on both proteins was mapped out, confirming that the X-ray structure of the complex is maintained in solution. Using NMR titrations and chemical shift perturbation analysis, we show that the interaction is independent of the CcP spin-state and is only weakly affected by the Cc redox state. Based on these findings, we argue that the complex of the ferrous Cc and the cyanide-bound CcP is a good mimic of the catalytically-active Cc-CcP compound I species. Finally, no chemical shift perturbations due to the Cc binding at the low-affinity CcP site were observed at low ionic strength. We discuss possible reasons for the absence of the effects and outline future research directions.

  18. APSY-NMR for protein backbone assignment in high-throughput structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

  19. Targeted natural product isolation guided by HPLC-SPE-NMR: constituents of Hubertia species.

    Science.gov (United States)

    Sprogøe, Kennett; Staerk, Dan; Jäger, Anna K; Adsersen, Anne; Hansen, Steen Honoré; Witt, Matthias; Landbo, Anne-Katrine R; Meyer, Anne S; Jaroszewski, Jerzy W

    2007-09-01

    The hyphenated technique, high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance spectroscopy (HPLC-SPE-NMR), has been applied for rapid identification of novel natural products in crude extracts of Hubertia ambavilla and Hubertia tomentosa. The technique allowed full or partial identification of all major extract constituents and demonstrated the presence of unusual quinic acid derivatives containing the (1-hydroxy-4-oxocyclohexa-2,5-dienyl)acetyl residue that exhibit strongly coupled ABXY patterns, the parameters of which were obtained by spin simulations. Using homo- and heteronuclear 2D NMR data acquired in the HPLC-SPE-NMR mode, complete structure determination of three new natural products, i.e., 3,5-di-O-caffeoyl-4-O-[(1-hydroxy-4-oxocyclohexa-2,5-dienyl)acetyl]quinic acid (1), its 2-hydroxy derivative (2), and 3,5-di-O-caffeoyl-4-O-[(4-hydroxyphenyl)acetyl]quinic acid (3), was performed. Finally, targeted isolation of 1 was achieved by SPE fractionation and preparative HPLC, followed by evaluation of its antioxidant and antimicrobial activity. In contrast to chlorogenic acid and 3,5-di-O-caffeoylquinic acid, which act as antioxidants, compound 1 proved at the same conditions to possess prooxidant activity in an assay evaluating the oxidation of human low-density lipoprotein induced by Cu(2+).

  20. Lagrangian multiforms and multidimensional consistency

    Energy Technology Data Exchange (ETDEWEB)

    Lobb, Sarah; Nijhoff, Frank [Department of Applied Mathematics, University of Leeds, Leeds LS2 9JT (United Kingdom)

    2009-10-30

    We show that well-chosen Lagrangians for a class of two-dimensional integrable lattice equations obey a closure relation when embedded in a higher dimensional lattice. On the basis of this property we formulate a Lagrangian description for such systems in terms of Lagrangian multiforms. We discuss the connection of this formalism with the notion of multidimensional consistency, and the role of the lattice from the point of view of the relevant variational principle.

  1. Cuba: Multidimensional numerical integration library

    Science.gov (United States)

    Hahn, Thomas

    2016-08-01

    The Cuba library offers four independent routines for multidimensional numerical integration: Vegas, Suave, Divonne, and Cuhre. The four algorithms work by very different methods, and can integrate vector integrands and have very similar Fortran, C/C++, and Mathematica interfaces. Their invocation is very similar, making it easy to cross-check by substituting one method by another. For further safeguarding, the output is supplemented by a chi-square probability which quantifies the reliability of the error estimate.

  2. REDOR NMR of stable-isotope-labeled protein binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, J. [Washington Univ., St. Louis, MO (United States)

    1994-12-01

    Rotational-echo, double resonance (REDOR) NMR, a new analytical spectroscopic technique for solids spinning at the magic angle, has been developed over the last 5 years. REDOR provides a direct measure of heteronuclear dipolar coupling between isolated pairs of labeled nuclei. In a solid with a {sup 13}C-{sup 15}N labeled pair, for example, the {sup 13}C rotational echoes that form each rotor period following a{sup 1}H-{sup 13}C cross-polarization transfer can be prevented from reaching full intensity by insertion of a {sup 15}N {pi} pulse each half rotor period. The REDOR difference (the difference between a {sup 13}C NMR spectrum obtained under these conditions and one obtained with no {sup 15}N {pi} pulses) has a strong dependence on the {sup 13}C-{sup 15}N dipolar coupling, and hence, the {sup 13}C-{sup 15}N internuclear distance. REDOR is described as double-resonance even though three radio frequencies (typically {sup 1}H, {sup 13}C, and {sup 15}N) are used because the protons are removed from the important evolution part of the experiment by resonant decoupling. The dephasing of magnetization in REDOR arises from a local dipolar {sup 13}C-{sup 15}N field gradient and involves no polarization transfer. REDOR has no dependence on {sup 13}C or {sup 15}N chemical-shift tensors and does not require resolution of a {sup 13}C-{sup 15}N coupling in the chemical-shift dimension.

  3. Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations

    International Nuclear Information System (INIS)

    Bernado, Pau; Fernandes, Miguel X.; Jacobs, Doris M.; Fiebig, Klaus; Garcia de la Torre, Jose; Pons, Miquel

    2004-01-01

    Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition. Heteronuclear NMR relaxation is sensitive to motions in the relevant time scales and could provide valuable information on the dynamics of multi-domain proteins. However, the standard analysis based on the separation of global tumbling and fast local motions is no longer valid for multi-domain proteins undergoing internal motions involving complete domains and that take place on the same time scale than the overall motion.The complexity of the motions experienced even for the simplest two-domain proteins are difficult to capture with simple extensions of the classical Lipari-Szabo approach. Hydrodynamic effects are expected to dominate the motion of the individual globular domains, as well as that of the complete protein. Using Pin1 as a test case, we have simulated its motion at the microsecond time scale, at a reasonable computational expense, using Brownian Dynamic simulations on simplified models. The resulting trajectories provide insight on the interplay between global and inter-domain motion and can be analyzed using the recently published method of isotropic Reorientational Mode Dynamics which offer a way of calculating their contribution to heteronuclear relaxation rates. The analysis of trajectories computed with Pin1 models of different flexibility provides a general framework to understand the dynamics of multi-domain proteins and explains some of the observed features in the relaxation rate profile of free Pin1

  4. Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Bernado, Pau [Institut de Biologie Structurale, Jean Pierre Ebel (France); Fernandes, Miguel X. [Universidad de Murcia, Departamento de Quimica Fisica, Facultad de Quimica (Spain); Jacobs, Doris M. [Johann Wolfgang Goethe-Universitaet Frankfurt, Institut fuer Organische Chemie und Chemische Biologie (Germany); Fiebig, Klaus [Affinium Pharmaceuticals (Canada); Garcia de la Torre, Jose [Universidad de Murcia, Departamento de Quimica Fisica, Facultad de Quimica (Spain); Pons, Miquel [Laboratori de RMN de Biomolecules, Parc Cientific de Barcelona (Spain)], E-mail: mpons@ub.edu

    2004-05-15

    Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition. Heteronuclear NMR relaxation is sensitive to motions in the relevant time scales and could provide valuable information on the dynamics of multi-domain proteins. However, the standard analysis based on the separation of global tumbling and fast local motions is no longer valid for multi-domain proteins undergoing internal motions involving complete domains and that take place on the same time scale than the overall motion.The complexity of the motions experienced even for the simplest two-domain proteins are difficult to capture with simple extensions of the classical Lipari-Szabo approach. Hydrodynamic effects are expected to dominate the motion of the individual globular domains, as well as that of the complete protein. Using Pin1 as a test case, we have simulated its motion at the microsecond time scale, at a reasonable computational expense, using Brownian Dynamic simulations on simplified models. The resulting trajectories provide insight on the interplay between global and inter-domain motion and can be analyzed using the recently published method of isotropic Reorientational Mode Dynamics which offer a way of calculating their contribution to heteronuclear relaxation rates. The analysis of trajectories computed with Pin1 models of different flexibility provides a general framework to understand the dynamics of multi-domain proteins and explains some of the observed features in the relaxation rate profile of free Pin1.

  5. A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells.

    Science.gov (United States)

    Hikone, Yuya; Hirai, Go; Mishima, Masaki; Inomata, Kohsuke; Ikeya, Teppei; Arai, Souichiro; Shirakawa, Masahiro; Sodeoka, Mikiko; Ito, Yutaka

    2016-10-01

    Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N-H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

  6. A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells

    Energy Technology Data Exchange (ETDEWEB)

    Hikone, Yuya [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Hirai, Go [RIKEN, Synthetic Organic Chemistry Laboratory (Japan); Mishima, Masaki [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Inomata, Kohsuke [RIKEN, Quantitative Biology Center (Japan); Ikeya, Teppei; Arai, Souichiro [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan); Shirakawa, Masahiro [Japan Agency for Medical Research and Development, AMED-CREST (Japan); Sodeoka, Mikiko [RIKEN, Synthetic Organic Chemistry Laboratory (Japan); Ito, Yutaka, E-mail: ito-yutaka@tmu.ac.jp [Tokyo Metropolitan University, Department of Chemistry, Graduate School of Science and Engineering (Japan)

    2016-10-15

    Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N–H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

  7. A new carbamidemethyl-linked lanthanoid chelating tag for PCS NMR spectroscopy of proteins in living HeLa cells

    International Nuclear Information System (INIS)

    Hikone, Yuya; Hirai, Go; Mishima, Masaki; Inomata, Kohsuke; Ikeya, Teppei; Arai, Souichiro; Shirakawa, Masahiro; Sodeoka, Mikiko; Ito, Yutaka

    2016-01-01

    Structural analyses of proteins under macromolecular crowding inside human cultured cells by in-cell NMR spectroscopy are crucial not only for explicit understanding of their cellular functions but also for applications in medical and pharmaceutical sciences. In-cell NMR experiments using human cultured cells however suffer from low sensitivity, thus pseudocontact shifts from protein-tagged paramagnetic lanthanoid ions, analysed using sensitive heteronuclear two-dimensional correlation NMR spectra, offer huge potential advantage in obtaining structural information over conventional NOE-based approaches. We synthesised a new lanthanoid-chelating tag (M8-CAM-I), in which the eight-fold, stereospecifically methylated DOTA (M8) scaffold was retained, while a stable carbamidemethyl (CAM) group was introduced as the functional group connecting to proteins. M8-CAM-I successfully fulfilled the requirements for in-cell NMR: high-affinity to lanthanoid, low cytotoxicity and the stability under reducing condition inside cells. Large PCSs for backbone N–H resonances observed for M8-CAM-tagged human ubiquitin mutant proteins, which were introduced into HeLa cells by electroporation, demonstrated that this approach readily provides the useful information enabling the determination of protein structures, relative orientations of domains and protein complexes within human cultured cells.

  8. Microprocessorized NMR measurement

    International Nuclear Information System (INIS)

    Rijllart, A.

    1984-01-01

    An MC68000 CAMAC microprocessor system for fast and accurate NMR signal measurement will be presented. A stand-alone CAMAC microprocessor system (MC68000 STAC) with a special purpose interface sweeps a digital frequency synthesizer and digitizes the NMR signal with a 16-bit ADC of 17 μs conversion time. It averages the NMR signal data over many sweeps and then transfers it through CAMAC to a computer for calculation of the signal parameters. The computer has full software control over the timing and sweep settings of this signal averager, and thus allows optimization of noise suppression. Several of these processor systems can be installed in the same crate for parallel processing, and the flexibility of the STAC also allows easy adaptation to other applications such as transient recording or phase-sensitive detection. (orig.)

  9. Non-uniform sampling of NMR relaxation data

    DEFF Research Database (Denmark)

    Schwarz-Linnet, Troels; Teilum, Kaare

    2016-01-01

    The use of non-uniform sampling of NMR spectra may give significant reductions in the data acquisition time. For quantitative experiments such as the measurement of spin relaxation rates, non-uniform sampling is however not widely used as inaccuracies in peak intensities may lead to errors...... in the extracted dynamic parameters. By systematic reducing the coverage of the Nyquist grid of (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion datasets for four different proteins and performing a full data analysis of the resulting non-uniform sampled datasets, we have compared the performance...... of the multi-dimensional decomposition and iterative re-weighted least-squares algorithms in reconstructing spectra with accurate peak intensities. As long as a single fully sampled spectrum is included in a series of otherwise non-uniform sampled two-dimensional spectra, multi-dimensional decomposition...

  10. Identification and quantification of flavonoids and ellagic acid derivatives in therapeutically important Drosera species by LC-DAD, LC-NMR, NMR, and LC-MS.

    Science.gov (United States)

    Zehl, Martin; Braunberger, Christina; Conrad, Jürgen; Crnogorac, Marija; Krasteva, Stanimira; Vogler, Bernhard; Beifuss, Uwe; Krenn, Liselotte

    2011-06-01

    Droserae herba is a drug commonly used for treatment of convulsive or whooping cough since the seventeenth century. Because of the contribution of flavonoids and ellagic acid derivatives to the therapeutic activity of Droserae herba, an LC-DAD method has been developed for quantification of these analytes in four Drosera species used in medicine (Drosera anglica, D. intermedia, D. madagascariensis, and D. rotundifolia). During elaboration of the method 13 compounds, including three substances not previously described for Drosera species, were detected and unambiguously identified by means of extensive LC-MS and LC-NMR experiments and by off-line heteronuclear 2D NMR after targeted isolation. The most prominent component of D. rotundifolia and D. anglica, 2″-O-galloylhyperoside, with myricetin-3-O-β-glucopyranoside and kaempferol-3-O-(2″-O-galloyl)-β-galactopyranoside, were identified for the very first time in this genus. The LC-DAD method for quantification was thoroughly validated, and enables, for the first time, separation and precise analysis of these analytes in Droserae herba. Simple sample preparation and use of a narrow-bore column guarantee low cost and simplicity of the suggested system, which is excellently suited to quality control of the drug or herbal medicinal products containing this drug.

  11. Fourier transform NMR

    International Nuclear Information System (INIS)

    Hallenga, K.

    1991-01-01

    This paper discusses the concept of Fourier transformation one of the many precious legacies of the French mathematician Jean Baptiste Joseph Fourier, essential for understanding the link between continuous-wave (CW) and Fourier transform (FT) NMR. Although in modern FT NMR the methods used to obtain a frequency spectrum from the time-domain signal may vary greatly, from the efficient Cooley-Tukey algorithm to very elaborate iterative least-square methods based other maximum entropy method or on linear prediction, the principles for Fourier transformation are unchanged and give invaluable insight into the interconnection of many pairs of physical entities called Fourier pairs

  12. Measures for a multidimensional multiverse

    Science.gov (United States)

    Chung, Hyeyoun

    2015-04-01

    We explore the phenomenological implications of generalizing the causal patch and fat geodesic measures to a multidimensional multiverse, where the vacua can have differing numbers of large dimensions. We consider a simple model in which the vacua are nucleated from a D -dimensional parent spacetime through dynamical compactification of the extra dimensions, and compute the geometric contribution to the probability distribution of observations within the multiverse for each measure. We then study how the shape of this probability distribution depends on the time scales for the existence of observers, for vacuum domination, and for curvature domination (tobs,tΛ , and tc, respectively.) In this work we restrict ourselves to bubbles with positive cosmological constant, Λ . We find that in the case of the causal patch cutoff, when the bubble universes have p +1 large spatial dimensions with p ≥2 , the shape of the probability distribution is such that we obtain the coincidence of time scales tobs˜tΛ˜tc . Moreover, the size of the cosmological constant is related to the size of the landscape. However, the exact shape of the probability distribution is different in the case p =2 , compared to p ≥3 . In the case of the fat geodesic measure, the result is even more robust: the shape of the probability distribution is the same for all p ≥2 , and we once again obtain the coincidence tobs˜tΛ˜tc . These results require only very mild conditions on the prior probability of the distribution of vacua in the landscape. Our work shows that the observed double coincidence of time scales is a robust prediction even when the multiverse is generalized to be multidimensional; that this coincidence is not a consequence of our particular Universe being (3 +1 )-dimensional; and that this observable cannot be used to preferentially select one measure over another in a multidimensional multiverse.

  13. Ordinal Comparison of Multidimensional Deprivation

    DEFF Research Database (Denmark)

    Sonne-Schmidt, Christoffer Scavenius; Tarp, Finn; Østerdal, Lars Peter

    This paper develops an ordinal method of comparison of multidimensional inequality. In our model, population distribution g is more unequal than f when the distributions have common median and can be obtained from f  by one or more shifts in population density that increase inequality. For our be...... benchmark 2x2 case (i.e. the case of two binary outcome variables), we derive an empirical method for making inequality comparisons. As an illustration, we apply the model to childhood poverty in Mozambique....

  14. International symposium on NMR spectroscopy

    International Nuclear Information System (INIS)

    The publication consists of 32 papers and presentations from the field of NMR spectroscopy applications submitted to the International Symposium on NMR Spectroscopy held at Smolenice between 29 Sep and 3 Oct, 1980. (B.S.)

  15. Quick, sensitive serial NMR experiments with Radon transform.

    Science.gov (United States)

    Dass, Rupashree; Kasprzak, Paweł; Kazimierczuk, Krzysztof

    2017-09-01

    The Radon transform is a potentially powerful tool for processing the data from serial spectroscopic experiments. It makes it possible to decode the rate at which frequencies of spectral peaks shift under the effect of changing conditions, such as temperature, pH, or solvent. In this paper we show how it also improves speed and sensitivity, especially in multidimensional experiments. This is particularly important in the case of low-sensitivity techniques, such as NMR spectroscopy. As an example, we demonstrate how Radon transform processing allows serial measurements of 15 N-HSQC spectra of unlabelled peptides that would otherwise be infeasible. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard

    2011-01-01

    Single-Sided NMR describes the design of the first functioning single-sided tomograph, the related measurement methods, and a number of applications. One of the key advantages to this method is the speed at which the images are obtained.

  17. Autonomous driving in NMR.

    Science.gov (United States)

    Perez, Manuel

    2017-01-01

    The automatic analysis of NMR data has been a much-desired endeavour for the last six decades, as it is the case with any other analytical technique. This need for automation has only grown as advances in hardware; pulse sequences and automation have opened new research areas to NMR and increased the throughput of data. Full automatic analysis is a worthy, albeit hard, challenge, but in a world of artificial intelligence, instant communication and big data, it seems that this particular fight is happening with only one technique at a time (let this be NMR, MS, IR, UV or any other), when the reality of most laboratories is that there are several types of analytical instrumentation present. Data aggregation, verification and elucidation by using complementary techniques (e.g. MS and NMR) is a desirable outcome to pursue, although a time-consuming one if performed manually; hence, the use of automation to perform the heavy lifting for users is required to make the approach attractive for scientists. Many of the decisions and workflows that could be implemented under automation will depend on the two-way communication with databases that understand analytical data, because it is desirable not only to query these databases but also to grow them in as much of an automatic manner as possible. How these databases are designed, set up and the data inside classified will determine what workflows can be implemented. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  18. NMR for chemists and biologists

    CERN Document Server

    Carbajo, Rodrigo J

    2013-01-01

    This book offers a concise introduction to the field of nuclear magnetic resonance or NMR. It presents the basic foundations of NMR in a non-mathematical way and provides an overview of both recent and important biological applications of NMR.

  19. Experiments and strategies for the assignment of fully13 C/15N-labelled polypeptides by solid state NMR

    International Nuclear Information System (INIS)

    Straus, Suzana K.; Bremi, Tobias; Ernst, Richard R.

    1998-01-01

    High-resolution heteronuclear NMR correlation experiments and strategies are proposed for the assignment of fully 13 C/ 15 N-labelled polypeptides in the solid state. By the combination of intra-residue and inter-residue 13 C- 15 N correlation experiments with 13 C- 13 C spin-diffusion studies, it becomes feasible to partially assign backbone and side-chain resonances in solid proteins. The performance of sequences using 15 N instead of 13 C detection is evaluated regarding sensitivity and resolution for a labelled dipeptide (L-Val-L-Phe). The techniques are used for a partial assignment of the 15 N and 13 C resonances in human ubiquitin

  20. 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.

  1. 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

  2. Perceptual Salience and Children's Multidimensional Problem Solving

    Science.gov (United States)

    Odom, Richard D.; Corbin, David W.

    1973-01-01

    Uni- and multidimensional processing of 6- to 9-year olds was studied using recall tasks in which an array of stimuli was reconstructed to match a model array. Results indicated that both age groups were able to solve multidimensional problems, but that solution rate was retarded by the unidimensional processing of highly salient dimensions.…

  3. Multidimensional fatigue and its correlates in hospitalised advanced cancer patients.

    NARCIS (Netherlands)

    Echteld, M.A.; Passchier, J.; Teunissen, S.; Claessen, S.; Wit, R. de; Rijt, C.C.D. van der

    2007-01-01

    Although fatigue is a multidimensional concept, multidimensional fatigue is rarely investigated in hospitalised cancer patients. We determined the levels and correlates of multidimensional fatigue in 100 advanced cancer patients admitted for symptom control. Fatigue dimensions were general fatigue

  4. SUSTAINABLE DEVELOPMENT, A MULTIDIMENSIONAL CONCEPT

    Directory of Open Access Journals (Sweden)

    TEODORESCU ANA MARIA

    2015-06-01

    Full Text Available Sustainable development imposed itself as a corollary of economic term "development". Sustainable development is meant to be the summation of economic, environmental and social considerations for the present and especially for the future. The concept of sustainable development plays an important role in european and global meetings since 1972, the year it has been set for the first time. Strategies necessary to achieve the objectives of sustainable development have been developed, indicators meant to indicate the result of the implementation of policies have been created, national plans were oriented towards achieving the proposed targets. I wanted to highlight the multidimensional character of the concept of sustainable development. Thus, using specialized national and international literature, I have revealed different approaches of one pillar to the detriment of another pillar depending on the specific field. In the different concepts of sustainable development, the consensus is undoubtedly agreed on its components: economic, social, environmental. Based on this fact, the concept of sustainability has different connotations depending on the specific content of each discipline: biology, economics, sociology, environmental ethics. The multidimensional valence of sustainable development consists of three pillars ability to act together for the benefit of present and future generations. Being a multidimensional concept, importance attached to a pillar over another is directed according to the particularities of each field: in economy profit prevails, in ecology care of natural resources is the most important, the social aims improving human living conditions. The challenge of sustainable development is to combine all the economic, environmental and social benefits and the present generation to come. Ecological approach is reflected in acceptance of limited natural resources by preserving natural capital. In terms of the importance of

  5. Natural abundant solid state NMR studies in designed tripeptides for differentiation of multiple conformers.

    Science.gov (United States)

    Jayanthi, S; Chatterjee, Bhaswati; Raghothama, S

    2009-10-01

    Solid state NMR (SSNMR) experiments on heteronuclei in natural abundance are described for three synthetically designed tripeptides Piv-(L)Pro-(L)Pro-(L)Phe-OMe (1), Piv-(D)Pro-(L)Pro-(L)Phe-OMe (2), and Piv-(D)Pro-(L)Pro-(L)Phe-NHMe (3). These peptides exist in different conformation as shown by solution state NMR and single crystal X-ray analysis (Chatterjee et al., Chem Eur J 2008, 14, 6192). In this study, SSNMR has been used to probe the conformations of these peptides in their powder form. The (13)C spectrum of peptide (1) showed doubling of resonances corresponding to cis/cis form, unlike in solution where the similar doubling is attributed to cis/trans form. This has been confirmed by the chemical shift differences of C(beta) and C(gamma) carbon of Proline in peptide (1) both in solution and SSNMR. Peptide (2) and (3) provided single set of resonances which represented all trans form across the di-Proline segment. The results are in agreement with the X-ray analysis. Solid state (15)N resonances, especially from Proline residues provided additional information, which is normally not observable in solution state NMR. (1)H chemical shifts are also obtained from a two-dimensional heteronuclear correlation experiment between (1)H--(13)C. The results confirm the utility of NMR as a useful tool for identifying different conformers in peptides in the solid state. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 851-860, 2009.

  6. Heuristics for Multidimensional Packing Problems

    DEFF Research Database (Denmark)

    Egeblad, Jens

    for a minimum height container required for the items. The main contributions of the thesis are three new heuristics for strip-packing and knapsack packing problems where items are both rectangular and irregular. In the two first papers we describe a heuristic for the multidimensional strip-packing problem...... that is based on a relaxed placement principle. The heuristic starts with a random overlapping placement of items and large container dimensions. From the overlapping placement overlap is reduced iteratively until a non-overlapping placement is found and a new problem is solved with a smaller container size...... of this heuristic are among the best published in the literature both for two- and three-dimensional strip-packing problems for irregular shapes. In the third paper, we introduce a heuristic for two- and three-dimensional rectangular knapsack packing problems. The two-dimensional heuristic uses the sequence pair...

  7. Applied multidimensional scaling and unfolding

    CERN Document Server

    Borg, Ingwer; Mair, Patrick

    2018-01-01

    This book introduces multidimensional scaling (MDS) and unfolding as data analysis techniques for applied researchers. MDS is used for the analysis of proximity data on a set of objects, representing the data as distances between points in a geometric space (usually of two dimensions). Unfolding is a related method that maps preference data (typically evaluative ratings of different persons on a set of objects) as distances between two sets of points (representing the persons and the objects, resp.). This second edition has been completely revised to reflect new developments and the coverage of unfolding has also been substantially expanded. Intended for applied researchers whose main interests are in using these methods as tools for building substantive theories, it discusses numerous applications (classical and recent), highlights practical issues (such as evaluating model fit), presents ways to enforce theoretical expectations for the scaling solutions, and addresses the typical mistakes that MDS/unfoldin...

  8. Minimal models of multidimensional computations.

    Directory of Open Access Journals (Sweden)

    Jeffrey D Fitzgerald

    2011-03-01

    Full Text Available The multidimensional computations performed by many biological systems are often characterized with limited information about the correlations between inputs and outputs. Given this limitation, our approach is to construct the maximum noise entropy response function of the system, leading to a closed-form and minimally biased model consistent with a given set of constraints on the input/output moments; the result is equivalent to conditional random field models from machine learning. For systems with binary outputs, such as neurons encoding sensory stimuli, the maximum noise entropy models are logistic functions whose arguments depend on the constraints. A constraint on the average output turns the binary maximum noise entropy models into minimum mutual information models, allowing for the calculation of the information content of the constraints and an information theoretic characterization of the system's computations. We use this approach to analyze the nonlinear input/output functions in macaque retina and thalamus; although these systems have been previously shown to be responsive to two input dimensions, the functional form of the response function in this reduced space had not been unambiguously identified. A second order model based on the logistic function is found to be both necessary and sufficient to accurately describe the neural responses to naturalistic stimuli, accounting for an average of 93% of the mutual information with a small number of parameters. Thus, despite the fact that the stimulus is highly non-Gaussian, the vast majority of the information in the neural responses is related to first and second order correlations. Our results suggest a principled and unbiased way to model multidimensional computations and determine the statistics of the inputs that are being encoded in the outputs.

  9. NMR studies of the fate of adenine nucleotides in glucose-starved erythrocytes

    International Nuclear Information System (INIS)

    Bubb, W.A.; Mulquiney, P.J.; Kuchel, P.W.; Rohwer, J.; De Atauri, P.

    2002-01-01

    Full text: As a consequence of many refinements during the past 30 years, we now have a detailed understanding of the glycolytic pathway in human erythrocytes. By comparison, and notwithstanding their central importance to four key steps in erythrocyte glycolysis, our knowledge of the catabolism of adenine nucleotides remains relatively limited. In particular, the mechanism for the degradation of AMP, whose concentration rises under conditions of oxidative stress or glucose deprivation, remains poorly understood, AMP degradation may proceed via two possible pathways which converge in the production of inosine. Analysis of the key intermediates for the respective pathways, adenosine and AMP, as well as determination of end products is not straightforward. High-resolution NMR spectroscopy affords a potentially simple analytical solution to this problem but is complicated by spectral overlap and the sensitivity of key resonances to variations in pH and the concentrations of cations such as Mg 2+ . We describe a multinuclear NMR approach towards characterising the intermediates and end-products of adenine nucleotide metabolism in glucose-starved human erythrocytes. Assignments based on homo- and heteronuclear correlation experiments for both 13 C and 31 P are presented

  10. Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase

    Energy Technology Data Exchange (ETDEWEB)

    Boonsri, Pornthip [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Herdendorf, Timothy J.; Miziorko, Henry M. [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Hannongbua, Supa [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Sem, Daniel S., E-mail: daniel.sem@cuw.edu [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.

  11. Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Takegoshi, K., E-mail: takeyan@kuchem.kyoto-u.ac.jp; Miyazawa, Norihiro [Division of Chemistry, Graduate School of Science, Kyoto University, 606-8502 Kyoto (Japan); Sharma, Kshama [TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500 075 (India); Madhu, P. K. [TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500 075 (India); Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India)

    2015-04-07

    We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order.

  12. Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

    Science.gov (United States)

    Takegoshi, K.; Miyazawa, Norihiro; Sharma, Kshama; Madhu, P. K.

    2015-04-01

    We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order.

  13. Comparison among Magnus/Floquet/Fer expansion schemes in solid-state NMR

    International Nuclear Information System (INIS)

    Takegoshi, K.; Miyazawa, Norihiro; Sharma, Kshama; Madhu, P. K.

    2015-01-01

    We here revisit expansion schemes used in nuclear magnetic resonance (NMR) for the calculation of effective Hamiltonians and propagators, namely, Magnus, Floquet, and Fer expansions. While all the expansion schemes are powerful methods there are subtle differences among them. To understand the differences, we performed explicit calculation for heteronuclear dipolar decoupling, cross-polarization, and rotary-resonance experiments in solid-state NMR. As the propagator from the Fer expansion takes the form of a product of sub-propagators, it enables us to appreciate effects of time-evolution under Hamiltonians with different orders separately. While 0th-order average Hamiltonian is the same for the three expansion schemes with the three cases examined, there is a case that the 2nd-order term for the Magnus/Floquet expansion is different from that obtained with the Fer expansion. The difference arises due to the separation of the 0th-order term in the Fer expansion. The separation enables us to appreciate time-evolution under the 0th-order average Hamiltonian, however, for that purpose, we use a so-called left-running Fer expansion. Comparison between the left-running Fer expansion and the Magnus expansion indicates that the sign of the odd orders in Magnus may better be reversed if one would like to consider its effect in order

  14. NMR, water and plants

    International Nuclear Information System (INIS)

    As, H. van.

    1982-01-01

    This thesis describes the application of a non-destructive pulsed proton NMR method mainly to measure water transport in the xylem vessels of plant stems and in some model systems. The results are equally well applicable to liquid flow in other biological objects than plants, e.g. flow of blood and other body fluids in human and animals. The method is based on a pulse sequence of equidistant π pulses in combination with a linear magnetic field gradient. (Auth.)

  15. Multidimensional singular integrals and integral equations

    CERN Document Server

    Mikhlin, Solomon Grigorievich; Stark, M; Ulam, S

    1965-01-01

    Multidimensional Singular Integrals and Integral Equations presents the results of the theory of multidimensional singular integrals and of equations containing such integrals. Emphasis is on singular integrals taken over Euclidean space or in the closed manifold of Liapounov and equations containing such integrals. This volume is comprised of eight chapters and begins with an overview of some theorems on linear equations in Banach spaces, followed by a discussion on the simplest properties of multidimensional singular integrals. Subsequent chapters deal with compounding of singular integrals

  16. Group contribution methodology based on the statistical associating fluid theory for heteronuclear molecules formed from Mie segments.

    Science.gov (United States)

    Papaioannou, Vasileios; Lafitte, Thomas; Avendaño, Carlos; Adjiman, Claire S; Jackson, George; Müller, Erich A; Galindo, Amparo

    2014-02-07

    A generalization of the recent version of the statistical associating fluid theory for variable range Mie potentials [Lafitte et al., J. Chem. Phys. 139, 154504 (2013)] is formulated within the framework of a group contribution approach (SAFT-γ Mie). Molecules are represented as comprising distinct functional (chemical) groups based on a fused heteronuclear molecular model, where the interactions between segments are described with the Mie (generalized Lennard-Jonesium) potential of variable attractive and repulsive range. A key feature of the new theory is the accurate description of the monomeric group-group interactions by application of a high-temperature perturbation expansion up to third order. The capabilities of the SAFT-γ Mie approach are exemplified by studying the thermodynamic properties of two chemical families, the n-alkanes and the n-alkyl esters, by developing parameters for the methyl, methylene, and carboxylate functional groups (CH3, CH2, and COO). The approach is shown to describe accurately the fluid-phase behavior of the compounds considered with absolute average deviations of 1.20% and 0.42% for the vapor pressure and saturated liquid density, respectively, which represents a clear improvement over other existing SAFT-based group contribution approaches. The use of Mie potentials to describe the group-group interaction is shown to allow accurate simultaneous descriptions of the fluid-phase behavior and second-order thermodynamic derivative properties of the pure fluids based on a single set of group parameters. Furthermore, the application of the perturbation expansion to third order for the description of the reference monomeric fluid improves the predictions of the theory for the fluid-phase behavior of pure components in the near-critical region. The predictive capabilities of the approach stem from its formulation within a group-contribution formalism: predictions of the fluid-phase behavior and thermodynamic derivative properties of

  17. Multidimensionally encoded magnetic resonance imaging.

    Science.gov (United States)

    Lin, Fa-Hsuan

    2013-07-01

    Magnetic resonance imaging (MRI) typically achieves spatial encoding by measuring the projection of a q-dimensional object over q-dimensional spatial bases created by linear spatial encoding magnetic fields (SEMs). Recently, imaging strategies using nonlinear SEMs have demonstrated potential advantages for reconstructing images with higher spatiotemporal resolution and reducing peripheral nerve stimulation. In practice, nonlinear SEMs and linear SEMs can be used jointly to further improve the image reconstruction performance. Here, we propose the multidimensionally encoded (MDE) MRI to map a q-dimensional object onto a p-dimensional encoding space where p > q. MDE MRI is a theoretical framework linking imaging strategies using linear and nonlinear SEMs. Using a system of eight surface SEM coils with an eight-channel radiofrequency coil array, we demonstrate the five-dimensional MDE MRI for a two-dimensional object as a further generalization of PatLoc imaging and O-space imaging. We also present a method of optimizing spatial bases in MDE MRI. Results show that MDE MRI with a higher dimensional encoding space can reconstruct images more efficiently and with a smaller reconstruction error when the k-space sampling distribution and the number of samples are controlled. Copyright © 2012 Wiley Periodicals, Inc.

  18. Magic Angle Spinning NMR Metabolomics

    Energy Technology Data Exchange (ETDEWEB)

    Zhi Hu, Jian

    2016-01-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is a non-destructive, quantitative, reproducible, untargeted and unbiased method that requires no or minimal sample preparation, and is one of the leading analytical tools for metabonomics research [1-3]. The easy quantification and the no need of prior knowledge about compounds present in a sample associated with NMR are advantageous over other techniques [1,4]. 1H NMR is especially attractive because protons are present in virtually all metabolites and its NMR sensitivity is high, enabling the simultaneous identification and monitoring of a wide range of low molecular weight metabolites.

  19. NMR in clinical practice

    International Nuclear Information System (INIS)

    Smith, F.W.

    1987-01-01

    The development of NMR for clinical use has been complicated by a number of controversies, the largest of these being the question of what is the optimum field strength for proton imaging. Many workers believe that diagnostically useful images can only be produced at high field strength (i.e. 0.5 - 2.0 T), where in fact diagnostically useful images are made using field strengths of as low as 0.02 T. Because the method is more complex than X-ray CT, which relies on the measurement of only one parameter, tissue density, many new users have difficulty in selecting the correct imaging pulse sequence to provide the most useful image for diagnosis. NMR imaging pulse sequence may be selected to produce images of the proton density, T/sub 1/ or T/sub 2/ signals, or combinations of them. When this facility is used, images which are T/sub 1/ or T/sub 2/ weighted can be selected. Inversion-recovery sequences are more appropriate for imaging the abdomen where by selecting a short TR interval the signal from subcutaneous fat, which is the major cause of image artefact in abdominal imaging, is suppressed thereby improving image quality. The use of surface receiver coils, which are applied closely to the area of the body being examined is becoming more widespread and is of particular value when examining the orbits, facial structures, neck, breast, spine and limbs. The use of these coils together with a discussion of patient selection for NMR imaging, image interpretation and data storage follow

  20. Discovering Multidimensional Structure in Relational Data

    DEFF Research Database (Denmark)

    Jensen, Mikael Rune; Holmgren, Thomas; Pedersen, Torben Bach

    2004-01-01

    On-Line Analytical Processing (OLAP) systems based on multidimensional databases are essential elements of decision support. However, most existing data is stored in “ordinary” relational OLTP databases, i.e., data has to be (re-) modeled as multidimensional cubes before the advantages of OLAP to...... algorithms for discovering multidimensional schemas from relational databases. The algorithms take a wide range of available metadata into account in the discovery process, including functional and inclusion dependencies, and key and cardinality information....... tools are available. In this paper we present an approach for the automatic construction of multidimensional OLAP database schemas from existing relational OLTP databases, enabling easy OLAP design and analysis for most existing data sources. This is achieved through a set of practical and effective...

  1. Two multi-dimensional uncertainty relations

    International Nuclear Information System (INIS)

    Skala, L; Kapsa, V

    2008-01-01

    Two multi-dimensional uncertainty relations, one related to the probability density and the other one related to the probability density current, are derived and discussed. Both relations are stronger than the usual uncertainty relations for the coordinates and momentum

  2. Multidimensional artificial field embedding with spatial sensitivity

    CSIR Research Space (South Africa)

    Lunga, D

    2013-06-01

    Full Text Available Multidimensional embedding is a technique useful for characterizing spectral signature relations in hyperspectral images. However, such images consist of disjoint similar spectral classes that are spatially sensitive, thus presenting challenges...

  3. CAMS: OLAPing Multidimensional Data Streams Efficiently

    Science.gov (United States)

    Cuzzocrea, Alfredo

    In the context of data stream research, taming the multidimensionality of real-life data streams in order to efficiently support OLAP analysis/mining tasks is a critical challenge. Inspired by this fundamental motivation, in this paper we introduce CAMS (C ube-based A cquisition model for M ultidimensional S treams), a model for efficiently OLAPing multidimensional data streams. CAMS combines a set of data stream processing methodologies, namely (i) the OLAP dimension flattening process, which allows us to obtain dimensionality reduction of multidimensional data streams, and (ii) the OLAP stream aggregation scheme, which aggregates data stream readings according to an OLAP-hierarchy-based membership approach. We complete our analytical contribution by means of experimental assessment and analysis of both the efficiency and the scalability of OLAPing capabilities of CAMS on synthetic multidimensional data streams. Both analytical and experimental results clearly connote CAMS as an enabling component for next-generation Data Stream Management Systems.

  4. Increasing the sensitivity of NMR diffusion measurements by paramagnetic longitudinal relaxation enhancement, with application to ribosome–nascent chain complexes

    International Nuclear Information System (INIS)

    Chan, Sammy H. S.; Waudby, Christopher A.; Cassaignau, Anaïs M. E.; Cabrita, Lisa D.; Christodoulou, John

    2015-01-01

    The translational diffusion of macromolecules can be examined non-invasively by stimulated echo (STE) NMR experiments to accurately determine their molecular sizes. These measurements can be important probes of intermolecular interactions and protein folding and unfolding, and are crucial in monitoring the integrity of large macromolecular assemblies such as ribosome–nascent chain complexes (RNCs). However, NMR studies of these complexes can be severely constrained by their slow tumbling, low solubility (with maximum concentrations of up to 10 μM), and short lifetimes resulting in weak signal, and therefore continuing improvements in experimental sensitivity are essential. Here we explore the use of the paramagnetic longitudinal relaxation enhancement (PLRE) agent NiDO2A on the sensitivity of 15 N XSTE and SORDID heteronuclear STE experiments, which can be used to monitor the integrity of these unstable complexes. We exploit the dependence of the PLRE effect on the gyromagnetic ratio and electronic relaxation time to accelerate recovery of 1 H magnetization without adversely affecting storage on N z during diffusion delays or introducing significant transverse relaxation line broadening. By applying the longitudinal relaxation-optimized SORDID pulse sequence together with NiDO2A to 70S Escherichia coli ribosomes and RNCs, NMR diffusion sensitivity enhancements of up to 4.5-fold relative to XSTE are achieved, alongside ∼1.9-fold improvements in two-dimensional NMR sensitivity, without compromising the sample integrity. We anticipate these results will significantly advance the use of NMR to probe dynamic regions of ribosomes and other large, unstable macromolecular assemblies.Graphical Abstract

  5. Trace level detection of compounds related to the chemical weapons convention by 1H-detected 13C NMR spectroscopy executed with a sensitivity-enhanced, cryogenic probehead.

    Science.gov (United States)

    Cullinan, David B; Hondrogiannis, George; Henderson, Terry J

    2008-04-15

    Two-dimensional 1H-13C HSQC (heteronuclear single quantum correlation) and fast-HMQC (heteronuclear multiple quantum correlation) pulse sequences were implemented using a sensitivity-enhanced, cryogenic probehead for detecting compounds relevant to the Chemical Weapons Convention present in complex mixtures. The resulting methods demonstrated exceptional sensitivity for detecting the analytes at trace level concentrations. 1H-13C correlations of target analytes at chemical shift information could be derived quickly and simultaneously from the resulting spectra. The fast-HMQC pulse sequences generated magnitude mode spectra suitable for detailed analysis in approximately 4.5 h and can be used in experiments to efficiently screen a large number of samples. The HSQC pulse sequences, on the other hand, required roughly twice the data acquisition time to produce suitable spectra. These spectra, however, were phase-sensitive, contained considerably more resolution in both dimensions, and proved to be superior for detecting analyte 1H-13C correlations. Furthermore, a HSQC spectrum collected with a multiplicity-edited pulse sequence provided additional structural information valuable for identifying target analytes. The HSQC pulse sequences are ideal for collecting high-quality data sets with overnight acquisitions and logically follow the use of fast-HMQC pulse sequences to rapidly screen samples for potential target analytes. Use of the pulse sequences considerably improves the performance of NMR spectroscopy as a complimentary technique for the screening, identification, and validation of chemical warfare agents and other small-molecule analytes present in complex mixtures and environmental samples.

  6. Multidimensional Poverty and Child Survival in India

    Science.gov (United States)

    Mohanty, Sanjay K.

    2011-01-01

    Background Though the concept of multidimensional poverty has been acknowledged cutting across the disciplines (among economists, public health professionals, development thinkers, social scientists, policy makers and international organizations) and included in the development agenda, its measurement and application are still limited. Objectives and Methodology Using unit data from the National Family and Health Survey 3, India, this paper measures poverty in multidimensional space and examine the linkages of multidimensional poverty with child survival. The multidimensional poverty is measured in the dimension of knowledge, health and wealth and the child survival is measured with respect to infant mortality and under-five mortality. Descriptive statistics, principal component analyses and the life table methods are used in the analyses. Results The estimates of multidimensional poverty are robust and the inter-state differentials are large. While infant mortality rate and under-five mortality rate are disproportionately higher among the abject poor compared to the non-poor, there are no significant differences in child survival among educationally, economically and health poor at the national level. State pattern in child survival among the education, economical and health poor are mixed. Conclusion Use of multidimensional poverty measures help to identify abject poor who are unlikely to come out of poverty trap. The child survival is significantly lower among abject poor compared to moderate poor and non-poor. We urge to popularize the concept of multiple deprivations in research and program so as to reduce poverty and inequality in the population. PMID:22046384

  7. Multidimensional poverty and child survival in India.

    Science.gov (United States)

    Mohanty, Sanjay K

    2011-01-01

    Though the concept of multidimensional poverty has been acknowledged cutting across the disciplines (among economists, public health professionals, development thinkers, social scientists, policy makers and international organizations) and included in the development agenda, its measurement and application are still limited. OBJECTIVES AND METHODOLOGY: Using unit data from the National Family and Health Survey 3, India, this paper measures poverty in multidimensional space and examine the linkages of multidimensional poverty with child survival. The multidimensional poverty is measured in the dimension of knowledge, health and wealth and the child survival is measured with respect to infant mortality and under-five mortality. Descriptive statistics, principal component analyses and the life table methods are used in the analyses. The estimates of multidimensional poverty are robust and the inter-state differentials are large. While infant mortality rate and under-five mortality rate are disproportionately higher among the abject poor compared to the non-poor, there are no significant differences in child survival among educationally, economically and health poor at the national level. State pattern in child survival among the education, economical and health poor are mixed. Use of multidimensional poverty measures help to identify abject poor who are unlikely to come out of poverty trap. The child survival is significantly lower among abject poor compared to moderate poor and non-poor. We urge to popularize the concept of multiple deprivations in research and program so as to reduce poverty and inequality in the population.

  8. Multidimensional poverty and child survival in India.

    Directory of Open Access Journals (Sweden)

    Sanjay K Mohanty

    Full Text Available Though the concept of multidimensional poverty has been acknowledged cutting across the disciplines (among economists, public health professionals, development thinkers, social scientists, policy makers and international organizations and included in the development agenda, its measurement and application are still limited. OBJECTIVES AND METHODOLOGY: Using unit data from the National Family and Health Survey 3, India, this paper measures poverty in multidimensional space and examine the linkages of multidimensional poverty with child survival. The multidimensional poverty is measured in the dimension of knowledge, health and wealth and the child survival is measured with respect to infant mortality and under-five mortality. Descriptive statistics, principal component analyses and the life table methods are used in the analyses.The estimates of multidimensional poverty are robust and the inter-state differentials are large. While infant mortality rate and under-five mortality rate are disproportionately higher among the abject poor compared to the non-poor, there are no significant differences in child survival among educationally, economically and health poor at the national level. State pattern in child survival among the education, economical and health poor are mixed.Use of multidimensional poverty measures help to identify abject poor who are unlikely to come out of poverty trap. The child survival is significantly lower among abject poor compared to moderate poor and non-poor. We urge to popularize the concept of multiple deprivations in research and program so as to reduce poverty and inequality in the population.

  9. Fine hierarchy of the V-O bonds by advanced solid state NMR: novel Pb4(VO2)(PO4)3 structure as a textbook case.

    Science.gov (United States)

    Tricot, Grégory; Mentré, Olivier; Cristol, Sylvain; Delevoye, Laurent

    2012-12-17

    We report here a complete structural characterization of a new lead Pb(4)(VO(2))(PO(4))(3) vanadophosphate compound by single crystal X-ray diffraction and (51)V and (31)P solid-state NMR spectroscopy. Although structural data are commonly used for the estimation of bond lengths and further delimitation of the true coordination number (e.g., octahedral: 6 versus 5 + 1 versus 4 + 2), we show here for the first time by solid-state NMR a more accurate appreciation of the V-O bonding scheme in this complex oxide which appears well adapted to the full series of vanado-phosphate materials. The direct characterization of V-O-P bridges through the J-mediated correlation (51)V{(31)P} heteronuclear multiple quantum coherence (J-HMQC) technique allows a contrasted hierarchy of the V-O electronic delocalization and indirectly supports the presence or not of the V-O bond. In the reported lead vanado-phosphate structure, the two vanadium polyhedra that have been assigned to octahedra from a bond length point of view have been finally reclassified as tetra- and penta-coordinated units on the basis of the solid-state NMR results. More generally, we believe that the improved characterization of interatomic bonds in various vanado-phosphate structures by solid-state NMR will contribute to a better understanding of the structure/property relationships in this important class of materials.

  10. 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.

  11. Improved multidimensional semiclassical tunneling theory.

    Science.gov (United States)

    Wagner, Albert F

    2013-12-12

    We show that the analytic multidimensional semiclassical tunneling formula of Miller et al. [Miller, W. H.; Hernandez, R.; Handy, N. C.; Jayatilaka, D.; Willets, A. Chem. Phys. Lett. 1990, 172, 62] is qualitatively incorrect for deep tunneling at energies well below the top of the barrier. The origin of this deficiency is that the formula uses an effective barrier weakly related to the true energetics but correctly adjusted to reproduce the harmonic description and anharmonic corrections of the reaction path at the saddle point as determined by second order vibrational perturbation theory. We present an analytic improved semiclassical formula that correctly includes energetic information and allows a qualitatively correct representation of deep tunneling. This is done by constructing a three segment composite Eckart potential that is continuous everywhere in both value and derivative. This composite potential has an analytic barrier penetration integral from which the semiclassical action can be derived and then used to define the semiclassical tunneling probability. The middle segment of the composite potential by itself is superior to the original formula of Miller et al. because it incorporates the asymmetry of the reaction barrier produced by the known reaction exoergicity. Comparison of the semiclassical and exact quantum tunneling probability for the pure Eckart potential suggests a simple threshold multiplicative factor to the improved formula to account for quantum effects very near threshold not represented by semiclassical theory. The deep tunneling limitations of the original formula are echoed in semiclassical high-energy descriptions of bound vibrational states perpendicular to the reaction path at the saddle point. However, typically ab initio energetic information is not available to correct it. The Supporting Information contains a Fortran code, test input, and test output that implements the improved semiclassical tunneling formula.

  12. Hydrogen and deuterium NMR of solids by magic-angle spinning

    International Nuclear Information System (INIS)

    Eckman, R.R.

    1982-10-01

    The nuclear magnetic resonance of solids has long been characterized by very large specral broadening which arises from internuclear dipole-dipole coupling or the nuclear electric quadrupole interaction. These couplings can obscure the smaller chemical shift interaction and make that information unavailable. Two important and difficult cases are that of hydrogen and deuterium. The development of cross polarization, heteronuclear radiofrequency decoupling, and coherent averaging of nuclear spin interactions has provided measurement of chemical shift tensors in solids. Recently, double quantum NMR and double quantum decoupling have led to measurement of deuterium and proton chemical shift tensors, respectively. A general problem of these experiments is the overlapping of the tensor powder pattern spectra of magnetically distinct sites which cannot be resolved. In this work, high resolution NMR of hydrogen and deuterium in solids is demonstrated. For both nuclei, the resonances are narrowed to obtain liquid-like isotropic spectra by high frequency rotation of the sample about an axis inclined at the magic angle, β/sub m/ = Arccos (3/sup -1/2/), with respect to the direction of the external magnetic field. For deuterium, the powder spectra were narrowed by over three orders of magnitude by magic angle rotation with precise control of β. A second approach was the observation of deuterium double quantum transitions under magic angle rotation. For hydrogen, magic angle rotation alone could be applied to obtain the isotropic spectrum when H/sub D/ was small. This often occurs naturally when the nuclei are semi-dilute or involved in internal motion. In the general case of large H/sub D/, isotropic spectra were obtained by dilution of 1 H with 2 H combined with magic angle rotation. The resolution obtained represents the practical limit for proton NMR of solids

  13. A pulse programmable parahydrogen polarizer using a tunable electromagnet and dual channel NMR spectrometer

    Science.gov (United States)

    Coffey, Aaron M.; Shchepin, Roman V.; Feng, Bibo; Colon, Raul D.; Wilkens, Ken; Waddell, Kevin W.; Chekmenev, Eduard Y.

    2017-11-01

    Applications of parahydrogen induced polarization (PHIP) often warrant conversion of the chemically-synthesized singlet-state spin order into net heteronuclear magnetization. In order to obtain optimal yields from the overall hyperpolarization process, catalytic hydrogenation must be tightly synchronized to subsequent radiofrequency (RF) transformations of spin order. Commercial NMR consoles are designed to synchronize applied waves on multiple channels and consequently are well-suited as controllers for these types of hyperpolarization experiments that require tight coordination of RF and non-RF events. Described here is a PHIP instrument interfaced to a portable NMR console operating with a static field electromagnet in the milliTesla regime. In addition to providing comprehensive control over chemistry and RF events, this setup condenses the PHIP protocol into a pulse-program that in turn can be readily shared in the manner of traditional pulse sequences. In this device, a TTL multiplexer was constructed to convert spectrometer TTL outputs into 24 VDC signals. These signals then activated solenoid valves to control chemical shuttling and reactivity in PHIP experiments. Consolidating these steps in a pulse-programming environment speeded calibration and improved quality assurance by enabling the B0/B1 fields to be tuned based on the direct acquisition of thermally polarized and hyperpolarized NMR signals. Performance was tested on the parahydrogen addition product of 2-hydroxyethyl propionate-1-13C-d3, where the 13C polarization was estimated to be P13C = 20 ± 2.5% corresponding to 13C signal enhancement approximately 25 million-fold at 9.1 mT or approximately 77,000-fold 13C enhancement at 3 T with respect to thermally induced polarization at room temperature.

  14. A novel strategy for NMR resonance assignment and protein structure determination

    International Nuclear Information System (INIS)

    Lemak, Alexander; Gutmanas, Aleksandras; Chitayat, Seth; Karra, Murthy; Farès, Christophe; Sunnerhagen, Maria; Arrowsmith, Cheryl H.

    2011-01-01

    The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1) spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition (MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size.

  15. NMR spectroscopy and drug development

    International Nuclear Information System (INIS)

    Craik, D.; Munro, S.

    1990-01-01

    The use of nuclear magnetic resonance (NMR) spectroscopy for structural and conformational studies on drug molecules, the three-dimensional investigation of proteins structure and their interactions with ligands are discussed. In-vivo NMR studies of the effects of drugs on metabolism in perfused organs and whole animals are also briefly presented. 5 refs., ills

  16. NMR in pulsed magnetic field

    KAUST Repository

    Abou-Hamad, Edy; Bontemps, P.; Rikken, Geert L J A

    2011-01-01

    Nuclear magnetic resonance (NMR) experiments in pulsed magnetic fields up to 30.4 T focused on 1H and 93Nb nuclei are reported. Here we discuss the advantage and limitation of pulsed field NMR and why this technique is able to become a promising research tool. © 2011 Elsevier Inc. All Rights Reserved.

  17. NMR imaging of osteoarticular pathology

    International Nuclear Information System (INIS)

    Frocrain, L.; Duvauferrier, R.; Gagey, N.

    1987-01-01

    NMR imaging is assuming an increasingly important role in the diagnosis of osteo-articular disorders. Semiological descriptions of the mean pathological disorders of the locomotor system are presented. Some investigation strategies are proposed to compare NMR imaging with other imaging techniques in various pathological states [fr

  18. Nuclear magnetic resonance (NMR) tomography

    International Nuclear Information System (INIS)

    Skalpe, I.O.

    1984-01-01

    A brief survey of the working principle of the NMR technique in diagnostical medicine is given. Its clinical usefulness for locating tumors, diagnosing various other diseases, such as some mental illnesses and multiple sclerosis, and its possibilities for studying biochemical processes in vivo are mentioned. The price of NMR image scanners and the problems of the strong magnetic field around the machines are mentioned

  19. NMR imaging studies of coal

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Z.R.; Zhang, P.Z.; Ding, G.L.; Li, L.Y.; Ye, C.H. [University of Science and Technology, Beijing (China). Dept. of Chemistry

    1996-06-01

    The permeation transportation and swelling behavior of solvents into coal are investigated by NMR imaging using pyridine-d{sub 5} and acetone-d{sub 6}. Images of coal swollen with deuterated solvents illuminate proton distributions of mobile phases within the coal macromolecular networks. More information about the chemical and physical structure of coal can be obtained using NMR imaging techniques.

  20. NMR in pulsed magnetic field

    KAUST Repository

    Abou-Hamad, Edy

    2011-09-01

    Nuclear magnetic resonance (NMR) experiments in pulsed magnetic fields up to 30.4 T focused on 1H and 93Nb nuclei are reported. Here we discuss the advantage and limitation of pulsed field NMR and why this technique is able to become a promising research tool. © 2011 Elsevier Inc. All Rights Reserved.

  1. Two dimensional NMR studies of polysaccharides

    International Nuclear Information System (INIS)

    Byrd, R.A.; Egan, W.; Summers, M.F.

    1987-01-01

    Polysaccharides are very important components in the immune response system. Capsular polysaccharides and lipopolysaccharides occupy cell surface sites of bacteria, play key roles in recognition and some have been used to develop vaccines. Consequently, the ability to determine chemical structures of these systems is vital to an understanding of their immunogenic action. The authors have been utilizing recently developed two-dimensional homonuclear and heteronuclear correlation spectroscopy for unambiguous assignment and structure determination of a number of polysaccharides. In particular, the 1 H-detected heteronuclear correlation experiments are essential to the rapid and sensitive determination of these structures. Linkage sites are determined by independent polarization transfer experiments and multiple quantum correlation experiments. These methods permit the complete structure determination on very small amounts of the polysaccharides. They present the results of a number of structural determinations and discuss the limits of these experiments in terms of their applications to polysaccharides

  2. Structural Biology: Practical NMR Applications

    CERN Document Server

    Teng, Quincy

    2005-01-01

    This textbook begins with an overview of NMR development and applications in biological systems. It describes recent developments in instrument hardware and methodology. Chapters highlight the scope and limitation of NMR methods. While detailed math and quantum mechanics dealing with NMR theory have been addressed in several well-known NMR volumes, chapter two of this volume illustrates the fundamental principles and concepts of NMR spectroscopy in a more descriptive manner. Topics such as instrument setup, data acquisition, and data processing using a variety of offline software are discussed. Chapters further discuss several routine stategies for preparing samples, especially for macromolecules and complexes. The target market for such a volume includes researchers in the field of biochemistry, chemistry, structural biology and biophysics.

  3. PR-CALC: A Program for the Reconstruction of NMR Spectra from Projections

    International Nuclear Information System (INIS)

    Coggins, Brian E.; Zhou Pei

    2006-01-01

    Projection-reconstruction NMR (PR-NMR) has attracted growing attention as a method for collecting multidimensional NMR data rapidly. The PR-NMR procedure involves measuring lower-dimensional projections of a higher-dimensional spectrum, which are then used for the mathematical reconstruction of the full spectrum. We describe here the program PR-CALC, for the reconstruction of NMR spectra from projection data. This program implements a number of reconstruction algorithms, highly optimized to achieve maximal performance, and manages the reconstruction process automatically, producing either full spectra or subsets, such as regions or slices, as requested. The ability to obtain subsets allows large spectra to be analyzed by reconstructing and examining only those subsets containing peaks, offering considerable savings in processing time and storage space. PR-CALC is straightforward to use, and integrates directly into the conventional pipeline for data processing and analysis. It was written in standard C+ + and should run on any platform. The organization is flexible, and permits easy extension of capabilities, as well as reuse in new software. PR-CALC should facilitate the widespread utilization of PR-NMR in biomedical research

  4. 15N NMR relaxation studies of calcium-loaded parvalbumin show tight dynamics compared to those of other EF-hand proteins

    DEFF Research Database (Denmark)

    Baldellon, C; Alattia, J R; Strub, M P

    1998-01-01

    Dynamics of the rat alpha-parvalbumin calcium-loaded form have been determined by measurement of 15N nuclear relaxation using proton-detected heteronuclear NMR spectroscopy. The relaxation data were analyzed using spectral density functions and the Lipari-Szabo formalism. The major dynamic features...... for the rat alpha-parvalbumin calcium-loaded form are (1) the extreme rigidity of the helix-loop-helix EF-hand motifs and the linker segment connecting them, (2) the N and C termini of the protein being restricted in their mobility, (3) a conformational exchange occurring at the kink of helix D, and (4...... properties which are conserved in the EF-hand domains from different members of this superfamily: (1) a tendency toward higher mobility of NH vectors at relative position 2 in the Ca2+-binding loop, (2) a restricted mobility for the other residues in the binding loop, and (3) an overall rigidity...

  5. nmr spectroscopic study and dft calculations of giao nmr shieldings

    African Journals Online (AJOL)

    Preferred Customer

    3Department of Physics, Arts and Science Faculty, Dumlupinar University, Kütahya, ... 1H, 13C NMR chemical shifts and 1JCH coupling constants of .... then estimated using the corresponding TMS shieldings calculated in advance at the same.

  6. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

    Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

    2013-01-01

    and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking...... compounds. Furthermore, metabolomics applications elucidating how the differential regulated genes affects milk composition are also reported. This review will highlight the recent advances in NMR-based metabolomics on milk, as well as give a brief summary of when NMR spectroscopy can be useful for gaining...

  7. Annual reports on NMR spectroscopy

    CERN Document Server

    Webb, Graham A; McCarthy, M J

    1995-01-01

    Over recent years, no other technique has grown to such importance as that of NMR spectroscopy. It is used in all branches of science where precise structural determination is required and where the nature of interactions and reactions in solution is being studied. Annual Reports on NMR Spectroscopy has established itself as a means for the specialist and non-specialist alike to become familiar with new applications of the technique in all branches of chemistry, including biochemistry, and pharmaceutics. This volume focuses on theoretical aspects of NMR nuclear shielding and on applications of

  8. Intuitionistic fuzzy (IF) evaluations of multidimensional model

    International Nuclear Information System (INIS)

    Valova, I.

    2012-01-01

    There are different logical methods for data structuring, but no one is perfect enough. Multidimensional model-MD of data is presentation of data in a form of cube (referred also as info-cube or hypercube) with data or in form of 'star' type scheme (referred as multidimensional scheme), by use of F-structures (Facts) and set of D-structures (Dimensions), based on the notion of hierarchy of D-structures. The data, being subject of analysis in a specific multidimensional model is located in a Cartesian space, being restricted by D-structures. In fact, the data is either dispersed or 'concentrated', therefore the data cells are not distributed evenly within the respective space. The moment of occurrence of any event is difficult to be predicted and the data is concentrated as per time periods, location of performed business event, etc. To process such dispersed or concentrated data, various technical strategies are needed. The basic methods for presentation of such data should be selected. The approaches of data processing and respective calculations are connected with different options for data representation. The use of intuitionistic fuzzy evaluations (IFE) provide us new possibilities for alternative presentation and processing of data, subject of analysis in any OLAP application. The use of IFE at the evaluation of multidimensional models will result in the following advantages: analysts will dispose with more complete information for processing and analysis of respective data; benefit for the managers is that the final decisions will be more effective ones; enabling design of more functional multidimensional schemes. The purpose of this work is to apply intuitionistic fuzzy evaluations of multidimensional model of data. (authors)

  9. Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex

    International Nuclear Information System (INIS)

    Nikonowicz, E.; Roongta, V.; Jones, C.R.; Gorenstein, D.G.

    1989-01-01

    Assignment of the 1H and 31P NMR spectra of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d(CGCAGAATTCGCG)2, has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The downfield 31P resonance previously noted by Patel et al. (1982) has been assigned by both 17O labeling of the phosphate as well as a pure absorption phase constant-time heteronuclear 31P-1H correlated spectrum and has been associated with the phosphate on the 3' side of the extrahelical adenosine. JH3'-P coupling constants for each of the phosphates of the tridecamer were obtained from the 1H-31P J-resolved selective proton-flip 2D spectrum. By use of a modified Karplus relationship the C4-C3'-O3-P torsional angles (epsilon) were obtained. There exists a good linear correlation between 31P chemical shifts and the epsilon torsional angle. The 31P chemical shifts and epsilon torsional angles follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. Because the extrahelical adenosine significantly distorts the deoxyribose phosphate backbone conformation even several bases distant from the extrahelical adenosine, 31P chemical shifts show complex site- and sequence-specific variations. Modeling and NOESY distance-restrained energy minimization and restrained molecular dynamics suggest that the extrahelical adenosine stacks into the duplex. However, a minor conformation is also observed in the 1H NMR, which could be associated with a structure in which the extrahelical adenosine loops out into solution

  10. Multi-Dimensional Aggregation for Temporal Data

    DEFF Research Database (Denmark)

    Böhlen, M. H.; Gamper, J.; Jensen, Christian Søndergaard

    2006-01-01

    Business Intelligence solutions, encompassing technologies such as multi-dimensional data modeling and aggregate query processing, are being applied increasingly to non-traditional data. This paper extends multi-dimensional aggregation to apply to data with associated interval values that capture...... that the data holds for each point in the interval, as well as the case where the data holds only for the entire interval, but must be adjusted to apply to sub-intervals. The paper reports on an implementation of the new operator and on an empirical study that indicates that the operator scales to large data...

  11. Simulation of a Multidimensional Input Quantum Perceptron

    Science.gov (United States)

    Yamamoto, Alexandre Y.; Sundqvist, Kyle M.; Li, Peng; Harris, H. Rusty

    2018-06-01

    In this work, we demonstrate the improved data separation capabilities of the Multidimensional Input Quantum Perceptron (MDIQP), a fundamental cell for the construction of more complex Quantum Artificial Neural Networks (QANNs). This is done by using input controlled alterations of ancillary qubits in combination with phase estimation and learning algorithms. The MDIQP is capable of processing quantum information and classifying multidimensional data that may not be linearly separable, extending the capabilities of the classical perceptron. With this powerful component, we get much closer to the achievement of a feedforward multilayer QANN, which would be able to represent and classify arbitrary sets of data (both quantum and classical).

  12. Multi-dimensional Laplace transforms and applications

    International Nuclear Information System (INIS)

    Mughrabi, T.A.

    1988-01-01

    In this dissertation we establish new theorems for computing certain types of multidimensional Laplace transform pairs from known one-dimensional Laplace transforms. The theorems are applied to the most commonly used special functions and so we obtain many two and three dimensional Laplace transform pairs. As applications, some boundary value problems involving linear partial differential equations are solved by the use of multi-dimensional Laplace transformation. Also we establish some relations between the Laplace transformation and other integral transformation in two variables

  13. AMORE-HX: a multidimensional optimization of radial enhanced NMR-sampled hydrogen exchange

    International Nuclear Information System (INIS)

    Gledhill, John M.; Walters, Benjamin T.; Wand, A. Joshua

    2009-01-01

    The Cartesian sampled three-dimensional HNCO experiment is inherently limited in time resolution and sensitivity for the real time measurement of protein hydrogen exchange. This is largely overcome by use of the radial HNCO experiment that employs the use of optimized sampling angles. The significant practical limitation presented by use of three-dimensional data is the large data storage and processing requirements necessary and is largely overcome by taking advantage of the inherent capabilities of the 2D-FT to process selective frequency space without artifact or limitation. Decomposition of angle spectra into positive and negative ridge components provides increased resolution and allows statistical averaging of intensity and therefore increased precision. Strategies for averaging ridge cross sections within and between angle spectra are developed to allow further statistical approaches for increasing the precision of measured hydrogen occupancy. Intensity artifacts potentially introduced by over-pulsing are effectively eliminated by use of the BEST approach

  14. β-NMR sample optimization

    CERN Document Server

    Zakoucka, Eva

    2013-01-01

    During my summer student programme I was working on sample optimization for a new β-NMR project at the ISOLDE facility. The β-NMR technique is well-established in solid-state physics and just recently it is being introduced for applications in biochemistry and life sciences. The β-NMR collaboration will be applying for beam time to the INTC committee in September for three nuclei: Cu, Zn and Mg. Sample optimization for Mg was already performed last year during the summer student programme. Therefore sample optimization for Cu and Zn had to be completed as well for the project proposal. My part in the project was to perform thorough literature research on techniques studying Cu and Zn complexes in native conditions, search for relevant binding candidates for Cu and Zn applicable for ß-NMR and eventually evaluate selected binding candidates using UV-VIS spectrometry.

  15. NMR Studies of Polymer Nanocomposites

    National Research Council Canada - National Science Library

    Greenbaum, Steve

    2001-01-01

    .... The primary tool is pulsed field gradient NMR. A static field gradient method was developed which makes possible variable pressure diffusion measurement, and the application to the important fuel cell membrane NAFION constitute the first results...

  16. Integrative NMR for biomolecular research

    International Nuclear Information System (INIS)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L.

    2016-01-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  17. Integrative NMR for biomolecular research

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-04-15

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download{sub p}ackages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  18. Interpretations of NMR images

    International Nuclear Information System (INIS)

    Shi, J.Z.; McFarland, W.D.; Chen, S.S.; Sadhu, V.K.

    1986-01-01

    Two color display schemes are generally considered in medical images: pseudo-color and color composite. Psuedo-color technique maps the intensity means of a single monochrome image into a three dimensional color space, the gray level is thus replaced by the assigned color. Such a psuedo-color assignment is somewhat arbitrary but may be advantageous if the monochrome image is composed of simple intensity patterns. A good example of psuedo-color application is in nuclear medicine: The change of gray levels can be simply determined and the isocounts from two regions with different surroundings can be readily recognized. However, the use of psuedo-color in CT or MR imaging is controversial because it does not give additional information and may exaggerate insignificant gray scale differences. The color composite technique maps three parametric image data into a three dimensional color space, and thus three monochrome images are merged to form a single color image. The color composite technique increases the number of ways information can be displayed and provides both quantitative and qualitative data about the object or event represented. This paper describes the application of color composite in NMR images

  19. NMR characterization of thin films

    Science.gov (United States)

    Gerald II, Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2010-06-15

    A method, apparatus, and system for characterizing thin film materials. The method, apparatus, and system includes a container for receiving a starting material, applying a gravitational force, a magnetic force, and an electric force or combinations thereof to at least the starting material, forming a thin film material, sensing an NMR signal from the thin film material and analyzing the NMR signal to characterize the thin film of material.

  20. NMR imaging of cerebral infarction

    International Nuclear Information System (INIS)

    Takusagawa, Yoshihiko; Yamaoka, Naoki; Doi, Kazuaki; Okada, Keisei

    1987-01-01

    One hundred and five patients with cerebral infarction were studied by nuclear magnetic resonance (NMR) CT (resistive type of magnet with strength of 0.1 tesla) and X-ray CT. Pulse sequences used saturation recovery (Tr = 600 mSec), Inversion recovery (Tr = 500 mSec, Td = 300 mSec) and spin echo (Tr = 1500 mSec, Te = 40, 80, 120, 160 mSec). Fifteen cases were examined by NMR-CT within 24 hours from onset. Proton NMR imaging could not detect cerebral ischemia as early as 2 hours after onset, but except could detect the lesions in Se image the area of cerebral infarct 3 hours after onset. After 5 hours from onset image changes in SE were evident and corresponded to the area of cerebral infarct, but image changes in IR could not fully delineate the infarcted area. NMR images of 41 year-old woman with cerebral embolism by MCA trunck occlusion associated with mitral stenosis were presented, and NMR-CT was examined 10 hours, 9th and 43th days after episode of MCA occlusion. Sixty patents (64 times) with lacunar infarction were studied by NMR-CT and X-ray CT. The inversion recovery images were used mainly for detection of lesions and comparison with X-ray CT. In 160 lesions which were detected by NMR-CT or X-ray CT, could 156 lesions be detected by NMR-CT and 78 lesions by X-ray CT. Inversion recovery images were more useful for detection of lacunes than X-ray CT. Calculated T1 and T2 values prolonged with time course from onset. (author)

  1. Optical pumping and xenon NMR

    International Nuclear Information System (INIS)

    Raftery, M.D.

    1991-11-01

    Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping 129 Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas to high magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the 131 Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen

  2. NMR characterization of thin films

    Science.gov (United States)

    Gerald, II, Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2008-11-25

    A method, apparatus, and system for characterizing thin film materials. The method, apparatus, and system includes a container for receiving a starting material, applying a gravitational force, a magnetic force, and an electric force or combinations thereof to at least the starting material, forming a thin film material, sensing an NMR signal from the thin film material and analyzing the NMR signal to characterize the thin film of material.

  3. Application of multidimensional IRT models to longitudinal data

    NARCIS (Netherlands)

    te Marvelde, J.M.; Glas, Cornelis A.W.; Van Landeghem, Georges; Van Damme, Jan

    2006-01-01

    The application of multidimensional item response theory (IRT) models to longitudinal educational surveys where students are repeatedly measured is discussed and exemplified. A marginal maximum likelihood (MML) method to estimate the parameters of a multidimensional generalized partial credit model

  4. The emergence and evolution of the multidimensional organization

    NARCIS (Netherlands)

    Strikwerda, J.; Stoelhorst, J.W.

    2009-01-01

    The article discusses multidimensional organizations and the evolution of complex organizations. The six characteristics of multidimensional organizations, disadvantages of the successful organizational structure that is categorized as a multidivisional, multi-unit or M-form, research by the

  5. Surface Properties of Squalene/Meibum Films and NMR Confirmation of Squalene in Tears

    Directory of Open Access Journals (Sweden)

    Slavyana Ivanova

    2015-09-01

    Full Text Available Squalene (SQ possesses a wide range of pharmacological activities (antioxidant, drug carrier, detoxifier, hydrating, emollient that can be of benefit to the ocular surface. It can come in contact with human meibum (hMGS; the most abundant component of the tear film lipid layer as an endogenous tear lipid or from exogenous sources as eyelid sebum or pharmaceuticals. The aims of this study were to determine (i if SQ is in tear lipids and (ii its influence on the surface properties of hMGS films. Heteronuclear single quantum correlation NMR confirmed 7 mol % SQ in Schirmer’s strips extracts. The properties of SQ/hMGS pseudo-binary films at the air/water interface were studied with Langmuir surface balance, stress-relaxation dilatational rheology and Brewster angle microscopy. SQ does not possess surfactant properties. When mixed with hMGS squalene (i localized over the layers’ thinner regions and (ii did not affect the film pressure at high compression. Therefore, tear SQ is unlikely to instigate dry eye, and SQ can be used as a safe and “inert” ingredient in formulations to protect against dry eye. The layering of SQ over the thinner film regions in addition to its pharmacological properties could contribute to the protection of the ocular surface.

  6. Multidimensional Screening as a Pharmacology Laboratory Experience.

    Science.gov (United States)

    Malone, Marvin H.; And Others

    1979-01-01

    A multidimensional pharmacodynamic screening experiment that addresses drug interaction is included in the pharmacology-toxicology laboratory experience of pharmacy students at the University of the Pacific. The student handout with directions for the procedure is reproduced, drug compounds tested are listed, and laboratory evaluation results are…

  7. Continued validation of the Multidimensional Perfectionism Scale.

    Science.gov (United States)

    Clavin, S L; Clavin, R H; Gayton, W F; Broida, J

    1996-06-01

    Scores on the Multidimensional Perfectionism Scale have been correlated with measures of obsessive-compulsive tendencies for women, so the validity of scores on this scale for 41 men was examined. Scores on the Perfectionism Scale were significantly correlated (.47-.03) with scores on the Maudsley Obsessive-Compulsive Inventory.

  8. Multi-dimensional indoor location information model

    NARCIS (Netherlands)

    Xiong, Q.; Zhu, Q.; Zlatanova, S.; Huang, L.; Zhou, Y.; Du, Z.

    2013-01-01

    Aiming at the increasing requirements of seamless indoor and outdoor navigation and location service, a Chinese standard of Multidimensional Indoor Location Information Model is being developed, which defines ontology of indoor location. The model is complementary to 3D concepts like CityGML and

  9. Multi-dimensional quasitoeplitz Markov chains

    Directory of Open Access Journals (Sweden)

    Alexander N. Dudin

    1999-01-01

    Full Text Available This paper deals with multi-dimensional quasitoeplitz Markov chains. We establish a sufficient equilibrium condition and derive a functional matrix equation for the corresponding vector-generating function, whose solution is given algorithmically. The results are demonstrated in the form of examples and applications in queues with BMAP-input, which operate in synchronous random environment.

  10. Multidimensional human dynamics in mobile phone communications.

    Science.gov (United States)

    Quadri, Christian; Zignani, Matteo; Capra, Lorenzo; Gaito, Sabrina; Rossi, Gian Paolo

    2014-01-01

    In today's technology-assisted society, social interactions may be expressed through a variety of techno-communication channels, including online social networks, email and mobile phones (calls, text messages). Consequently, a clear grasp of human behavior through the diverse communication media is considered a key factor in understanding the formation of the today's information society. So far, all previous research on user communication behavior has focused on a sole communication activity. In this paper we move forward another step on this research path by performing a multidimensional study of human sociality as an expression of the use of mobile phones. The paper focuses on user temporal communication behavior in the interplay between the two complementary communication media, text messages and phone calls, that represent the bi-dimensional scenario of analysis. Our study provides a theoretical framework for analyzing multidimensional bursts as the most general burst category, that includes one-dimensional bursts as the simplest case, and offers empirical evidence of their nature by following the combined phone call/text message communication patterns of approximately one million people over three-month period. This quantitative approach enables the design of a generative model rooted in the three most significant features of the multidimensional burst - the number of dimensions, prevalence and interleaving degree - able to reproduce the main media usage attitude. The other findings of the paper include a novel multidimensional burst detection algorithm and an insight analysis of the human media selection process.

  11. Multidimensional stochastic approximation using locally contractive functions

    Science.gov (United States)

    Lawton, W. M.

    1975-01-01

    A Robbins-Monro type multidimensional stochastic approximation algorithm which converges in mean square and with probability one to the fixed point of a locally contractive regression function is developed. The algorithm is applied to obtain maximum likelihood estimates of the parameters for a mixture of multivariate normal distributions.

  12. Multidimensional human dynamics in mobile phone communications.

    Directory of Open Access Journals (Sweden)

    Christian Quadri

    Full Text Available In today's technology-assisted society, social interactions may be expressed through a variety of techno-communication channels, including online social networks, email and mobile phones (calls, text messages. Consequently, a clear grasp of human behavior through the diverse communication media is considered a key factor in understanding the formation of the today's information society. So far, all previous research on user communication behavior has focused on a sole communication activity. In this paper we move forward another step on this research path by performing a multidimensional study of human sociality as an expression of the use of mobile phones. The paper focuses on user temporal communication behavior in the interplay between the two complementary communication media, text messages and phone calls, that represent the bi-dimensional scenario of analysis. Our study provides a theoretical framework for analyzing multidimensional bursts as the most general burst category, that includes one-dimensional bursts as the simplest case, and offers empirical evidence of their nature by following the combined phone call/text message communication patterns of approximately one million people over three-month period. This quantitative approach enables the design of a generative model rooted in the three most significant features of the multidimensional burst - the number of dimensions, prevalence and interleaving degree - able to reproduce the main media usage attitude. The other findings of the paper include a novel multidimensional burst detection algorithm and an insight analysis of the human media selection process.

  13. MCMC estimation of multidimensional IRT models

    NARCIS (Netherlands)

    Beguin, Anton; Glas, Cornelis A.W.

    1998-01-01

    A Bayesian procedure to estimate the three-parameter normal ogive model and a generalization to a model with multidimensional ability parameters are discussed. The procedure is a generalization of a procedure by J. Albert (1992) for estimating the two-parameter normal ogive model. The procedure will

  14. Natural abundance 15N NMR assignments delineate structural differences between intact and reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    Science.gov (United States)

    Krishnamoorthi, R; Nemmers, S; Tobias, B

    1992-06-15

    15N NMR assignments were made to the backbone amide nitrogen atoms at natural isotopic abundance of intact and reactive-site (Arg5-Ile6) hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III and CMTI-III*, respectively) by means of 2D proton-detected heteronuclear single bond chemical shift correlation (HSBC) spectroscopy, utilizing the previously made sequence-specific 1H NMR assignments (Krishnamoorthi et al. (1992) Biochemistry 31, 898-904). Comparison of the 15N chemical shifts of the two forms of the inhibitor molecule revealed significant changes not only for residues located near the reactive-site region, but also for those distantly located. Residues Cys3, Arg5, Leu7, Met8, Cys10, Cys16, Glu19, His25, Tyr27, Cys28 and Gly29 showed significant chemical shift changes ranging from 0.3 to 6.1 ppm, thus indicating structural perturbations that were transmitted throughout the molecule. These findings confirm the earlier conclusions based on 1H NMR investigations.

  15. Multidimensional Data Model and Query Language for Informetrics.

    Science.gov (United States)

    Niemi, Timo; Hirvonen, Lasse; Jarvelin, Kalervo

    2003-01-01

    Discusses multidimensional data analysis, or online analytical processing (OLAP), which offer a single subject-oriented source for analyzing summary data based on various dimensions. Develops a conceptual/logical multidimensional model for supporting the needs of informetrics, including a multidimensional query language whose basic idea is to…

  16. Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

    Energy Technology Data Exchange (ETDEWEB)

    Matwiyoff, N.A.

    1983-01-01

    The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs.

  17. Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

    International Nuclear Information System (INIS)

    Matwiyoff, N.A.

    1983-01-01

    The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs

  18. Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz

    International Nuclear Information System (INIS)

    Bundle, D.R.; Cherwonogrodzky, J.W.; Perry, M.B.

    1987-01-01

    The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-α-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers of the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz 1 H and 125-MHz 13 C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent β-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-lined 4,6-dideoxy-4-formamido-α-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-α-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants

  19. Measurement and Characterization of Hydrogen-Deuterium Exchange Chemistry Using Relaxation Dispersion NMR Spectroscopy.

    Science.gov (United States)

    Khirich, Gennady; Holliday, Michael J; Lin, Jasper C; Nandy, Aditya

    2018-03-01

    One-dimensional heteronuclear relaxation dispersion NMR spectroscopy at 13 C natural abundance successfully characterized the dynamics of the hydrogen-deuterium exchange reaction occurring at the N ε position in l-arginine by monitoring C δ in varying amounts of D 2 O. A small equilibrium isotope effect was observed and quantified, corresponding to ΔG = -0.14 kcal mol -1 . A bimolecular rate constant of k D = 5.1 × 10 9 s -1 M -1 was determined from the pH*-dependence of k ex (where pH* is the direct electrode reading of pH in 10% D 2 O and k ex is the nuclear spin exchange rate constant), consistent with diffusion-controlled kinetics. The measurement of ΔG serves to bridge the millisecond time scale lifetimes of the detectable positively charged arginine species with the nanosecond time scale lifetime of the nonobservable low-populated neutral arginine intermediate species, thus allowing for characterization of the equilibrium lifetimes of the various arginine species in solution as a function of fractional solvent deuterium content. Despite the system being in fast exchange on the chemical shift time scale, the magnitude of the secondary isotope shift due to the exchange reaction at N ε was accurately measured to be 0.12 ppm directly from curve-fitting D 2 O-dependent dispersion data collected at a single static field strength. These results indicate that relaxation dispersion NMR spectroscopy is a robust and general method for studying base-catalyzed hydrogen-deuterium exchange chemistry at equilibrium.

  20. Simulations of NMR pulse sequences during equilibrium and non-equilibrium chemical exchange

    International Nuclear Information System (INIS)

    Helgstrand, Magnus; Haerd, Torleif; Allard, Peter

    2000-01-01

    The McConnell equations combine the differential equations for a simple two-state chemical exchange process with the Bloch differential equations for a classical description of the behavior of nuclear spins in a magnetic field. This equation system provides a useful starting point for the analysis of slow, intermediate and fast chemical exchange studied using a variety of NMR experiments. The McConnell equations are in the mathematical form of an inhomogeneous system of first-order differential equations. Here we rewrite the McConnell equations in a homogeneous form in order to facilitate fast and simple numerical calculation of the solution to the equation system. The McConnell equations can only treat equilibrium chemical exchange. We therefore also present a homogeneous equation system that can handle both equilibrium and non-equilibrium chemical processes correctly, as long as the kinetics is of first-order. Finally, the same method of rewriting the inhomogeneous form of the McConnell equations into a homogeneous form is applied to a quantum mechanical treatment of a spin system in chemical exchange. In order to illustrate the homogeneous McConnell equations, we have simulated pulse sequences useful for measuring exchange rates in slow, intermediate and fast chemical exchange processes. A stopped-flow NMR experiment was simulated using the equations for non-equilibrium chemical exchange. The quantum mechanical treatment was tested by the simulation of a sensitivity enhanced 15 N-HSQC with pulsed field gradients during slow chemical exchange and by the simulation of the transfer efficiency of a two-dimensional heteronuclear cross-polarization based experiment as a function of both chemical shift difference and exchange rate constants

  1. Determination of structural topology of a membrane protein in lipid bilayers using polarization optimized experiments (POE) for static and MAS solid state NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mote, Kaustubh R. [University of Minnesota, Department of Chemistry (United States); Gopinath, T. [University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics (United States); Veglia, Gianluigi, E-mail: vegli001@umn.edu [University of Minnesota, Department of Chemistry (United States)

    2013-10-15

    The low sensitivity inherent to both the static and magic angle spinning techniques of solid-state NMR (ssNMR) spectroscopy has thus far limited the routine application of multidimensional experiments to determine the structure of membrane proteins in lipid bilayers. Here, we demonstrate the advantage of using a recently developed class of experiments, polarization optimized experiments, for both static and MAS spectroscopy to achieve higher sensitivity and substantial time-savings for 2D and 3D experiments. We used sarcolipin, a single pass membrane protein, reconstituted in oriented bicelles (for oriented ssNMR) and multilamellar vesicles (for MAS ssNMR) as a benchmark. The restraints derived by these experiments are then combined into a hybrid energy function to allow simultaneous determination of structure and topology. The resulting structural ensemble converged to a helical conformation with a backbone RMSD {approx}0.44 A, a tilt angle of 24 Degree-Sign {+-} 1 Degree-Sign , and an azimuthal angle of 55 Degree-Sign {+-} 6 Degree-Sign . This work represents a crucial first step toward obtaining high-resolution structures of large membrane proteins using combined multidimensional oriented solid-state NMR and magic angle spinning solid-state NMR.

  2. Hyphenation of solid-phase extraction with liquid chromatography and nuclear magnetic resonance: application of HPLC-DAD-SPE-NMR to identification of constituents of Kanahia laniflora.

    Science.gov (United States)

    Clarkson, Cailean; Staerk, Dan; Hansen, Steen Honoré; Jaroszewski, Jerzy W

    2005-06-01

    The introduction of on-line solid-phase extraction (SPE) in HPLC-NMR has dramatically enhanced the sensitivity of this technique by concentration of the analytes in a small-volume NMR flow cell and by increasing the amount of the analyte by multiple peak trapping. In this study, the potential of HPLC-DAD-SPE-NMR hyphenation was demonstrated by structure determination of complex constituents of flower, leaf, root, and stem extracts of an African medicinal plant Kanahia laniflora. The technique was shown to allow acquisition of high-quality homo- and heteronuclear 2D NMR data following analytical-scale HPLC separation of extract constituents. Four flavonol glycosides [kaempferol 3-O-(6-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside; kaempferol 3-O-(2,6-di-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside; quercetin 3-O-(2,6-di-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside (rutin); and isorhamnetin, 3-O-(6-O-alpha-l-rhamnopyranosyl)-beta-d-glucopyranoside] and three 5alpha-cardenolides [coroglaucigenin 3-O-6-deoxy-beta-d-allopyranoside; coroglaucigenin 3-O-(4-O-beta-d-glucopyranosyl)-6-deoxy-beta-d-glucopyranoside; 3'-O-acetyl-3'-epiafroside] were identified, with complete assignments of 1H and 13C resonances based on HSQC and HMBC spectra whenever required. Confirmation of the structures was provided by HPLC-MS data. The HPLC-DAD-SPE-NMR technique therefore speeds up the dereplication of complex mixtures of natural origin significantly, by characterization of individual extract components prior to preparative isolation work.

  3. Carbon-13 NMR of flavinoids

    International Nuclear Information System (INIS)

    Agrawal, P.K.

    1989-01-01

    The present book has been written with the objective of introducing the organic chemists with the conceptual and experimental basis required for interpretation of 13 C NMR spectra of a flavonoid and to a discussion of general usefulness of the technique in solving flavonoid structural problem. After a brief general introduction to the essential aspects of flavonoids and 13 C NMR spectroscopy, considerable emphasis has been placed in chapter 2 on the various experimental methods and the interpretation of spectral details which enable individual resonance lines to be associated with the appropriate carbons in a molecule. The whole bulk of the literature, published on 13 C NMR of flavonoids in the major journals upto 1986 alongwith some recent references of 1987 has been classified in several categories such as: flavonoids, isflavonoids, other flavonoids, flavonoid glycosides, chalconoids and flavanoids. Each category constitutes a chapter. Finally the last chapter is devoted largely to a discussion for the differentiation of various categories and subcategories of flavonoids and for the establishment of aromatic substitution pattern in these compounds. It should be emphasized that the book is a data book and only concerned with the actual analysis of 13 C NMR spectra, thus a reasonable familiarity with basic instrumentation of 13 C NMR and general pattern of nuclear chemical shifts has been assumed. (author). refs.; figs.; tabs

  4. TG/DTG, FT-ICR Mass Spectrometry, and NMR Spectroscopy Study of Heavy Fuel Oil

    KAUST Repository

    Elbaz, Ayman M.

    2015-11-12

    There is an increasing interest in the comprehensive study of heavy fuel oil (HFO) due to its growing use in furnaces, boilers, marines, and recently in gas turbines. In this work, the thermal combustion characteristics and chemical composition of HFO were investigated using a range of techniques. Thermogravimetric analysis (TGA) was conducted to study the nonisothermal HFO combustion behavior. Chemical characterization of HFO was accomplished using various standard methods in addition to direct infusion atmospheric pressure chemical ionization Fourier transform ion cyclotron resonance mass spectrometry (APCI-FTICR MS), high resolution 1H nuclear magnetic resonance (NMR), 13C NMR, and two-dimensional heteronuclear multiple bond correlation (HMBC) spectroscopy. By analyzing thermogravimetry and differential thermogravimetry (TG/DTG) results, three different reaction regions were identified in the combustion of HFO with air, specifically, low temperature oxidation region (LTO), fuel deposition (FD), and high temperature oxidation (HTO) region. At the high end of the LTO region, a mass transfer resistance (skin effect) was evident. Kinetic analysis in LTO and HTO regions was conducted using two different kinetic models to calculate the apparent activation energy. In both models, HTO activation energies are higher than those for LTO. The FT-ICR MS technique resolved thousands of aromatic and sulfur containing compounds in the HFO sample and provided compositional details for individual molecules of three major class species. The major classes of compounds included species with one sulfur atom (S1), with two sulfur atoms (S2), and purely hydrocarbons (HC). The DBE (double bond equivalent) abundance plots established for S1 and HC provided additional information on their distributions in the HFO sample. The 1H NMR and 13C NMR results revealed that nearly 59% of the 1H nuclei were distributed as paraffinic CH2 and 5% were in aromatic groups. Nearly 21% of 13C nuclei were

  5. NMR investigation of coal extracts

    Energy Technology Data Exchange (ETDEWEB)

    Lang, I; Sebor, G [Ceskoslovenska Akademie Ved, Prague. Hornicky Ustav; Sebor, G Jr; Hajek, M; Mostecky, J [Vysoka Skola Chemicko-Technologicka, Prague (Czechoslovakia)

    1978-07-01

    Proton NMR spectroscopy was used for the evaluation of 10% coal extract solutions in deuterated pyridine. Four types of Czechoslovak coal were analyzed. Agreement was found between the aromaticity of coal extracts calculated from /sup 1/H NMR data using Brown's method and Ladner's and Williams' method and the characterization of an average molecule of the coal extract by the number of non-bridge carbon atoms of aromatic rings, by the overall number of aromatic ring carbon atoms and the number of aromatic rings, determined by the Williams and Ferris methods. The methods for calculating carbon distribution from /sup 1/H NMR data, however, contain some constants theoretically estimated or experimentally found using the method which still remain to be verified.

  6. Multidimensional integral representations problems of analytic continuation

    CERN Document Server

    Kytmanov, Alexander M

    2015-01-01

    The monograph is devoted to integral representations for holomorphic functions in several complex variables, such as Bochner-Martinelli, Cauchy-Fantappiè, Koppelman, multidimensional logarithmic residue etc., and their boundary properties. The applications considered are problems of analytic continuation of functions from the boundary of a bounded domain in C^n. In contrast to the well-known Hartogs-Bochner theorem, this book investigates functions with the one-dimensional property of holomorphic extension along complex lines, and includes the problems of receiving multidimensional boundary analogs of the Morera theorem.   This book is a valuable resource for specialists in complex analysis, theoretical physics, as well as graduate and postgraduate students with an understanding of standard university courses in complex, real and functional analysis, as well as algebra and geometry.

  7. Applications of Convex Analysis to Multidimensional Scaling

    OpenAIRE

    Jan de Leeuw

    2011-01-01

    In this paper we discuss the convergence of an algorithm for metric and nonmetric multidimensional scaling that is very similar to the C-matrix algorithm of Guttman. The paper improves some earlier results in two respects. In the first place the analysis is extended to cover general Minkovski metrics, in the second place a more elementary proof of convergence based on results of Robert is presented.

  8. Multidimensional Scaling Visualization using Parametric Similarity Indices

    OpenAIRE

    Machado, J. A. Tenreiro; Lopes, António M.; Galhano, A.M.

    2015-01-01

    In this paper, we apply multidimensional scaling (MDS) and parametric similarity indices (PSI) in the analysis of complex systems (CS). Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, an...

  9. Two-dimensional NMR spectrometry

    International Nuclear Information System (INIS)

    Farrar, T.C.

    1987-01-01

    This article is the second in a two-part series. In part one (ANALYTICAL CHEMISTRY, May 15) the authors discussed one-dimensional nuclear magnetic resonance (NMR) spectra and some relatively advanced nuclear spin gymnastics experiments that provide a capability for selective sensitivity enhancements. In this article and overview and some applications of two-dimensional NMR experiments are presented. These powerful experiments are important complements to the one-dimensional experiments. As in the more sophisticated one-dimensional experiments, the two-dimensional experiments involve three distinct time periods: a preparation period, t 0 ; an evolution period, t 1 ; and a detection period, t 2

  10. Solid state NMR of materials

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Sharon A; Ferguson, David B; Haw, James F [Texas A and M Univ., College Station, TX (United States). Dept. of Chemistry

    1994-12-31

    In situ NMR experiments are studied, including probe of several structures such as the structures of the organic adsorbates, Broensted acid sites, other nuclei associated with active sites, and other framework sites. The authors report that in the absence of high concentrations of paramagnetic sites or metal particles, high resolution MAS spectra are relatively easy to obtain and interpret. It is also concluded that NMR can measure spatial distributions and rates of diffusion; and are able to characterize equilibrium structures and the frequencies and amplitudes of molecular motion

  11. Frost Multidimensional Perfectionism Scale: the portuguese version

    Directory of Open Access Journals (Sweden)

    Ana Paula Monteiro Amaral

    2013-01-01

    Full Text Available BACKGROUND: The Frost Multidimensional Perfectionism Scale is one of the most world widely used measures of perfectionism. OBJECTIVE: To analyze the psychometric properties of the Portuguese version of the Frost Multidimensional Perfectionism Scale. METHODS: Two hundred and seventeen (178 females students from two Portuguese Universities filled in the scale, and a subgroup (n = 166 completed a retest with a four weeks interval. RESULTS: The scale reliability was good (Cronbach alpha = .857. Corrected item-total correlations ranged from .019 to .548. The scale test-retest reliability suggested a good temporal stability with a test-retest correlation of .765. A principal component analysis with Varimax rotation was performed and based on the Scree plot, two robust factorial structures were found (four and six factors. The principal component analyses, using Monte Carlo PCA for parallel analyses confirmed the six factor solution. The concurrent validity with Hewitt and Flett MPS was high, as well as the discriminant validity of positive and negative affect (Profile of Mood Stats-POMS. DISCUSSION: The two factorial structures (of four and six dimensions of the Portuguese version of Frost Multidimensional Perfectionism Scale replicate the results from different authors, with different samples and cultures. This suggests this scale is a robust instrument to assess perfectionism, in several clinical and research settings as well as in transcultural studies.

  12. Push-through Direction Injectin NMR Automation

    Science.gov (United States)

    Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the two major spectroscopic techniques successfully used in metabolomics studies. The non-invasive, quantitative and reproducible characteristics make NMR spectroscopy an excellent technique for detection of endogeno...

  13. Stereoselective and stereospecific effects in the formation of heteronuclear tartrate complexes of 3d- and 4f-elements from proton magnetic relaxation data

    International Nuclear Information System (INIS)

    Sal'nikov, Yu.I.; Chevela, V.V.

    1987-01-01

    A new approach to identification of stereoselective and stereospecific effects in the formation of heteronuclear tartrate complexes of 3d- and 4f-elements according to proton magnetic relaxation data is developed. At the first stage comparison of experimental dependences of the property measured (relaxation efficiency coefficient, Bjerrum function etc.) on the consentrational parameters is conducted. Their different course in systems with dH 4 L (d-tartaric acid) and dlH 4 L (dl-tartaric acid) points out to the presence of stereoeffects. Then, using mathematical simulation the most true stoichiometry of complex particles is determined as well as optimized values of their stability constants and intensity factors. The method is used when investigating the following systems: Fe 3+ -dH 4 L(dlH 4 L), Ln 3+ -dH 4 L(dlH 4 L), Fe 3+ -Ln 3+ -dH 4 L(dlH 4 L)(Ln 3+ -Gd 3+ , Ho 3+ , Er 3+ , Tm 3+ )

  14. Fourier transform n.m.r. spectroscopy

    International Nuclear Information System (INIS)

    Shaw, D.

    1976-01-01

    This book is orientated to techniques rather than applications. The basic theory of n.m.r. is dealt with in a unified approach to the Fourier theory. The middle section of the book concentrates on the practical aspects of Fourier n.m.r., both instrumental and experimental. The final chapters briefly cover general application of n.m.r., but concentrate strongly on those areas where Fourier n.m.r. can give information which is not available by conventional techniques

  15. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  16. PSYCHE Pure Shift NMR Spectroscopy.

    Science.gov (United States)

    Foroozandeh, Mohammadali; Morris, Gareth; Nilsson, Mathias

    2018-03-13

    Broadband homodecoupling techniques in NMR, also known as "pure shift" methods, aim to enhance spectral resolution by suppressing the effects of homonuclear coupling interactions to turn multiplet signals into singlets. Such techniques typically work by selecting a subset of "active" nuclear spins to observe, and selectively inverting the remaining, "passive", spins to reverse the effects of coupling. Pure Shift Yielded by Chirp Excitation (PSYCHE) is one such method; it is relatively recent, but has already been successfully implemented in a range of different NMR experiments. Paradoxically, PSYCHE is one of the trickiest of pure shift NMR techniques to understand but one of the easiest to use. Here we offer some insights into theoretical and practical aspects of the method, and into the effects and importance of the experimental parameters. Some recent improvements that enhance the spectral purity of PSYCHE spectra will be presented, and some experimental frameworks including examples in 1D and 2D NMR spectroscopy, for the implementation of PSYCHE will be introduced. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Simultaneous acquisition for T2 -T2 Exchange and T1 -T2 correlation NMR experiments

    Science.gov (United States)

    Montrazi, Elton T.; Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G.; Barsi-Andreeta, Mariane; Bonagamba, Tito J.

    2018-04-01

    The NMR measurements of longitudinal and transverse relaxation times and its multidimensional correlations provide useful information about molecular dynamics. However, these experiments are very time-consuming, and many researchers proposed faster experiments to reduce this issue. This paper presents a new way to simultaneously perform T2 -T2 Exchange and T1 -T2 correlation experiments by taking the advantage of the storage time and the two steps phase cycling used for running the relaxation exchange experiment. The data corresponding to each step is either summed or subtracted to produce the T2 -T2 and T1 -T2 data, enhancing the information obtained while maintaining the experiment duration. Comparing the results from this technique with traditional NMR experiments it was possible to validate the method.

  18. 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

  19. Sensitivity enhancement in NMR of macromolecules by application of optimal control theory

    International Nuclear Information System (INIS)

    Frueh, Dominique P.; Ito, Takuhiro; Li, J.-S.; Wagner, Gerhard; Glaser, Steffen J.; Khaneja, Navin

    2005-01-01

    NMR of macromolecules is limited by large transverse relaxation rates. In practice, this results in low efficiency of coherence transfer steps in multidimensional NMR experiments, leading to poor sensitivity and long acquisition times. The efficiency of coherence transfer can be maximized by design of relaxation optimized pulse sequences using tools from optimal control theory. In this paper, we demonstrate that this approach can be adopted for studies of large biological systems, such as the 800 kDa chaperone GroEL. For this system, the 1 H- 15 N coherence transfer module presented here yields an average sensitivity enhancement of 20-25% for cross-correlated relaxation induced polarization transfer (CRIPT) experiments

  20. 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

  1. NMRNet: A deep learning approach to automated peak picking of protein NMR spectra.

    Science.gov (United States)

    Klukowski, Piotr; Augoff, Michal; Zieba, Maciej; Drwal, Maciej; Gonczarek, Adam; Walczak, Michal J

    2018-03-14

    Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy. In particular, deep learning has proven to systematically achieve human-level performance in various recognition tasks, and thus emerges as an ideal tool to address automated identification of NMR signals. We have applied a convolutional neural network for visual analysis of multidimensional NMR spectra. A comprehensive test on 31 manually-annotated spectra has demonstrated top-tier average precision (AP) of 0.9596, 0.9058 and 0.8271 for backbone, side-chain and NOESY spectra, respectively. Furthermore, a combination of extracted peak lists with automated assignment routine, FLYA, outperformed other methods, including the manual one, and led to correct resonance assignment at the levels of 90.40%, 89.90% and 90.20% for three benchmark proteins. The proposed model is a part of a Dumpling software (platform for protein NMR data analysis), and is available at https://dumpling.bio/. michaljerzywalczak@gmail.compiotr.klukowski@pwr.edu.pl. Supplementary data are available at Bioinformatics online.

  2. The emergence and evolution of the multidimensional organization

    OpenAIRE

    Strikwerda, J.; Stoelhorst, J.W.

    2009-01-01

    The article discusses multidimensional organizations and the evolution of complex organizations. The six characteristics of multidimensional organizations, disadvantages of the successful organizational structure that is categorized as a multidivisional, multi-unit or M-form, research by the Foundation for Management Studies which suggests that synergies across business divisions can be exploited by the M-form, a team approach to creating economic value, examples of multidimensional firms suc...

  3. An Improved Multidimensional MPA Procedure for Bidirectional Earthquake Excitations

    OpenAIRE

    Wang, Feng; Sun, Jian-Gang; Zhang, Ning

    2014-01-01

    Presently, the modal pushover analysis procedure is extended to multidimensional analysis of structures subjected to multidimensional earthquake excitations. an improved multidimensional modal pushover analysis (IMMPA) method is presented in the paper in order to estimate the response demands of structures subjected to bidirectional earthquake excitations, in which the unidirectional earthquake excitation applied on equivalent SDOF system is replaced by the direct superposition of two compone...

  4. Multidimensional Risk Management for Underground Electricity Networks

    Directory of Open Access Journals (Sweden)

    Garcez Thalles V.

    2014-08-01

    Full Text Available In the paper we consider an electricity provider company that makes decision on allocating resources on electric network maintenance. The investments decrease malfunction rate of network nodes. An accidental event (explosion, fire, etc. or a malfunctioning on underground system can have various consequences and in different perspectives, such as deaths and injuries of pedestrians, fires in nearby locations, disturbances in the flow of vehicular traffic, loss to the company image, operating and financial losses, etc. For this reason it is necessary to apply an approach of the risk management that considers the multidimensional view of the consequences. Furthermore an analysis of decision making should consider network dependencies between the nodes of the electricity distribution system. In the paper we propose the use of the simulation to assess the network effects (such as the increase of the probability of other accidental event and the occurrence of blackouts of the dependent nodes in the multidimensional risk assessment in electricity grid. The analyzed effects include node overloading due to malfunction of adjacent nodes and blackouts that take place where there is temporarily no path in the grid between the power plant and a node. The simulation results show that network effects have crucial role for decisions in the network maintenance – outcomes of decisions to repair a particular node in the network can have significant influence on performance of other nodes. However, those dependencies are non-linear. The effects of network connectivity (number of connections between nodes on its multidimensional performance assessment depend heavily on the overloading effect level. The simulation results do not depend on network type structure (random or small world – however simulation outcomes for random networks have shown higher variance compared to small-world networks.

  5. Trust and credibility: measured by multidimensional scaling

    International Nuclear Information System (INIS)

    Warg, L.E.; Bodin, L.

    1998-01-01

    Full text of publication follows: in focus of much of today's research interest in risk communication, is the fact that the communities do not trust policy and decision makers such as politicians, government or industry people. This is especially serious in the years to come when we are expecting risk issues concerning for example the nuclear industry, global warming and hazardous waste, to be even higher on the political and social agenda all over the world. Despite the research efforts devoted to trust, society needs an in depth understanding of trust for conducting successful communication regarding environmental hazards. The present abstract is about an experimental study in psychology where focus has been on the possibility to use the multidimensional scaling technique to explore the characteristics people consider to be of importance when they say that certain persons are credible. In the study, a total of 61 students of the University of Oerebro, Sweden, were required to make comparisons of the similarity between 12 well-known swedish persons from politics science, media, industry, 'TV-world' and literature (two persons at a time), regarding their credibility when making statements about risks in society. In addition, the subjects were rating the importance of 19 factors for the credibility of a source. These 61 persons comprised three groups of students: pedagogists, business economists, and chemists. There were 61 % women and 39% men and the mean age was 23 years. The results will be analyzed using multidimensional scaling technique. Differences between the three groups will be analyzed and presented as well as those between men and women. In addition, the 19 factors will be discussed and considered when trying to label the dimensions accounted for by the multidimensional scaling technique. The result from this study will contribute to our understanding of important factors behind human judgments concerning trust and credibility. It will also point to a

  6. Multidimensional flux-limited advection schemes

    International Nuclear Information System (INIS)

    Thuburn, J.

    1996-01-01

    A general method for building multidimensional shape preserving advection schemes using flux limiters is presented. The method works for advected passive scalars in either compressible or incompressible flow and on arbitrary grids. With a minor modification it can be applied to the equation for fluid density. Schemes using the simplest form of the flux limiter can cause distortion of the advected profile, particularly sideways spreading, depending on the orientation of the flow relative to the grid. This is partly because the simple limiter is too restrictive. However, some straightforward refinements lead to a shape-preserving scheme that gives satisfactory results, with negligible grid-flow angle-dependent distortion

  7. Point Information Gain and Multidimensional Data Analysis

    Directory of Open Access Journals (Sweden)

    Renata Rychtáriková

    2016-10-01

    Full Text Available We generalize the point information gain (PIG and derived quantities, i.e., point information gain entropy (PIE and point information gain entropy density (PIED, for the case of the Rényi entropy and simulate the behavior of PIG for typical distributions. We also use these methods for the analysis of multidimensional datasets. We demonstrate the main properties of PIE/PIED spectra for the real data with the examples of several images and discuss further possible utilizations in other fields of data processing.

  8. New method for solving multidimensional scattering problem

    International Nuclear Information System (INIS)

    Melezhik, V.S.

    1991-01-01

    A new method is developed for solving the quantum mechanical problem of scattering of a particle with internal structure. The multichannel scattering problem is formulated as a system of nonlinear functional equations for the wave function and reaction matrix. The method is successfully tested for the scattering from a nonspherical potential well and a long-range nonspherical scatterer. The method is also applicable to solving the multidimensional Schroedinger equation with a discrete spectrum. As an example the known problem of a hydrogen atom in a homogeneous magnetic field is analyzed

  9. An example of multidimensional analysis: Discriminant analysis

    International Nuclear Information System (INIS)

    Lutz, P.

    1990-01-01

    Among the approaches on the data multi-dimensional analysis, lectures on the discriminant analysis including theoretical and practical aspects are presented. The discrimination problem, the analysis steps and the discrimination categories are stressed. Examples on the descriptive historical analysis, the discrimination for decision making, the demonstration and separation of the top quark are given. In the linear discriminant analysis the following subjects are discussed: Huyghens theorem, projection, discriminant variable, geometrical interpretation, case for g=2, classification method, separation of the top events. Criteria allowing the obtention of relevant results are included [fr

  10. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1999-01-01

    High Resolution NMR provides a broad treatment of the principles and theory of nuclear magnetic resonance (NMR) as it is used in the chemical sciences. It is written at an "intermediate" level, with mathematics used to augment, rather than replace, clear verbal descriptions of the phenomena. The book is intended to allow a graduate student, advanced undergraduate, or researcher to understand NMR at a fundamental level, and to see illustrations of the applications of NMR to the determination of the structure of small organic molecules and macromolecules, including proteins. Emphasis is on the study of NMR in liquids, but the treatment also includes high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. Careful attention is given to developing and interrelating four approaches - steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The presentation is based on the assumption that the reader has an acquaintan...

  11. Segmental isotope labeling of proteins for NMR structural study using a protein S tag for higher expression and solubility

    International Nuclear Information System (INIS)

    Kobayashi, Hiroshi; Swapna, G. V. T.; Wu, Kuen-Phon; Afinogenova, Yuliya; Conover, Kenith; Mao, Binchen; Montelione, Gaetano T.; Inouye, Masayori

    2012-01-01

    A common obstacle to NMR studies of proteins is sample preparation. In many cases, proteins targeted for NMR studies are poorly expressed and/or expressed in insoluble forms. Here, we describe a novel approach to overcome these problems. In the protein S tag-intein (PSTI) technology, two tandem 92-residue N-terminal domains of protein S (PrS 2 ) from Myxococcus xanthus is fused at the N-terminal end of a protein to enhance its expression and solubility. Using intein technology, the isotope-labeled PrS 2 -tag is replaced with non-isotope labeled PrS 2 -tag, silencing the NMR signals from PrS 2 -tag in isotope-filtered 1 H-detected NMR experiments. This method was applied to the E. coli ribosome binding factor A (RbfA), which aggregates and precipitates in the absence of a solubilization tag unless the C-terminal 25-residue segment is deleted (RbfAΔ25). Using the PrS 2 -tag, full-length well-behaved RbfA samples could be successfully prepared for NMR studies. PrS 2 (non-labeled)-tagged RbfA (isotope-labeled) was produced with the use of the intein approach. The well-resolved TROSY-HSQC spectrum of full-length PrS 2 -tagged RbfA superimposes with the TROSY-HSQC spectrum of RbfAΔ25, indicating that PrS 2 -tag does not affect the structure of the protein to which it is fused. Using a smaller PrS-tag, consisting of a single N-terminal domain of protein S, triple resonance experiments were performed, and most of the backbone 1 H, 15 N and 13 C resonance assignments for full-length E. coli RbfA were determined. Analysis of these chemical shift data with the Chemical Shift Index and heteronuclear 1 H– 15 N NOE measurements reveal the dynamic nature of the C-terminal segment of the full-length RbfA protein, which could not be inferred using the truncated RbfAΔ25 construct. CS-Rosetta calculations also demonstrate that the core structure of full-length RbfA is similar to that of the RbfAΔ25 construct.

  12. PVT Degradation Studies: NMR Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Herman M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kouzes, Richard T. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2017-06-06

    Under certain environmental conditions, polyvinyl toluene (PVT) plastic scintillator has been observed to undergo internal fogging. Nuclear magnetic resonance spectroscopy has been used to elucidate the state of water inside the PVT. The deuterium NMR results show that water absorbed by PVT under warm, humid conditions enters several distinct environments, and when the PVT is transferred from incubation to ambient temperature and humidity the water is lost on a time scale of a few hours from these samples. Most of the deuterium NMR peaks can be assigned to bulk liquid water, but almost 35% of the detected signal intensity is contained in a resonance that resembles spectra of water contained in nanometer-scale pores in mesoporous carbon.

  13. NMR imaging of human atherosclerosis

    International Nuclear Information System (INIS)

    Toussaint, J.F.

    1995-01-01

    Diagnosis and prognosis of atherosclerosis can no longer be evaluated with morphological parameters only. A description of atherosclerotic plaque composition is necessary to study the mechanisms of plaque rupture, which depends on collagenous cap and lipid core thicknesses. NMR, as a biochemical imaging technique, allows visualization of these components using T1 contrast (mobile lipids), T2 contrast (cap vs. core), spin density (calcifications), diffusion imaging, 1H and 13C spectroscopy. Today, these imaging sequences allow to study in vitro the effects of interventional techniques such as angioplasty or atherectomy. Clinical investigations begin, which will attempt to develop in vivo microscopy and test the ability of NMR to predict plaque rupture. (author). 13 refs., 7 figs

  14. Simplifying the complex 1H NMR spectra of fluorine-substituted benzamides by spin system filtering and spin-state selection: multiple-quantum-single-quantum correlation.

    Science.gov (United States)

    Baishya, Bikash; Reddy, G N Manjunatha; Prabhu, Uday Ramesh; Row, T N Guru; Suryaprakash, N

    2008-10-23

    The proton NMR spectra of fluorine-substituted benzamides are very complex (Figure 1) due to severe overlap of (1)H resonances from the two aromatic rings, in addition to several short and long-range scalar couplings experienced by each proton. With no detectable scalar couplings between the inter-ring spins, the (1)H NMR spectra can be construed as an overlap of spectra from two independent phenyl rings. In the present study we demonstrate that it is possible to separate the individual spectrum for each aromatic ring by spin system filtering employing the multiple-quantum-single-quantum correlation methodology. Furthermore, the two spin states of fluorine are utilized to simplify the spectrum corresponding to each phenyl ring by the spin-state selection. The demonstrated technique reduces spectral complexity by a factor of 4, in addition to permitting the determination of long-range couplings of less than 0.2 Hz and the relative signs of heteronuclear couplings. The technique also aids the judicious choice of the spin-selective double-quantum-single-quantum J-resolved experiment to determine the long-range homonuclear couplings of smaller magnitudes.

  15. Structural characterization of chemical warfare agent degradation products in decontamination solutions with proton band-selective (1)H-(31)P NMR spectroscopy.

    Science.gov (United States)

    Koskela, Harri; Hakala, Ullastiina; Vanninen, Paula

    2010-06-15

    Decontamination solutions, which are usually composed of strong alkaline chemicals, are used for efficient detoxification of chemical warfare agents (CWAs). The analysis of CWA degradation products directly in decontamination solutions is challenging due to the nature of the matrix. Furthermore, occasionally an unforeseen degradation pathway can result in degradation products which could be eluded to in standard analyses. Here, we present the results of the application of proton band-selective (1)H-(31)P NMR spectroscopy, i.e., band-selective 1D (1)H-(31)P heteronuclear single quantum coherence (HSQC) and band-selective 2D (1)H-(31)P HSQC-total correlation spectroscopy (TOCSY), for ester side chain characterization of organophosphorus nerve agent degradation products in decontamination solutions. The viability of the approach is demonstrated with a test mixture of typical degradation products of nerve agents sarin, soman, and VX. The proton band-selective (1)H-(31)P NMR spectroscopy is also applied in characterization of unusual degradation products of VX in GDS 2000 solution.

  16. High resolution NMR in zeolites

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, Anix [INTEVEP, Filial de Petroleos de Venezuela, SA, Caracas (Venezuela). Dept. de Analisis y Evalucion

    1992-12-31

    In this work {sup 29} Si and {sup 27} Al NMR spectroscopy was used to study various types of zeolites. The corresponding spectra were used to measure the Si/Al ratios, to follow chemical modifications induced by acid and hydrothermal treatments, to determine non-equivalent crystallographic sites in highly dealuminated mordenites, and to detect modifications of faujasites due to the insertion of titanium atoms in the lattice. (author) 7 refs., 7 figs., 2 tabs.

  17. High resolution NMR in zeolites

    International Nuclear Information System (INIS)

    Diaz, Anix

    1991-01-01

    In this work 29 Si and 27 Al NMR spectroscopy was used to study various types of zeolites. The corresponding spectra were used to measure the Si/Al ratios, to follow chemical modifications induced by acid and hydrothermal treatments, to determine non-equivalent crystallographic sites in highly dealuminated mordenites, and to detect modifications of faujasites due to the insertion of titanium atoms in the lattice. (author)

  18. Benchmarking the Multidimensional Stellar Implicit Code MUSIC

    Science.gov (United States)

    Goffrey, T.; Pratt, J.; Viallet, M.; Baraffe, I.; Popov, M. V.; Walder, R.; Folini, D.; Geroux, C.; Constantino, T.

    2017-04-01

    We present the results of a numerical benchmark study for the MUltidimensional Stellar Implicit Code (MUSIC) based on widely applicable two- and three-dimensional compressible hydrodynamics problems relevant to stellar interiors. MUSIC is an implicit large eddy simulation code that uses implicit time integration, implemented as a Jacobian-free Newton Krylov method. A physics based preconditioning technique which can be adjusted to target varying physics is used to improve the performance of the solver. The problems used for this benchmark study include the Rayleigh-Taylor and Kelvin-Helmholtz instabilities, and the decay of the Taylor-Green vortex. Additionally we show a test of hydrostatic equilibrium, in a stellar environment which is dominated by radiative effects. In this setting the flexibility of the preconditioning technique is demonstrated. This work aims to bridge the gap between the hydrodynamic test problems typically used during development of numerical methods and the complex flows of stellar interiors. A series of multidimensional tests were performed and analysed. Each of these test cases was analysed with a simple, scalar diagnostic, with the aim of enabling direct code comparisons. As the tests performed do not have analytic solutions, we verify MUSIC by comparing it to established codes including ATHENA and the PENCIL code. MUSIC is able to both reproduce behaviour from established and widely-used codes as well as results expected from theoretical predictions. This benchmarking study concludes a series of papers describing the development of the MUSIC code and provides confidence in future applications.

  19. MULTIDIMENSIONAL MODELING OF CORONAL RAIN DYNAMICS

    Energy Technology Data Exchange (ETDEWEB)

    Fang, X.; Xia, C.; Keppens, R. [Centre for mathematical Plasma Astrophysics, Department of Mathematics, KU Leuven, B-3001 Leuven (Belgium)

    2013-07-10

    We present the first multidimensional, magnetohydrodynamic simulations that capture the initial formation and long-term sustainment of the enigmatic coronal rain phenomenon. We demonstrate how thermal instability can induce a spectacular display of in situ forming blob-like condensations which then start their intimate ballet on top of initially linear force-free arcades. Our magnetic arcades host a chromospheric, transition region, and coronal plasma. Following coronal rain dynamics for over 80 minutes of physical time, we collect enough statistics to quantify blob widths, lengths, velocity distributions, and other characteristics which directly match modern observational knowledge. Our virtual coronal rain displays the deformation of blobs into V-shaped features, interactions of blobs due to mostly pressure-mediated levitations, and gives the first views of blobs that evaporate in situ or are siphoned over the apex of the background arcade. Our simulations pave the way for systematic surveys of coronal rain showers in true multidimensional settings to connect parameterized heating prescriptions with rain statistics, ultimately allowing us to quantify the coronal heating input.

  20. Multidimensional Learner Model In Intelligent Learning System

    Science.gov (United States)

    Deliyska, B.; Rozeva, A.

    2009-11-01

    The learner model in an intelligent learning system (ILS) has to ensure the personalization (individualization) and the adaptability of e-learning in an online learner-centered environment. ILS is a distributed e-learning system whose modules can be independent and located in different nodes (servers) on the Web. This kind of e-learning is achieved through the resources of the Semantic Web and is designed and developed around a course, group of courses or specialty. An essential part of ILS is learner model database which contains structured data about learner profile and temporal status in the learning process of one or more courses. In the paper a learner model position in ILS is considered and a relational database is designed from learner's domain ontology. Multidimensional modeling agent for the source database is designed and resultant learner data cube is presented. Agent's modules are proposed with corresponding algorithms and procedures. Multidimensional (OLAP) analysis guidelines on the resultant learner module for designing dynamic learning strategy have been highlighted.

  1. Multidimensional biochemical information processing of dynamical patterns.

    Science.gov (United States)

    Hasegawa, Yoshihiko

    2018-02-01

    Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

  2. MULTIDIMENSIONAL MODELING OF CORONAL RAIN DYNAMICS

    International Nuclear Information System (INIS)

    Fang, X.; Xia, C.; Keppens, R.

    2013-01-01

    We present the first multidimensional, magnetohydrodynamic simulations that capture the initial formation and long-term sustainment of the enigmatic coronal rain phenomenon. We demonstrate how thermal instability can induce a spectacular display of in situ forming blob-like condensations which then start their intimate ballet on top of initially linear force-free arcades. Our magnetic arcades host a chromospheric, transition region, and coronal plasma. Following coronal rain dynamics for over 80 minutes of physical time, we collect enough statistics to quantify blob widths, lengths, velocity distributions, and other characteristics which directly match modern observational knowledge. Our virtual coronal rain displays the deformation of blobs into V-shaped features, interactions of blobs due to mostly pressure-mediated levitations, and gives the first views of blobs that evaporate in situ or are siphoned over the apex of the background arcade. Our simulations pave the way for systematic surveys of coronal rain showers in true multidimensional settings to connect parameterized heating prescriptions with rain statistics, ultimately allowing us to quantify the coronal heating input.

  3. Testlet-Based Multidimensional Adaptive Testing.

    Science.gov (United States)

    Frey, Andreas; Seitz, Nicki-Nils; Brandt, Steffen

    2016-01-01

    Multidimensional adaptive testing (MAT) is a highly efficient method for the simultaneous measurement of several latent traits. Currently, no psychometrically sound approach is available for the use of MAT in testlet-based tests. Testlets are sets of items sharing a common stimulus such as a graph or a text. They are frequently used in large operational testing programs like TOEFL, PISA, PIRLS, or NAEP. To make MAT accessible for such testing programs, we present a novel combination of MAT with a multidimensional generalization of the random effects testlet model (MAT-MTIRT). MAT-MTIRT compared to non-adaptive testing is examined for several combinations of testlet effect variances (0.0, 0.5, 1.0, and 1.5) and testlet sizes (3, 6, and 9 items) with a simulation study considering three ability dimensions with simple loading structure. MAT-MTIRT outperformed non-adaptive testing regarding the measurement precision of the ability estimates. Further, the measurement precision decreased when testlet effect variances and testlet sizes increased. The suggested combination of the MTIRT model therefore provides a solution to the substantial problems of testlet-based tests while keeping the length of the test within an acceptable range.

  4. Testlet-based Multidimensional Adaptive Testing

    Directory of Open Access Journals (Sweden)

    Andreas Frey

    2016-11-01

    Full Text Available Multidimensional adaptive testing (MAT is a highly efficient method for the simultaneous measurement of several latent traits. Currently, no psychometrically sound approach is available for the use of MAT in testlet-based tests. Testlets are sets of items sharing a common stimulus such as a graph or a text. They are frequently used in large operational testing programs like TOEFL, PISA, PIRLS, or NAEP. To make MAT accessible for such testing programs, we present a novel combination of MAT with a multidimensional generalization of the random effects testlet model (MAT-MTIRT. MAT-MTIRT compared to non-adaptive testing is examined for several combinations of testlet effect variances (0.0, 0.5, 1.0, 1.5 and testlet sizes (3 items, 6 items, 9 items with a simulation study considering three ability dimensions with simple loading structure. MAT-MTIRT outperformed non-adaptive testing regarding the measurement precision of the ability estimates. Further, the measurement precision decreased when testlet effect variances and testlet sizes increased. The suggested combination of the MTIRT model therefore provides a solution to the substantial problems of testlet-based tests while keeping the length of the test within an acceptable range.

  5. A Multidimensional Theory of Suicide.

    Science.gov (United States)

    Leenaars, Antoon A; Dieserud, Gudrun; Wenckstern, Susanne; Dyregrov, Kari; Lester, David; Lyke, Jennifer

    2018-04-05

    Theory is the foundation of science; this is true in suicidology. Over decades of studies of suicide notes, Leenaars developed a multidimensional model of suicide, with international (crosscultural) studies and independent verification. To corroborate Leenaars's theory with a psychological autopsy (PA) study, examining age and sex of the decedent, and survivor's relationship to deceased. A PA study in Norway, with 120 survivors/informants was undertaken. Leenaars' theoretical-conceptual (protocol) analysis was undertaken of the survivors' narratives and in-depth interviews combined. Substantial interjudge reliability was noted (κ = .632). Overall, there was considerable confirmatory evidence of Leenaars's intrapsychic and interpersonal factors in suicide survivors' narratives. Differences were found in the age of the decedent, but not in sex, nor in the survivor's closeness of the relationship. Older deceased people were perceived to exhibit more heightened unbearable intrapsychic pain, associated with the suicide. Leenaars's theory has corroborative verification, through the decedents' suicide notes and the survivors' narratives. However, the multidimensional model needs further testing to develop a better evidence-based way of understanding suicide.

  6. [Multidimensional family therapy: which influences, which specificities?].

    Science.gov (United States)

    Bonnaire, C; Bastard, N; Couteron, J-P; Har, A; Phan, O

    2014-10-01

    Among illegal psycho-active drugs, cannabis is the most consumed by French adolescents. Multidimensional family therapy (MDFT) is a family-based outpatient therapy which has been developed for adolescents with drug and behavioral problems. MDFT has shown its effectiveness in adolescents with substance abuse disorders (notably cannabis abuse) not only in the United States but also in Europe (International Cannabis Need of Treatment project). MDFT is a multidisciplinary approach and an evidence-based treatment, at the crossroads of developmental psychology, ecological theories and family therapy. Its psychotherapeutic techniques find its roots in a variety of approaches which include systemic family therapy and cognitive therapy. The aims of this paper are: to describe all the backgrounds of MDFT by highlighting its characteristics; to explain how structural and strategy therapies have influenced this approach; to explore the links between MDFT, brief strategic family therapy and multi systemic family therapy; and to underline the specificities of this family therapy method. The multidimensional family therapy was created on the bases of 1) the integration of multiple therapeutic techniques stemming from various family therapy theories; and 2) studies which have shown family therapy efficiency. Several trials have shown a better efficiency of MDFT compared to group treatment, cognitive-behavioral therapy and home-based treatment. Studies have also highlighted that MDFT led to superior treatment outcomes, especially among young people with severe drug use and psychiatric co-morbidities. In the field of systemic family therapies, MDFT was influenced by: 1) the structural family therapy (S. Minuchin), 2) the strategic family theory (J. Haley), and 3) the intergenerational family therapy (Bowen and Boszormenyi-Nagy). MDFT has specific aspects: MDFT therapists think in a multidimensional perspective (because an adolescent's drug abuse is a multidimensional disorder), they

  7. Advanced NMR technology for bioscience and biotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Hammel, P.C.; Hernandez, G.; Trewhella, J.; Unkefer, C.J. [Los Alamos National Lab., NM (US); Boumenthal, D.K. [Univ. of Utah, Salt Lake City, UT (US); Kennedy, M.A. [Pacific Northwest National Lab., Richland, WA (US); Moore, G.J. [Wayne State Univ., Detroit, MI (US)

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). NMR plays critical roles in bioscience and biotechnology in both imaging and structure determination. NMR is limited, however, by the inherent low sensitivity of the NMR experiment and the demands for spectral resolution required to study biomolecules. The authors addressed both of these issues by working on the development of NMR force microscopy for molecular imaging, and high field NMR with isotope labeling to overcome limitations in the size of biomolecules that can be studied using NMR. A novel rf coil design for NMR force microscopy was developed that increases the limits of sensitivity in magnetic resonance detection for imaging, and the authors demonstrated sub-surface spatial imaging capabilities. The authors also made advances in the miniaturization of two critical NMR force microscope components. They completed high field NMR and isotope labeling studies of a muscle protein complex which is responsible for regulating muscle contraction and is too large for study using conventional NMR approaches.

  8. Solid-state NMR of inorganic semiconductors.

    Science.gov (United States)

    Yesinowski, James P

    2012-01-01

    Studies of inorganic semiconductors by solid-state NMR vary widely in terms of the nature of the samples investigated, the techniques employed to observe the NMR signal, and the types of information obtained. Compared with the NMR of diamagnetic non-semiconducting substances, important differences often result from the presence of electron or hole carriers that are the hallmark of semiconductors, and whose theoretical interpretation can be involved. This review aims to provide a broad perspective on the topic for the non-expert by providing: (1) a basic introduction to semiconductor physical concepts relevant to NMR, including common crystal structures and the various methods of making samples; (2) discussions of the NMR spin Hamiltonian, details of some of the NMR techniques and strategies used to make measurements and theoretically predict NMR parameters, and examples of how each of the terms in the Hamiltonian has provided useful information in bulk semiconductors; (3) a discussion of the additional considerations needed to interpret the NMR of nanoscale semiconductors, with selected examples. The area of semiconductor NMR is being revitalized by this interest in nanoscale semiconductors, the great improvements in NMR detection sensitivity and resolution that have occurred, and the current interest in optical pumping and spintronics-related studies. Promising directions for future research will be noted throughout.

  9. 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

  10. Two-dimensional 1H and 31P NMR spectra of a decamer oligodeoxyribonucleotide duplex and a quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex

    International Nuclear Information System (INIS)

    Powers, R.; Olsen, R.K.; Gorenstein, D.G.

    1989-01-01

    Assignment of the 1H and 31P NMR spectra of a decamer oligodeoxyribonucleotide duplex, d(CCCGATCGGG), and its quinoxaline ([MeCys3, MeCys7]TANDEM) drug duplex complex has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The 31P chemical shifts of this 10 base pair oligonucleotide follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. While the 31P chemical shifts show sequence-specific variations, they also do not generally follow the Calladine rules previously demonstrated. 31P NMR also provides a convenient monitor of the phosphate ester backbone conformational changes upon binding of the drug to the duplex. Although the quinoxaline drug, [MeCys3, MeCys7]TANDEM, is generally expected to bind to duplex DNA by bis-intercalation, only small 31P chemical shift changes are observed upon binding the drug to duplex d(CCCGATCGGG). Additionally, only small perturbations in the 1H NMR and UV spectra are observed upon binding the drug to the decamer, although association of the drug stabilizes the duplex form relative to the other states. These results are consistent with a non-intercalative mode of association of the drug. Modeling and molecular mechanics energy minimization demonstrate that a novel structure in which the two quinoxaline rings of the drug binds in the minor groove of the duplex is possible

  11. Resolution Improvement in Multidimensional Nuclear Magnetic Resonance Spectroscopy of Proteins; Amelioration de la resolution dans la resonance magnetique nucleaire multidimensionnelle des proteines

    Energy Technology Data Exchange (ETDEWEB)

    Duma, L

    2004-07-01

    The work presented in this thesis is concerned with both liquid-state and solid-state nuclear magnetic resonance (NMR) spectroscopy. Most of this work is devoted to the investigation by solid-state NMR of C{sup 13}-enriched compounds with the principal aim of presenting techniques devised for further improving the spectral resolution in multidimensional NMR of microcrystalline proteins. In fully C{sup 13}-labelled compounds, the J-coupling induces a broadening of the carbon lineshapes. We show that spin-state-selective technique called IPAP can be successfully combined with standard polarisation transfer schemes in order to remove the J-broadening in multidimensional solid-state NMR correlation experiments of fully C{sup 13}-enriched proteins. We present subsequently two techniques tailored for liquid-state NMR spectroscopy. The carbon directly detected techniques provide chemical shift information for all backbone hetero-nuclei. They are very attracting for the study of large bio-molecular systems or for the investigation of paramagnetic proteins. In the last part of this thesis, we study the spin-echo J-modulation for homonuclear two-spin 1/2 systems. Under magic-angle spinning, the theory of J-induced spin-echo modulation allows to derive a set of modulation regimes which give a spin-echo modulation exactly equal to the J-coupling. We show that the chemical-shift anisotropy and the dipolar interaction tend to stabilize the spin-echo J-modulation. The theoretical conclusions are supported by numerical simulations and experimental results obtained for three representative samples containing C{sup 13} spin pairs. (author)

  12. Improving personality facet scores with multidimensional computer adaptive testing

    DEFF Research Database (Denmark)

    Makransky, Guido; Mortensen, Erik Lykke; Glas, Cees A W

    2013-01-01

    personality tests contain many highly correlated facets. This article investigates the possibility of increasing the precision of the NEO PI-R facet scores by scoring items with multidimensional item response theory and by efficiently administering and scoring items with multidimensional computer adaptive...

  13. Multidimensional Computerized Adaptive Testing for Indonesia Junior High School Biology

    Science.gov (United States)

    Kuo, Bor-Chen; Daud, Muslem; Yang, Chih-Wei

    2015-01-01

    This paper describes a curriculum-based multidimensional computerized adaptive test that was developed for Indonesia junior high school Biology. In adherence to the Indonesian curriculum of different Biology dimensions, 300 items was constructed, and then tested to 2238 students. A multidimensional random coefficients multinomial logit model was…

  14. The Tunneling Method for Global Optimization in Multidimensional Scaling.

    Science.gov (United States)

    Groenen, Patrick J. F.; Heiser, Willem J.

    1996-01-01

    A tunneling method for global minimization in multidimensional scaling is introduced and adjusted for multidimensional scaling with general Minkowski distances. The method alternates a local search step with a tunneling step in which a different configuration is sought with the same STRESS implementation. (SLD)

  15. Multidimensional Physical Self-Concept of Athletes with Physical Disabilities

    Science.gov (United States)

    Shapiro, Deborah R.; Martin, Jeffrey J.

    2010-01-01

    The purposes of this investigation were first to predict reported PA (physical activity) behavior and self-esteem using a multidimensional physical self-concept model and second to describe perceptions of multidimensional physical self-concept (e.g., strength, endurance, sport competence) among athletes with physical disabilities. Athletes (N =…

  16. Multidimensional filter banks and wavelets research developments and applications

    CERN Document Server

    Levy, Bernard

    1997-01-01

    Multidimensional Filter Banks and Wavelets: Reserach Developments and Applications brings together in one place important contributions and up-to-date research results in this important area. Multidimensional Filter Banks and Wavelets: Research Developments and Applications serves as an excellent reference, providing insight into some of the most important research issues in the field.

  17. Multidimensional First-Order Dominance Comparisons of Population Wellbeing

    DEFF Research Database (Denmark)

    Siersbæk, Nikolaj; Østerdal, Lars Peter Raahave; Arndt, Thomas Channing

    2017-01-01

    This chapter conveys the concept of first-order dominance (FOD) with particular focus on applications to multidimensional population welfare comparisons. It gives an account of the fundamental equivalent definitions of FOD both in the one-dimensional and multidimensional setting, illustrated...

  18. Supervised and Unsupervised Learning of Multidimensional Acoustic Categories

    Science.gov (United States)

    Goudbeek, Martijn; Swingley, Daniel; Smits, Roel

    2009-01-01

    Learning to recognize the contrasts of a language-specific phonemic repertoire can be viewed as forming categories in a multidimensional psychophysical space. Research on the learning of distributionally defined visual categories has shown that categories defined over 1 dimension are easy to learn and that learning multidimensional categories is…

  19. Teaching NMR spectra analysis with nmr.cheminfo.org.

    Science.gov (United States)

    Patiny, Luc; Bolaños, Alejandro; Castillo, Andrés M; Bernal, Andrés; Wist, Julien

    2018-06-01

    Teaching spectra analysis and structure elucidation requires students to get trained on real problems. This involves solving exercises of increasing complexity and when necessary using computational tools. Although desktop software packages exist for this purpose, nmr.cheminfo.org platform offers students an online alternative. It provides a set of exercises and tools to help solving them. Only a small number of exercises are currently available, but contributors are invited to submit new ones and suggest new types of problems. Copyright © 2018 John Wiley & Sons, Ltd.

  20. Multidimensional quantum entanglement with large-scale integrated optics.

    Science.gov (United States)

    Wang, Jianwei; Paesani, Stefano; Ding, Yunhong; Santagati, Raffaele; Skrzypczyk, Paul; Salavrakos, Alexia; Tura, Jordi; Augusiak, Remigiusz; Mančinska, Laura; Bacco, Davide; Bonneau, Damien; Silverstone, Joshua W; Gong, Qihuang; Acín, Antonio; Rottwitt, Karsten; Oxenløwe, Leif K; O'Brien, Jeremy L; Laing, Anthony; Thompson, Mark G

    2018-04-20

    The ability to control multidimensional quantum systems is central to the development of advanced quantum technologies. We demonstrate a multidimensional integrated quantum photonic platform able to generate, control, and analyze high-dimensional entanglement. A programmable bipartite entangled system is realized with dimensions up to 15 × 15 on a large-scale silicon photonics quantum circuit. The device integrates more than 550 photonic components on a single chip, including 16 identical photon-pair sources. We verify the high precision, generality, and controllability of our multidimensional technology, and further exploit these abilities to demonstrate previously unexplored quantum applications, such as quantum randomness expansion and self-testing on multidimensional states. Our work provides an experimental platform for the development of multidimensional quantum technologies. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  1. Dynamic pulsed-field-gradient NMR

    CERN Document Server

    Sørland, Geir Humborstad

    2014-01-01

    Dealing with the basics, theory and applications of dynamic pulsed-field-gradient NMR NMR (PFG NMR), this book describes the essential theory behind diffusion in heterogeneous media that can be combined with NMR measurements to extract important information of the system being investigated. This information could be the surface to volume ratio, droplet size distribution in emulsions, brine profiles, fat content in food stuff, permeability/connectivity in porous materials and medical applications currently being developed. Besides theory and applications it will provide the readers with background knowledge on the experimental set-ups, and most important, deal with the pitfalls that are numerously present in work with PFG-NMR. How to analyze the NMR data and some important basic knowledge on the hardware will be explained, too.

  2. Probing membrane protein structure using water polarization transfer solid-state NMR.

    Science.gov (United States)

    Williams, Jonathan K; Hong, Mei

    2014-10-01

    Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected (1)H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of this method to various biological systems. Three polarization transfer mechanisms, chemical exchange, spin diffusion and NOE, manifest themselves at different temperatures, magic-angle-spinning frequencies, and pulse irradiations. Chemical exchange is ubiquitous in all systems examined so far, and spin diffusion plays the key role in polarization transfer within the macromolecule. Tightly bound water molecules with long residence times are rare in proteins at ambient temperature. The water polarization-transfer technique has been used to study the hydration of microcrystalline proteins, lipid membranes, and plant cell wall polysaccharides, and to derive atomic-resolution details of the kinetics and mechanism of ion conduction in channels and pumps. Using this approach, we have measured the water polarization transfer to the transmembrane domain of the influenza M2 protein to obtain information on the structure of this tetrameric proton channel. At short mixing times, the polarization transfer rates are site-specific and depend on the pH, labile protons, sidechain conformation, as well as the radial position of the residues in this four-helix bundle. Despite the multiple dependences, the initial transfer rates reflect the periodic nature of the residue positions from the water-filled pore, thus this technique provides a way of gleaning secondary structure information, helix tilt angle, and the oligomeric structure of membrane proteins. Copyright © 2014 Elsevier Inc. All

  3. An Inversion Recovery NMR Kinetics Experiment

    OpenAIRE

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this article will enable instructors to use inversion recovery as a laboratory activity in applied NMR classes and provide research students with a conveni...

  4. Optical Multidimensional Switching for Data Center Networks

    DEFF Research Database (Denmark)

    Kamchevska, Valerija

    2017-01-01

    . Software controlled switching using an on-chip integrated fiber switch is demonstrated and enabling of additional network functionalities such as multicast and optical grooming is experimentally confirmed. Altogether this work demonstrates the potential of optical switching technologies...... for the purpose of deploying optical switching within the network. First, the Hi-Ring data center architecture is proposed. It is based on optical multidimensional switching nodes that provide switching in hierarchically layered space, wavelength and time domain. The performance of the Hi-Ring architecture...... is evaluated experimentally and successful switching of both high capacity wavelength connections and time-shared subwavelengthconnections is demonstrated. Error-free performance is also achieved when transmitting 7 Tbit/s using multicore fiber, confirming the ability to scale the network. Moreover...

  5. A complete set of multidimensional Bell inequalities

    International Nuclear Information System (INIS)

    Arnault, François

    2012-01-01

    We give a multidimensional generalization of the complete set of Bell-correlation inequalities given by Werner and Wolf (2001 Phys. Rev. A 64 032112) and by Zukowski and Brukner (2002 Phys. Rev. Lett. 88 210401), for the two-dimensional case. Our construction applies to the n-party, two-observable case, where each observable is d-valued. The d d n inequalities obtained involve homogeneous polynomials. They define the facets of a polytope in a complex vector space of dimension d n . We detail the inequalities obtained in the case d = 3 and, from them, we recover known inequalities. We finally explain how the violations of our inequalities by quantum mechanics can be computed and could be observed, when using unitary observables. (paper)

  6. The simulation of multidimensional multiphase flows

    International Nuclear Information System (INIS)

    Lahey, Richard T.

    2005-01-01

    This paper presents an assessment of various models which can be used for the multidimensional simulation of multiphase flows, such as may occur in nuclear reactors. In particular, a model appropriate for the direct numerical simulation (DNS) of multiphase flows and a mechanistically based, three-dimensional, four-field, turbulent, two-fluid computational multiphase fluid dynamics (CMFD) model are discussed. A two-fluid bubbly flow model, which was derived using potential flow theory, can be extended to other flow regimes, but this will normally involve ensemble-averaging the results from direct numerical simulations (DNS) of various flow regimes to provide the detailed numerical data necessary for the development of flow-regime-specific interfacial and wall closure laws

  7. Constraint theory multidimensional mathematical model management

    CERN Document Server

    Friedman, George J

    2017-01-01

    Packed with new material and research, this second edition of George Friedman’s bestselling Constraint Theory remains an invaluable reference for all engineers, mathematicians, and managers concerned with modeling. As in the first edition, this text analyzes the way Constraint Theory employs bipartite graphs and presents the process of locating the “kernel of constraint” trillions of times faster than brute-force approaches, determining model consistency and computational allowability. Unique in its abundance of topological pictures of the material, this book balances left- and right-brain perceptions to provide a thorough explanation of multidimensional mathematical models. Much of the extended material in this new edition also comes from Phan Phan’s PhD dissertation in 2011, titled “Expanding Constraint Theory to Determine Well-Posedness of Large Mathematical Models.” Praise for the first edition: "Dr. George Friedman is indisputably the father of the very powerful methods of constraint theory...

  8. Path integral approach to multidimensional quantum tunnelling

    International Nuclear Information System (INIS)

    Balantekin, A.B.; Takigawa, N.

    1985-01-01

    Path integral formulation of the coupled channel problem in the case of multidimensional quantum tunneling is presented and two-time influence functionals are introduced. The two-time influence functionals are calculated explicitly for the three simplest cases: Harmonic oscillators linearly or quadratically coupled to the translational motion and a system with finite number of equidistant energy levels linearly coupled to the translational motion. The effects of these couplings on the transmission probability are studied for two limiting cases, adiabatic case and when the internal system has a degenerate energy spectrum. The condition for the transmission probability to show a resonant structure is discussed and exemplified. Finally, the properties of the dissipation factor in the adiabatic limit and its correlation with the friction coefficient in the classically accessible region are studied

  9. Security Contents: Politico-Military or Multidimensional?

    Directory of Open Access Journals (Sweden)

    Pere Vilanova

    1997-12-01

    Full Text Available The description of security problems has dramatically changed since the end of the bipolar system, and there are difficulties in building new concepts to comprehend a new and not yet defined international system. In the bipolar world, based on the North-South and East-West axes, security was described as systemic stability built upon deterrence and the defense of the statu quo. After the end of the Cold War, a new concept of multidimensional security was formulated. It lay emphasis on political, social (economic development andinternational (peaceful international relations democracy and the rule of law, putting aside too rapidly the military dimension. Vilanova argues that what have been identified as sources of new threats –narcotrafficking, ecology, migration, terrorism and fundamentalism– are not really new. There is a need to formulate political responses to these risks factors by means of public policies and intergovernmental and supranational action.

  10. Multidimensional splines for modeling FET nonlinearities

    Energy Technology Data Exchange (ETDEWEB)

    Barby, J A

    1986-01-01

    Circuit simulators like SPICE and timing simulators like MOTIS are used extensively for critical path verification of integrated circuits. MOSFET model evaluation dominates the run time of these simulators. Changes in technology results in costly updates, since modifications require reprogramming of the functions and their derivatives. The computational cost of MOSFET models can be reduced by using multidimensional polynomial splines. Since simulators based on the Newton Raphson algorithm require the function and first derivative, quadratic splines are sufficient for this purpose. The cost of updating the MOSFET model due to technology changes is greatly reduced since splines are derived from a set of points. Crucial for convergence speed of simulators is the fact that MOSFET characteristic equations are monotonic. This must be maintained by any simulation model. The splines the author designed do maintain monotonicity.

  11. Multidimensional Scaling for Orthodontic Root Resorption

    Directory of Open Access Journals (Sweden)

    Cristina Teodora Preoteasa

    2013-01-01

    Full Text Available The paper investigates the risk factors for the severity of orthodontic root resorption. The multidimensional scaling (MDS visualization method is used to investigate the experimental data from patients who received orthodontic treatment at the Department of Orthodontics and Dentofacial Orthopedics, Faculty of Dentistry, “Carol Davila” University of Medicine and Pharmacy, during a period of 4 years. The clusters emerging in the MDS plots reveal features and properties not easily captured by classical statistical tools. The results support the adoption of MDS for tackling the dentistry information and overcoming noise embedded into the data. The method introduced in this paper is rapid, efficient, and very useful for treating the risk factors for the severity of orthodontic root resorption.

  12. Multidimensional student skills with collaborative filtering

    Science.gov (United States)

    Bergner, Yoav; Rayyan, Saif; Seaton, Daniel; Pritchard, David E.

    2013-01-01

    Despite the fact that a physics course typically culminates in one final grade for the student, many instructors and researchers believe that there are multiple skills that students acquire to achieve mastery. Assessment validation and data analysis in general may thus benefit from extension to multidimensional ability. This paper introduces an approach for model determination and dimensionality analysis using collaborative filtering (CF), which is related to factor analysis and item response theory (IRT). Model selection is guided by machine learning perspectives, seeking to maximize the accuracy in predicting which students will answer which items correctly. We apply the CF to response data for the Mechanics Baseline Test and combine the results with prior analysis using unidimensional IRT.

  13. Gender Ideologies in Europe: A Multidimensional Framework.

    Science.gov (United States)

    Grunow, Daniela; Begall, Katia; Buchler, Sandra

    2018-02-01

    The authors argue, in line with recent research, that operationalizing gender ideology as a unidimensional construct ranging from traditional to egalitarian is problematic and propose an alternative framework that takes the multidimensionality of gender ideologies into account. Using latent class analysis, they operationalize their gender ideology framework based on data from the 2008 European Values Study, of which eight European countries reflecting the spectrum of current work-family policies were selected. The authors examine the form in which gender ideologies cluster in the various countries. Five ideology profiles were identified: egalitarian, egalitarian essentialism, intensive parenting, moderate traditional, and traditional. The five ideology profiles were found in all countries, but with pronounced variation in size. Ideologies mixing gender essentialist and egalitarian views appear to have replaced traditional ideologies, even in countries offering some institutional support for gendered separate spheres.

  14. Transport stochastic multi-dimensional media

    International Nuclear Information System (INIS)

    Haran, O.; Shvarts, D.

    1996-01-01

    Many physical phenomena evolve according to known deterministic rules, but in a stochastic media in which the composition changes in space and time. Examples to such phenomena are heat transfer in turbulent atmosphere with non uniform diffraction coefficients, neutron transfer in boiling coolant of a nuclear reactor and radiation transfer through concrete shields. The results of measurements conducted upon such a media are stochastic by nature, and depend on the specific realization of the media. In the last decade there has been a considerable efforts to describe linear particle transport in one dimensional stochastic media composed of several immiscible materials. However, transport in two or three dimensional stochastic media has been rarely addressed. The important effect in multi-dimensional transport that does not appear in one dimension is the ability to bypass obstacles. The current work is an attempt to quantify this effect. (authors)

  15. Multidimensional scaling of musical time estimations.

    Science.gov (United States)

    Cocenas-Silva, Raquel; Bueno, José Lino Oliveira; Molin, Paul; Bigand, Emmanuel

    2011-06-01

    The aim of this study was to identify the psycho-musical factors that govern time evaluation in Western music from baroque, classic, romantic, and modern repertoires. The excerpts were previously found to represent variability in musical properties and to induce four main categories of emotions. 48 participants (musicians and nonmusicians) freely listened to 16 musical excerpts (lasting 20 sec. each) and grouped those that seemed to have the same duration. Then, participants associated each group of excerpts to one of a set of sine wave tones varying in duration from 16 to 24 sec. Multidimensional scaling analysis generated a two-dimensional solution for these time judgments. Musical excerpts with high arousal produced an overestimation of time, and affective valence had little influence on time perception. The duration was also overestimated when tempo and loudness were higher, and to a lesser extent, timbre density. In contrast, musical tension had little influence.

  16. Transport stochastic multi-dimensional media

    Energy Technology Data Exchange (ETDEWEB)

    Haran, O; Shvarts, D [Israel Atomic Energy Commission, Beersheba (Israel). Nuclear Research Center-Negev; Thiberger, R [Ben-Gurion Univ. of the Negev, Beersheba (Israel)

    1996-12-01

    Many physical phenomena evolve according to known deterministic rules, but in a stochastic media in which the composition changes in space and time. Examples to such phenomena are heat transfer in turbulent atmosphere with non uniform diffraction coefficients, neutron transfer in boiling coolant of a nuclear reactor and radiation transfer through concrete shields. The results of measurements conducted upon such a media are stochastic by nature, and depend on the specific realization of the media. In the last decade there has been a considerable efforts to describe linear particle transport in one dimensional stochastic media composed of several immiscible materials. However, transport in two or three dimensional stochastic media has been rarely addressed. The important effect in multi-dimensional transport that does not appear in one dimension is the ability to bypass obstacles. The current work is an attempt to quantify this effect. (authors).

  17. Multidimensional fractional Schrödinger equation

    Science.gov (United States)

    Rodrigues, M. M.; Vieira, N.

    2012-11-01

    This work is intended to investigate the multi-dimensional space-time fractional Schrödinger equation of the form (CDt0+αu)(t,x) = iħ/2m(C∇βu)(t,x), with ħ the Planck's constant divided by 2π, m is the mass and u(t,x) is a wave function of the particle. Here (CDt0+α,C∇β are operators of the Caputo fractional derivatives, where α ∈]0,1] and β ∈]1,2]. The wave function is obtained using Laplace and Fourier transforms methods and a symbolic operational form of solutions in terms of the Mittag-Leffler functions is exhibited. It is presented an expression for the wave function and for the quantum mechanical probability density. Using Banach fixed point theorem, the existence and uniqueness of solutions is studied for this kind of fractional differential equations.

  18. Multidimensional evaluation on FR cycle systems

    International Nuclear Information System (INIS)

    Nakai, Ryodai; Fujii, Sumio; Takakuma, Katsuyuki; Katoh, Atsushi; Ono, Kiyoshi; Ohtaki, Akira; Shiotani, Hiroki

    2004-01-01

    This report explains some results of the multidimensional evaluation on various fast reactor cycle system concepts from an interim report of the 2nd phase of ''Feasibility Study on Commercialized FR Cycle System''. This method is designed to give more objective and more quantitative evaluations to clarify commercialized system candidate concepts. Here we brief current evaluation method from the five viewpoints of safety, economy, environment, resource and non-proliferation, with some trial evaluation results for some cycles consist of promising technologies in reactor, core and fuel, reprocessing and fuel manufacture. Moreover, we describe FR cycle deployment scenarios which describe advantages and disadvantages of the cycles from the viewpoints of uranium resource and radioactive waste based on long-term nuclear material mass flow analyses and advantages of the deployment of FR cycle itself from the viewpoints of the comparison with alternative power supplies as well as cost and benefit. (author)

  19. Gender Ideologies in Europe: A Multidimensional Framework

    Science.gov (United States)

    Begall, Katia; Buchler, Sandra

    2018-01-01

    The authors argue, in line with recent research, that operationalizing gender ideology as a unidimensional construct ranging from traditional to egalitarian is problematic and propose an alternative framework that takes the multidimensionality of gender ideologies into account. Using latent class analysis, they operationalize their gender ideology framework based on data from the 2008 European Values Study, of which eight European countries reflecting the spectrum of current work–family policies were selected. The authors examine the form in which gender ideologies cluster in the various countries. Five ideology profiles were identified: egalitarian, egalitarian essentialism, intensive parenting, moderate traditional, and traditional. The five ideology profiles were found in all countries, but with pronounced variation in size. Ideologies mixing gender essentialist and egalitarian views appear to have replaced traditional ideologies, even in countries offering some institutional support for gendered separate spheres. PMID:29491532

  20. Recombinant proteins incorporating short non-native extensions may display increased aggregation propensity as detected by high resolution NMR spectroscopy

    International Nuclear Information System (INIS)

    Zanzoni, Serena; D’Onofrio, Mariapina; Molinari, Henriette; Assfalg, Michael

    2012-01-01

    Highlights: ► Bile acid binding proteins from different constructs retain structural integrity. ► NMR 15 N-T 1 relaxation data of BABPs show differences if LVPR extension is present. ► Deviations from a 15 N-T 1 /molecular-weight calibration curve indicate aggregation. -- Abstract: The use of a recombinant protein to investigate the function of the native molecule requires that the former be obtained with the same amino acid sequence as the template. However, in many cases few additional residues are artificially introduced for cloning or purification purposes, possibly resulting in altered physico-chemical properties that may escape routine characterization. For example, increased aggregation propensity without visible protein precipitation is hardly detected by most analytical techniques but its investigation may be of great importance for optimizing the yield of recombinant protein production in biotechnological and structural biology applications. In this work we show that bile acid binding proteins incorporating the common C-terminal LeuValProArg extension display different hydrodynamic properties from those of the corresponding molecules without such additional amino acids. The proteins were produced enriched in nitrogen-15 for analysis via heteronuclear NMR spectroscopy. Residue-specific spin relaxation rates were measured and related to rotational tumbling time and molecular size. While the native-like recombinant proteins show spin-relaxation rates in agreement with those expected for monomeric globular proteins of their mass, our data indicate the presence of larger adducts for samples of proteins with very short amino acid extensions. The used approach is proposed as a further screening method for the quality assessment of biotechnological protein products.

  1. Recombinant proteins incorporating short non-native extensions may display increased aggregation propensity as detected by high resolution NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Zanzoni, Serena; D' Onofrio, Mariapina; Molinari, Henriette [Department of Biotechnology, University of Verona, 37134 Verona (Italy); Assfalg, Michael, E-mail: michael.assfalg@univr.it [Department of Biotechnology, University of Verona, 37134 Verona (Italy)

    2012-10-26

    Highlights: Black-Right-Pointing-Pointer Bile acid binding proteins from different constructs retain structural integrity. Black-Right-Pointing-Pointer NMR {sup 15}N-T{sub 1} relaxation data of BABPs show differences if LVPR extension is present. Black-Right-Pointing-Pointer Deviations from a {sup 15}N-T{sub 1}/molecular-weight calibration curve indicate aggregation. -- Abstract: The use of a recombinant protein to investigate the function of the native molecule requires that the former be obtained with the same amino acid sequence as the template. However, in many cases few additional residues are artificially introduced for cloning or purification purposes, possibly resulting in altered physico-chemical properties that may escape routine characterization. For example, increased aggregation propensity without visible protein precipitation is hardly detected by most analytical techniques but its investigation may be of great importance for optimizing the yield of recombinant protein production in biotechnological and structural biology applications. In this work we show that bile acid binding proteins incorporating the common C-terminal LeuValProArg extension display different hydrodynamic properties from those of the corresponding molecules without such additional amino acids. The proteins were produced enriched in nitrogen-15 for analysis via heteronuclear NMR spectroscopy. Residue-specific spin relaxation rates were measured and related to rotational tumbling time and molecular size. While the native-like recombinant proteins show spin-relaxation rates in agreement with those expected for monomeric globular proteins of their mass, our data indicate the presence of larger adducts for samples of proteins with very short amino acid extensions. The used approach is proposed as a further screening method for the quality assessment of biotechnological protein products.

  2. NMR studies of two spliced leader RNAs using isotope labeling

    Energy Technology Data Exchange (ETDEWEB)

    Lapham, J.; Crothers, D.M. [Yale Univ., New Haven, CT (United States)

    1994-12-01

    Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions between the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.

  3. NMR in structure-based drug design.

    Science.gov (United States)

    Carneiro, Marta G; Ab, Eiso; Theisgen, Stephan; Siegal, Gregg

    2017-11-08

    NMR spectroscopy is a powerful technique that can provide valuable structural information for drug discovery endeavors. Here, we discuss the strengths (and limitations) of NMR applications to structure-based drug discovery, highlighting the different levels of resolution and throughput obtainable. Additionally, the emerging field of paramagnetic NMR in drug discovery and recent developments in approaches to speed up and automate protein-observed NMR data collection and analysis are discussed. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  4. NMR spectroscopy using liquid crystal solvents

    CERN Document Server

    Emsley, JW

    2013-01-01

    NMR Spectroscopy using Liquid Crystal Solvents covers the importance of using a liquid crystal solvent in NMR to derive nuclear dipolar spin-spin coupling constants. This book is composed of ten chapters, and begins with a brief description of the features and benefits of liquid crystal in NMR spectroscopic analysis. The succeeding chapters deal with the mode of operation of nuclear spin Hamiltonian for partially oriented molecules and the analysis of NMR spectra of partially oriented molecules, as well as the determination of rigid molecule structure. These topics are followed by discussions

  5. Solution NMR structure determination of proteins revisited

    International Nuclear Information System (INIS)

    Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

    2008-01-01

    This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

  6. Ligand-receptor Interactions by NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Novak. P.

    2008-04-01

    Full Text Available Today NMR spectroscopy is a method of choice for elucidation of interactions between biomolecules and the potential ligands. Knowledge on these interactions is an essential prerequisite for the rational drug design. The most important contribution of NMR to drug design a few years ago was the 3D structure determination of proteins. Besides delivering the 3D structures of the free proteins as a raw material for the modeling studies on ligand binding, NMR can directly yield valuable experimental data on the biologically important protein-ligand complexes. In addition to X-ray diffraction, NMR spectroscopy can provide information on the internal protein dynamics ordynamics of intermolecular interactions. Changes in NMR parameters allow us to detect ("SAR by NMR" and quantitatively determine binding affinities (titration, diffusion NMR experiments, etc. of potential ligands. Also, it is possible to determine the binding site and conformations of ligands, receptors and receptor-ligand complexes with the help of NMR methods such as tr-NOESY. Epitopes or functional groups responsible for binding of ligands to the receptor can be identified by employing STD or WaterLOGSY experiments. In this review are described some of the most frequent NMR methods for the characterization of the interactions between biomolecules and ligands, together with their advantages and disadvantages.

  7. The necessity-concerns framework: a multidimensional theory benefits from multidimensional analysis.

    Science.gov (United States)

    Phillips, L Alison; Diefenbach, Michael A; Kronish, Ian M; Negron, Rennie M; Horowitz, Carol R

    2014-08-01

    Patients' medication-related concerns and necessity-beliefs predict adherence. Evaluation of the potentially complex interplay of these two dimensions has been limited because of methods that reduce them to a single dimension (difference scores). We use polynomial regression to assess the multidimensional effect of stroke-event survivors' medication-related concerns and necessity beliefs on their adherence to stroke-prevention medication. Survivors (n = 600) rated their concerns, necessity beliefs, and adherence to medication. Confirmatory and exploratory polynomial regression determined the best-fitting multidimensional model. As posited by the necessity-concerns framework (NCF), the greatest and lowest adherence was reported by those necessity weak concerns and strong concerns/weak Necessity-Beliefs, respectively. However, as could not be assessed using a difference-score model, patients with ambivalent beliefs were less adherent than those exhibiting indifference. Polynomial regression allows for assessment of the multidimensional nature of the NCF. Clinicians/Researchers should be aware that concerns and necessity dimensions are not polar opposites.

  8. The Necessity-Concerns-Framework: A Multidimensional Theory Benefits from Multidimensional Analysis

    Science.gov (United States)

    Phillips, L. Alison; Diefenbach, Michael; Kronish, Ian M.; Negron, Rennie M.; Horowitz, Carol R.

    2014-01-01

    Background Patients’ medication-related concerns and necessity-beliefs predict adherence. Evaluation of the potentially complex interplay of these two dimensions has been limited because of methods that reduce them to a single dimension (difference scores). Purpose We use polynomial regression to assess the multidimensional effect of stroke-event survivors’ medication-related concerns and necessity-beliefs on their adherence to stroke-prevention medication. Methods Survivors (n=600) rated their concerns, necessity-beliefs, and adherence to medication. Confirmatory and exploratory polynomial regression determined the best-fitting multidimensional model. Results As posited by the Necessity-Concerns Framework (NCF), the greatest and lowest adherence was reported by those with strong necessity-beliefs/weak concerns and strong concerns/weak necessity-beliefs, respectively. However, as could not be assessed using a difference-score model, patients with ambivalent beliefs were less adherent than those exhibiting indifference. Conclusions Polynomial regression allows for assessment of the multidimensional nature of the NCF. Clinicians/Researchers should be aware that concerns and necessity dimensions are not polar opposites. PMID:24500078

  9. NMR characterization of pituitary tumors

    International Nuclear Information System (INIS)

    Osbakken, M.; Gonzales, J.; Page, R.

    1984-01-01

    Twelve patients (5 male, 7 female, mean age 37.9 +- 20) with pituitary tumors were extensively evaluated with NMR imaging using a 1.5K gauss resistive magnet. Saturation recovery (SR), inversion recovery (IR) and spin echo (SE) pulse sequences were used for qualitative characterization of the lesions. T/sub 1/ calculations were also performed for brain and pituitary. Tumor histology and endocrine status were correlated with NMR data. All tumors were large with suprasellar extension (6 with prolactin secretion, 6 without). Pituitary T/sub 1/'s ranged from .2 to .64, the mean T/sub 1/ being longer than that of brain (Brain = .4 +- .04; Pit = .48 +- .14). 3 patients with histological evidence of homogeneous adenomas had long T/sub 1/'s (0.58 +- .05). 3 patients with evidence of recent or old hemorhage into the pituitary had much shorter T/sub 1/'s (0.29 +- .12). There was no relationship between prolactin secretion and T/sub 1/. Qualitative T/sub 1/ and T/sub 2/ information can be obtained by using a combination of SR, IR, and SE images. Using this method in the patients, homogeneous adenomas had similar T/sub 1/'s and longer T/sub 2/'s compared to the brain, while patients with bleeds had shorter T/sub 1/'s and T/sub 2/'s. Image T/sub 1/ characteristics correlated well with the calculated T/sub 1/ values. The range of T/sub 1/ (and potentially T/sub 2/) values which occur in apparently similar lesions are most likely due to anatomical and pathophysiological variations in these lesions. It may be ultimately possible to separate different types of pathological processes based on NMR image T/sub 1/ and T/sub 2/ characteristics after careful comparative studies of NMR and histological data are completed. The combination of calculated T/sub 1/ and T/sub 2/ with image T/sub 1/ and T/sub 2/ information may also be useful in further characterization of lesions

  10. Short recovery time NMR probe

    International Nuclear Information System (INIS)

    Ramia, M.E.; Martin, C.A.; Jeandrevin, S.

    2011-01-01

    A NMR probe for low frequency and short recovery time is presented in this work. The probe contains the tuning circuit, diode expanders and quarter wavelength networks to protect the receiver from both the amplifier noise and the coil ringing following the transmitter power pulse. It also possesses a coil damper which is activated by of non active components. The probe performance shows a recovery time of about of 15μs a sensitive Q factor reduction and an increase of the signal to noise ratio of about 68% during the reception at a work frequency of 2 MHz. (author)

  11. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    NARCIS (Netherlands)

    Van Der Schot, Gijs; Bonvin, Alexandre M J J

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on

  12. Exploring the metal coordination properties of the pyrimidine part of purine nucleobases: isomerization reactions in heteronuclear Pt(II)/Pd(II) of 9-methyladenine.

    Science.gov (United States)

    Ibáñez, Susana; Albertí, Francisca M; Sanz Miguel, Pablo J; Lippert, Bernhard

    2011-10-17

    The synthesis and characterization of three heteronuclear Pt(2)Pd(2) (4, 5) and PtPd(2) (6) complexes of the model nucleobase 9-methyladenine (9-MeA) is reported. The compounds were prepared by reacting [Pt(NH(3))(3)(9-MeA-N7)](ClO(4))(2) (1) with [Pd(en)(H(2)O)(2)](ClO(4))(2) at different ratios r between Pt and Pd, with the goal to probe Pd(II) binding to any of the three available nitrogen atoms, N1, N3, N6 or combinations thereof. Pd(II) coordination occurs at N1 and at the deprotonated N6 positions, yet not at N3. 4 and 5 are isomers of [{(en)Pd}(2){N1,N6-9-MeA(-)-N7)Pt(NH(3))(3)}(2)](ClO(4))(6)·nH(2)O, with a head-head orientation of the two bridging 9-MeA(-) ligands in 4 and a head-tail orientation in 5. 6 is [{(en)Pd}(2)(OH)(N1,N6-9MeA(-)-N7)Pt(NH(3))(3)](ClO(4))(4)·4H(2)O, hence a condensation product between [Pt(NH(3))(3)(9-MeA-N7)](2+) and a μ-OH bridged dinuclear (en)Pd-OH-Pd(en) unit, which connects the N1 and N6 positions of 9-MeA(-) in an intramolecular fashion. 4 and 5, which slowly interconvert in aqueous solution, display distinct structural differences such as significantly different intramolecular Pd···Pd contacts (3.124 0(16) Å in 4; 2.986 6(14) Å in 5), among others. Binding of (en)Pd(II) to the exocyclic N6 atom in 4 and 5 is accompanied by a large movement of Pd(II) out of the 9-MeA(-) plane and a trend to a further shortening of the C6-N6 bond as compared to free 9-MeA. The packing patterns of 4 and 5 reveal substantial anion-π interactions.

  13. 1H-NMR urinalysis

    International Nuclear Information System (INIS)

    Yamamoto, Hideaki; Yamaguchi, Shuichi

    1988-01-01

    In an effort to examine the usefulness of 1 H-nuclear magnetic resonance (NMR) urinalysis in the diagnosis of congenital metabolic disorders, 70 kinds of urinary metabolites were analysed in relation to the diagnosis of inborn errors of amino acid and organic acid disorders. Homogated decoupling (HMG) method failed to analyze six metabolites within the undetectable range. When non-decoupling method (NON), in which the materials are dissolved in dimethyl sulfoxide, was used, the identification of signals became possible. The combination of HMG and NON methods was, therefore, considered to identify all of the metabolites. When the urine samples, which were obtained from patients with hyperglycerolemia, hyperornithinemia, glutaric acidemia type II, or glycerol kinase deficiency, were analysed by using both HMG and NON methods, abnormally increased urinary metabolites were detected. 1 H-NMR urinalysis, if used in the combination of HMG and NON methods, may allow simultanenous screening of inborn errors of metabolism of amino acid and organic acid disorders. (Namekawa, K.)

  14. A study of multidimensional modeling approaches for data warehouse

    Science.gov (United States)

    Yusof, Sharmila Mat; Sidi, Fatimah; Ibrahim, Hamidah; Affendey, Lilly Suriani

    2016-08-01

    Data warehouse system is used to support the process of organizational decision making. Hence, the system must extract and integrate information from heterogeneous data sources in order to uncover relevant knowledge suitable for decision making process. However, the development of data warehouse is a difficult and complex process especially in its conceptual design (multidimensional modeling). Thus, there have been various approaches proposed to overcome the difficulty. This study surveys and compares the approaches of multidimensional modeling and highlights the issues, trend and solution proposed to date. The contribution is on the state of the art of the multidimensional modeling design.

  15. A Conceptual Model for Multidimensional Analysis of Documents

    Science.gov (United States)

    Ravat, Franck; Teste, Olivier; Tournier, Ronan; Zurlfluh, Gilles

    Data warehousing and OLAP are mainly used for the analysis of transactional data. Nowadays, with the evolution of Internet, and the development of semi-structured data exchange format (such as XML), it is possible to consider entire fragments of data such as documents as analysis sources. As a consequence, an adapted multidimensional analysis framework needs to be provided. In this paper, we introduce an OLAP multidimensional conceptual model without facts. This model is based on the unique concept of dimensions and is adapted for multidimensional document analysis. We also provide a set of manipulation operations.

  16. Early history of NMR at Los Alamos

    International Nuclear Information System (INIS)

    Jackson, J.A.

    1985-11-01

    Nuclear magnetic resonance (NMR) spectroscopy has developed into an important research tool in chemistry. More recently, NMR imaging and in vivo spectroscopy promise to produce a revolution in medicine and biochemistry. Early experiments at Los Alamos led to DOE programs involving stable isotopes of importance to biology and to medicine. These events are briefly recounted. 2 refs

  17. Characterization of natural bentonite by NMR

    International Nuclear Information System (INIS)

    Leite, Sidnei Q.M.; Dieguez, Lidia C.; Menezes, Sonia M.C.; San Gil, Rosane A.S.

    1993-01-01

    Solid state NMR as well as several other instrumental chemical analysis techniques were used in order to characterize two natural occurring bentonite. The methodology is described. The NMR spectra, together with the other used techniques suggest that the observed differences are due to iron inclusions in tetrahedral and octahedral sites

  18. Using Cloud Storage for NMR Data Distribution

    Science.gov (United States)

    Soulsby, David

    2012-01-01

    An approach using Google Groups as method for distributing student-acquired NMR data has been implemented. We describe how to configure NMR spectrometer software so that data is uploaded to a laboratory section specific Google Group, thereby removing bottlenecks associated with printing and processing at the spectrometer workstation. Outside of…

  19. Quartz Crystal Temperature Sensor for MAS NMR

    Science.gov (United States)

    Simon, Gerald

    1997-10-01

    Quartz crystal temperature sensors (QCTS) were tested for the first time as wireless thermometers in NMR MAS rotors utilizing the NMR RF technique itself for exiting and receiving electro-mechanical quartz resonances. This new tool in MAS NMR has a high sensitivity, linearity, and precision. When compared to the frequently used calibration of the variable temperature in the NMR system by a solid state NMR chemical shift thermometer (CST), such as lead nitrate, QCTS shows a number of advantages. It is an inert thermometer in close contact with solid samples operating parallel to the NMR experiment. QCTS can be manufactured for any frequency to be near a NMR frequency of interest (typically 1 to 2 MHz below or above). Due to the strong response of the crystal, signal detection is possible without changing the tuning of the MAS probe. The NMR signal is not influenced due to the relative sharp crystal resonance, restricted excitation by finite pulses, high probeQvalues, and commonly used audio filters. The quadratic dependence of the temperature increase on spinning speed is the same for the QCTS and for the CST lead nitrate and is discussed in terms of frictional heat in accordance with the literature about lead nitrate and with the results of a simple rotor speed jump experiment with differently radial located lead nitrate in the rotor.

  20. NMR studies of the structure of glasses

    International Nuclear Information System (INIS)

    Bray, P.J.; Gravina, S.J.; Stallworth, P.E.; Szu, S.P.; Jianhui Zhong

    1988-01-01

    Earlier continuous wave (CW) NMR studies of chemical bonding and structure in glasses are summarized. Examples are given of this use of the quadrupolar interaction and chemical shift to obtain structural information. New NMR data and analyses are presented for alkali borate and gallate glasses. Extensions to other elements (e.g. molybdenum, lanthanum) are suggested. 44 refs. (author)

  1. An Inversion Recovery NMR Kinetics Experiment

    Science.gov (United States)

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this…

  2. Selective sensitivity enhancement in FT-NMR

    International Nuclear Information System (INIS)

    Farrar, T.C.

    1987-01-01

    In this article the basic two-spin nuclear magnetic resonance (NMR) experiment and the new sensitivity enhancement experiments are reviewed. In part two of this two-part series an overview of two-dimensional NMR experiments will be presented. Part two will appear in the June 1 issue of Analytical Chemistry

  3. 2D NMR studies of biomolecules

    International Nuclear Information System (INIS)

    Lamerichs, R.M.J.N.

    1989-01-01

    The work described in this thesis comprises two related subjects. The first part describes methods to derive high-resolution structures of proteins in solution using two-dimensional (2-D) NMR. The second part describes 2-D NMR studies on the interaction between proteins and DNA. (author). 261 refs.; 52 figs.; 23 tabs

  4. Synthesis and NMR Elucidation of Novel Pentacycloundecane ...

    African Journals Online (AJOL)

    Herein we report the synthesis and NMR elucidation of five novel pentacycloundecane (PCU)-derived short peptides as potential HIV protease inhibitors. 1H and 13C spectral analysis show major overlapping of methine resonance of the PCU 'cage' thereby making it extremely difficult to assign the NMR signals. Attachment ...

  5. Development and applications of quantitative NMR spectroscopy

    International Nuclear Information System (INIS)

    Yamazaki, Taichi

    2016-01-01

    Recently, quantitative NMR spectroscopy has attracted attention as an analytical method which can easily secure traceability to SI unit system, and discussions about its accuracy and inaccuracy are also started. This paper focuses on the literatures on the advancement of quantitative NMR spectroscopy reported between 2009 and 2016, and introduces both NMR measurement conditions and actual analysis cases in quantitative NMR. The quantitative NMR spectroscopy using an internal reference method enables accurate quantitative analysis with a quick and versatile way in general, and it is possible to obtain the precision sufficiently applicable to the evaluation of pure substances and standard solutions. Since the external reference method can easily prevent contamination to samples and the collection of samples, there are many reported cases related to the quantitative analysis of biologically related samples and highly scarce natural products in which NMR spectra are complicated. In the precision of quantitative NMR spectroscopy, the internal reference method is superior. As the quantitative NMR spectroscopy widely spreads, discussions are also progressing on how to utilize this analytical method as the official methods in various countries around the world. In Japan, this method is listed in the Pharmacopoeia and Japanese Standard of Food Additives, and it is also used as the official method for purity evaluation. In the future, this method will be expected to spread as the general-purpose analysis method that can ensure traceability to SI unit system. (A.O.)

  6. NMR imaging of soft tissue tumors

    International Nuclear Information System (INIS)

    Laval-Jeantet, M.; Tobolsk, F.; Delepine, N.; Delepine, G.; Roger, B.; Cabanis, E.A.

    1986-01-01

    Preliminary findings on NMR imaging of 30 soft tissue tumors demonstrated the indispensable value of this examination (particularly when a surface antenna is used) for preoperative investigation and diagnosis of tumoral recurrence when compared with other radiologic techniques. The possible potential of NMR imaging for characterization of tissues, apart from lipoma or liposarcoma, cannot be evaluated at the present time [fr

  7. Characterization of lithium coordination sites with magic-angle spinning NMR

    Science.gov (United States)

    Haimovich, A.; Goldbourt, A.

    2015-05-01

    Lithium, in the form of lithium carbonate, is one of the most common drugs for bipolar disorder. Lithium is also considered to have an effect on many other cellular processes hence it possesses additional therapeutic as well as side effects. In order to quantitatively characterize the binding mode of lithium, it is required to identify the interacting species and measure their distances from the metal center. Here we use magic-angle spinning (MAS) solid-state NMR to study the binding site of lithium in complex with glycine and water (LiGlyW). Such a compound is a good enzyme mimetic since lithium is four-coordinated to one water molecule and three carboxylic groups. Distance measurements to carbons are performed using a 2D transferred echo double resonance (TEDOR) MAS solid-state NMR experiment, and water binding is probed by heteronuclear high-resolution proton-lithium and proton-carbon correlation (wPMLG-HETCOR) experiments. Both HETCOR experiments separate the main complex from impurities and non-specifically bound lithium species, demonstrating the sensitivity of the method to probe the species in the binding site. Optimizations of the TEDOR pulse scheme in the case of a quadrupolar nucleus with a small quadrupole coupling constant show that it is most efficient when pulses are positioned on the spin-1/2 (carbon-13) nucleus. Since the intensity of the TEDOR signal is not normalized, careful data analysis that considers both intensity and dipolar oscillations has to be performed. Nevertheless we show that accurate distances can be extracted for both carbons of the bound glycine and that these distances are consistent with the X-ray data and with lithium in a tetrahedral environment. The lithium environment in the complex is very similar to the binding site in inositol monophosphatase, an enzyme associated with bipolar disorder and the putative target for lithium therapy. A 2D TEDOR experiment applied to the bacterial SuhB gene product of this enzyme was designed

  8. Systematic Evaluation of Non-Uniform Sampling Parameters in the Targeted Analysis of Urine Metabolites by 1H,1H 2D NMR Spectroscopy.

    Science.gov (United States)

    Schlippenbach, Trixi von; Oefner, Peter J; Gronwald, Wolfram

    2018-03-09

    Non-uniform sampling (NUS) allows the accelerated acquisition of multidimensional NMR spectra. The aim of this contribution was the systematic evaluation of the impact of various quantitative NUS parameters on the accuracy and precision of 2D NMR measurements of urinary metabolites. Urine aliquots spiked with varying concentrations (15.6-500.0 µM) of tryptophan, tyrosine, glutamine, glutamic acid, lactic acid, and threonine, which can only be resolved fully by 2D NMR, were used to assess the influence of the sampling scheme, reconstruction algorithm, amount of omitted data points, and seed value on the quantitative performance of NUS in 1 H, 1 H-TOCSY and 1 H, 1 H-COSY45 NMR spectroscopy. Sinusoidal Poisson-gap sampling and a compressed sensing approach employing the iterative re-weighted least squares method for spectral reconstruction allowed a 50% reduction in measurement time while maintaining sufficient quantitative accuracy and precision for both types of homonuclear 2D NMR spectroscopy. Together with other advances in instrument design, such as state-of-the-art cryogenic probes, use of 2D NMR spectroscopy in large biomedical cohort studies seems feasible.

  9. A DYNAMIC INDEXING SCHEME FOR MULTIDIMENSIONAL DATA

    Directory of Open Access Journals (Sweden)

    Manuk G. Manukyan

    2018-03-01

    Full Text Available We present a new dynamic index structure for multidimensional data. The considered index structure is based on an extended grid file concept. Strengths and weaknesses of the grid files were analyzed. Based on that analysis we proposed to strengthen the concept of grid files by considering their stripes as linear hash tables, introducing the concept of chunk and representing the grid file structure as a graph. As a result we significantly reduced the amount of disk operations. Efficient algorithms for storage and access of index directory are proposed, in order to minimize memory usage and lookup operations complexities. Estimations of complexities for these algorithms are presented. A comparison of our approach to support effective grid file structure with other known approaches is presented. This comparison shows effectiveness of suggested metadata storage environment. An estimation of directory size is presented. A prototype to support of our grid file concept has been created and experimentally compared with MongoDB (a renowned NoSQL database. Comparison results show effectiveness of our approach in the cases of given point lookup, lookup by wide ranges and closest objects lookup when considering more than one dimension, and also better memory usage.

  10. Statistical segmentation of multidimensional brain datasets

    Science.gov (United States)

    Desco, Manuel; Gispert, Juan D.; Reig, Santiago; Santos, Andres; Pascau, Javier; Malpica, Norberto; Garcia-Barreno, Pedro

    2001-07-01

    This paper presents an automatic segmentation procedure for MRI neuroimages that overcomes part of the problems involved in multidimensional clustering techniques like partial volume effects (PVE), processing speed and difficulty of incorporating a priori knowledge. The method is a three-stage procedure: 1) Exclusion of background and skull voxels using threshold-based region growing techniques with fully automated seed selection. 2) Expectation Maximization algorithms are used to estimate the probability density function (PDF) of the remaining pixels, which are assumed to be mixtures of gaussians. These pixels can then be classified into cerebrospinal fluid (CSF), white matter and grey matter. Using this procedure, our method takes advantage of using the full covariance matrix (instead of the diagonal) for the joint PDF estimation. On the other hand, logistic discrimination techniques are more robust against violation of multi-gaussian assumptions. 3) A priori knowledge is added using Markov Random Field techniques. The algorithm has been tested with a dataset of 30 brain MRI studies (co-registered T1 and T2 MRI). Our method was compared with clustering techniques and with template-based statistical segmentation, using manual segmentation as a gold-standard. Our results were more robust and closer to the gold-standard.

  11. Proposed empirical gas geothermometer using multidimensional approach

    Energy Technology Data Exchange (ETDEWEB)

    Supranto; Sudjatmiko; Toha, Budianto; Wintolo, Djoko; Alhamid, Idrus

    1996-01-24

    Several formulas of surface gas geothermometer have been developed to utilize in geothermal exploration, i.e. by D'Amore and Panichi (1980) and by Darling and Talbot (1992). This paper presents an empirical gas geothermometer formula using multidimensional approach. The formula was derived from 37 selected chemical data of the 5 production wells from the Awibengkok Geothermal Volcanic Field in West Java. Seven components, i.e., gas volume percentage, CO2, H2S, CH4, H2, N2, and NH3, from these data are utilize to developed three model equations which represent relationship between temperature and gas compositions. These formulas are then tested by several fumarolic chemical data from Sibual-buali Area (North Sumatera) and from Ringgit Area (South Sumatera). Preliminary result indicated that gas volume percentage, H2S and CO2 concentrations have a significant role in term of gas geothermometer. Further verification is currently in progress.

  12. Multi-dimensional cosmology and GUP

    Energy Technology Data Exchange (ETDEWEB)

    Zeynali, K.; Motavalli, H. [Department of Theoretical Physics and Astrophysics, University of Tabriz, 51666-16471, Tabriz (Iran, Islamic Republic of); Darabi, F., E-mail: k.zeinali@arums.ac.ir, E-mail: f.darabi@azaruniv.edu, E-mail: motavalli@tabrizu.ac.ir [Department of Physics, Azarbaijan Shahid Madani University, 53714-161, Tabriz (Iran, Islamic Republic of)

    2012-12-01

    We consider a multidimensional cosmological model with FRW type metric having 4-dimensional space-time and d-dimensional Ricci-flat internal space sectors with a higher dimensional cosmological constant. We study the classical cosmology in commutative and GUP cases and obtain the corresponding exact solutions for negative and positive cosmological constants. It is shown that for negative cosmological constant, the commutative and GUP cases result in finite size universes with smaller size and longer ages, and larger size and shorter age, respectively. For positive cosmological constant, the commutative and GUP cases result in infinite size universes having late time accelerating behavior in good agreement with current observations. The accelerating phase starts in the GUP case sooner than the commutative case. In both commutative and GUP cases, and for both negative and positive cosmological constants, the internal space is stabilized to the sub-Planck size, at least within the present age of the universe. Then, we study the quantum cosmology by deriving the Wheeler-DeWitt equation, and obtain the exact solutions in the commutative case and the perturbative solutions in GUP case, to first order in the GUP small parameter, for both negative and positive cosmological constants. It is shown that good correspondence exists between the classical and quantum solutions.

  13. Multi-dimensional cosmology and GUP

    International Nuclear Information System (INIS)

    Zeynali, K.; Motavalli, H.; Darabi, F.

    2012-01-01

    We consider a multidimensional cosmological model with FRW type metric having 4-dimensional space-time and d-dimensional Ricci-flat internal space sectors with a higher dimensional cosmological constant. We study the classical cosmology in commutative and GUP cases and obtain the corresponding exact solutions for negative and positive cosmological constants. It is shown that for negative cosmological constant, the commutative and GUP cases result in finite size universes with smaller size and longer ages, and larger size and shorter age, respectively. For positive cosmological constant, the commutative and GUP cases result in infinite size universes having late time accelerating behavior in good agreement with current observations. The accelerating phase starts in the GUP case sooner than the commutative case. In both commutative and GUP cases, and for both negative and positive cosmological constants, the internal space is stabilized to the sub-Planck size, at least within the present age of the universe. Then, we study the quantum cosmology by deriving the Wheeler-DeWitt equation, and obtain the exact solutions in the commutative case and the perturbative solutions in GUP case, to first order in the GUP small parameter, for both negative and positive cosmological constants. It is shown that good correspondence exists between the classical and quantum solutions

  14. Convergence almost everywhere of multidimensional vectors

    International Nuclear Information System (INIS)

    El Berdan, Kassem; Zeineddine, Hassan

    2000-01-01

    Let X be a reflexive Banach space, Ω a measure space, T 1 ,...,T d be linear not commuting operators on L 1 (Ω,X)=L 1 (X) which are strictly contracting in L 1 (X) (i.e. there exist αjbelong to ]0,1[ such that ||T j f||≤αj||f|| for all j=1....,d and f belong to L 1 (X), and contracting in L ∞ (X). We prove a maximal equality for the averages: A n (T 1 ,...,T d )f= n d /1 i1=0 Σ n-1 ... id=0 Σ n-1 T 1 i1 ...T d id f and the convergence almost everywhere of it for all f in L 1 (X). This result generalizes Chacon's theorem (Chacon 19620 to the multidimensional case for this operators class. Finally, we give two operators which are strictly contracting in L 1 (X) and contracting in L ∞ (X) such that the convergence of the averages is not trivial. (author)

  15. Multidimensional Scaling Visualization Using Parametric Similarity Indices

    Directory of Open Access Journals (Sweden)

    J. A. Tenreiro Machado

    2015-03-01

    Full Text Available In this paper, we apply multidimensional scaling (MDS and parametric similarity indices (PSI in the analysis of complex systems (CS. Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, and we generate the corresponding MDS maps of ‘points’. Third, we use Procrustes analysis to linearly transform the MDS charts for maximum superposition and to build a globalMDS map of “shapes”. This final plot captures the time evolution of the phenomena and is sensitive to the PSI adopted. The generalized correlation, theMinkowski distance and four entropy-based indices are tested. The proposed approach is applied to the Dow Jones Industrial Average stock market index and the Europe Brent Spot Price FOB time-series.

  16. Energy Poverty in Europe: A Multidimensional Approach

    Directory of Open Access Journals (Sweden)

    Carlo Andrea Bollino

    2017-12-01

    Full Text Available With the European Commission’s “Third Energy Package”, the challenges posed by energy poverty have been recently acknowledged by European legislation. The paper develops a synthetic indicator of energy poverty for the purpose of assessing households’ well-being across different domains of inequality in access to energy services and to a healthy domestic environment. These dimensions are broadly defined in terms of energy affordability and thermal efficiency, two of the main manifestations of energy poverty. The analysis focuses on Europe and expands on existing economic literature by employing a fuzzy analysis for the definition of a multidimensional energy poverty index, which is then used to investigate the role of individual and household characteristics in shaping energy poverty. We find that during the European crisis energy poverty has been more stable than monetary poverty, and that thermal efficiency plays a crucial role in shaping individual and countries’ average degrees of energy poverty. JEL codes: I32; Q41; D10; D63

  17. Control of multidimensional systems on complex network

    Science.gov (United States)

    Bagnoli, Franco; Battistelli, Giorgio; Chisci, Luigi; Fanelli, Duccio

    2017-01-01

    Multidimensional systems coupled via complex networks are widespread in nature and thus frequently invoked for a large plethora of interesting applications. From ecology to physics, individual entities in mutual interactions are grouped in families, homogeneous in kind. These latter interact selectively, through a sequence of self-consistently regulated steps, whose deeply rooted architecture is stored in the assigned matrix of connections. The asymptotic equilibrium eventually attained by the system, and its associated stability, can be assessed by employing standard nonlinear dynamics tools. For many practical applications, it is however important to externally drive the system towards a desired equilibrium, which is resilient, hence stable, to external perturbations. To this end we here consider a system made up of N interacting populations which evolve according to general rate equations, bearing attributes of universality. One species is added to the pool of interacting families and used as a dynamical controller to induce novel stable equilibria. Use can be made of the root locus method to shape the needed control, in terms of intrinsic reactivity and adopted protocol of injection. The proposed method is tested on both synthetic and real data, thus enabling to demonstrate its robustness and versatility. PMID:28892493

  18. Indexación multidimensional configurable

    Directory of Open Access Journals (Sweden)

    José L. Zechinelli M.

    2004-01-01

    Full Text Available Existe una gran cantidad de métodos de indexado para datos multidimensionales. La idea fundamental de éstos es generar estructuras dinámicas para organizar objetos complejos, de tal manera que se puedan consultar de forma rápida y efectiva. Aunque existen taxonomías que definen las propiedades de cada método de indexado. A un usuario no experto le es difícil decidir cuál método podría ser apropiado para un conjunto particular de datos. En este artículo describimos la arquitectura de un framework el cual ofrece herramientas de análisis e implementación de diversos métodos de indexado multidimensional y que ayuda a un usuario a determinar el método más adecuado, para un conjunto de datos. Además se analizan ciertas propiedades de los mismos y el tipo de consultas que se llevarán a cabo en ellos.

  19. Phase space eigenfunctions of multidimensional quadratic Hamiltonians

    International Nuclear Information System (INIS)

    Dodonov, V.V.; Man'ko, V.I.

    1986-01-01

    We obtain the explicit expressions for phace space eigenfunctions (PSE),i.e. Weyl's symbols of dyadic operators like vertical stroken> ,vertical strokem>, being the solution of the Schroedinger equation with the Hamiltonian which is a quite arbitrary multidimensional quadratic form of the operators of Cartesian coordinates and conjugated to them momenta with time-dependent coefficients. It is shown that for an arbitrary quadratic Hamiltonian one can always construct the set of completely factorized PSE which are products of N factors, each factor being dependent only on two arguments for nnot=m and on a single argument for n=m. These arguments are nothing but constants of motion of the correspondent classical system. PSE are expressed in terms of the associated Laguerre polynomials in the case of a discrete spectrum and in terms of the Airy functions in the continuous spectrum case. Three examples are considered: a harmonic oscillator with a time-dependent frequency, a charged particle in a nonstationary uniform magnetic field, and a particle in a time-dependent uniform potential field. (orig.)

  20. Experimental verification of multidimensional quantum steering

    Science.gov (United States)

    Li, Che-Ming; Lo, Hsin-Pin; Chen, Liang-Yu; Yabushita, Atsushi

    2018-03-01

    Quantum steering enables one party to communicate with another remote party even if the sender is untrusted. Such characteristics of quantum systems not only provide direct applications to quantum information science, but are also conceptually important for distinguishing between quantum and classical resources. While concrete illustrations of steering have been shown in several experiments, quantum steering has not been certified for higher dimensional systems. Here, we introduce a simple method to experimentally certify two different kinds of quantum steering: Einstein-Podolsky-Rosen (EPR) steering and single-system (SS) steering (i.e., temporal steering), for dimensionality (d) up to d = 16. The former reveals the steerability among bipartite systems, whereas the latter manifests itself in single quantum objects. We use multidimensional steering witnesses to verify EPR steering of polarization-entangled pairs and SS steering of single photons. The ratios between the measured witnesses and the maximum values achieved by classical mimicries are observed to increase with d for both EPR and SS steering. The designed scenario offers a new method to study further the genuine multipartite steering of large dimensionality and potential uses in quantum information processing.

  1. Analysis of Multidimensional Poverty: Theory and Case Studies ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2009-08-18

    Aug 18, 2009 ... ... of applying a factorial technique, Multiple Correspondence Analysis, to poverty analysis. ... Analysis of Multidimensional Poverty: Theory and Case Studies ... agreement to support joint research projects in December 2017.

  2. The Multicultural Personality Questionnaire : A multidimensional instrument of multicultural effectiveness

    NARCIS (Netherlands)

    Van der Zee, KI; Van Oudenhoven, JP

    2000-01-01

    In today's global business environment, executive work is becoming more international in orientation. Several skills and traits may underlie executive success in an inter national environment. The Multicultural Personality Questionnaire was developed as a multidimensional instrument aimed at

  3. Capturing Complex Multidimensional Data in Location-Based Data Warehouses

    DEFF Research Database (Denmark)

    Timko, Igor; Pedersen, Torben Bach

    2004-01-01

    Motivated by the increasing need to handle complex multidimensional data inlocation-based data warehouses, this paper proposes apowerful data model that is able to capture the complexities of such data. The model provides a foundation for handling complex transportationinfrastructures...

  4. Benefits of Multidimensional Measures of Child Well Being in China.

    Science.gov (United States)

    Gatenio Gabel, Shirley; Zhang, Yiwei

    2017-11-06

    In recent decades, measures of child well-being have evolved from single dimension to multidimensional measures. Multi-dimensional measures deepen and broaden our understanding of child well-being and inform us of areas of neglect. Child well-being in China today is measured through proxy measures of household need. This paper discusses the evolution of child well-being measures more generally, explores the benefits of positive indicators and multiple dimensions in formulating policy, and then reviews efforts to date by the Chinese government, researchers, and non-governmental and intergovernmental organizations to develop comprehensive multidimensional measures of child well-being in China. The domains and their potential interactions, as well as data sources and availability, are presented. The authors believe that child well-being in China would benefit from the development of a multidimensional index and that there is sufficient data to develop such an index.

  5. A multidimensional subdiffusion model: An arbitrage-free market

    International Nuclear Information System (INIS)

    Li Guo-Hua; Zhang Hong; Luo Mao-Kang

    2012-01-01

    To capture the subdiffusive characteristics of financial markets, the subordinated process, directed by the inverse α-stale subordinator S α (t) for 0 < α < 1, has been employed as the model of asset prices. In this article, we introduce a multidimensional subdiffusion model that has a bond and K correlated stocks. The stock price process is a multidimensional subdiffusion process directed by the inverse α-stable subordinator. This model describes the period of stagnation for each stock and the behavior of the dependency between multiple stocks. Moreover, we derive the multidimensional fractional backward Kolmogorov equation for the subordinated process using the Laplace transform technique. Finally, using a martingale approach, we prove that the multidimensional subdiffusion model is arbitrage-free, and also gives an arbitrage-free pricing rule for contingent claims associated with the martingale measure. (interdisciplinary physics and related areas of science and technology)

  6. On new physics searches with multidimensional differential shapes

    Science.gov (United States)

    Ferreira, Felipe; Fichet, Sylvain; Sanz, Veronica

    2018-03-01

    In the context of upcoming new physics searches at the LHC, we investigate the impact of multidimensional differential rates in typical LHC analyses. We discuss the properties of shape information, and argue that multidimensional rates bring limited information in the scope of a discovery, but can have a large impact on model discrimination. We also point out subtleties about systematic uncertainties cancellations and the Cauchy-Schwarz bound on interference terms.

  7. An Analysis of Multi-dimensional Gender Inequality in Pakistan

    OpenAIRE

    Abdul Hamid; Aisha M. Ahmed

    2011-01-01

    Women make almost half of the population of Pakistan. They also contribute significantly to economic and social growth. However, in developing countries like Pakistan, women usually suffer from multidimensional inequality of opportunities leading to multidimensional poverty. The dimensions of family, women identity, health, education and women access to economic resources and employment contribute significantly to the discrimination of women. The provision of more opportunities to women in th...

  8. On multidimensional item response theory -- a coordinate free approach

    OpenAIRE

    Antal, Tamás

    2007-01-01

    A coordinate system free definition of complex structure multidimensional item response theory (MIRT) for dichotomously scored items is presented. The point of view taken emphasizes the possibilities and subtleties of understanding MIRT as a multidimensional extension of the ``classical'' unidimensional item response theory models. The main theorem of the paper is that every monotonic MIRT model looks the same; they are all trivial extensions of univariate item response theory.

  9. Background elimination methods for multidimensional coincidence γ-ray spectra

    International Nuclear Information System (INIS)

    Morhac, M.

    1997-01-01

    In the paper new methods to separate useful information from background in one, two, three and multidimensional spectra (histograms) measured in large multidetector γ-ray arrays are derived. The sensitive nonlinear peak clipping algorithm is the basis of the methods for estimation of the background in multidimensional spectra. The derived procedures are simple and therefore have a very low cost in terms of computing time. (orig.)

  10. Modelling of multidimensional quantum systems by the numerical functional integration

    International Nuclear Information System (INIS)

    Lobanov, Yu.Yu.; Zhidkov, E.P.

    1990-01-01

    The employment of the numerical functional integration for the description of multidimensional systems in quantum and statistical physics is considered. For the multiple functional integrals with respect to Gaussian measures in the full separable metric spaces the new approximation formulas exact on a class of polynomial functionals of a given summary degree are constructed. The use of the formulas is demonstrated on example of computation of the Green function and the ground state energy in multidimensional Calogero model. 15 refs.; 2 tabs

  11. Fatigue and multidimensional disease severity in chronic obstructive pulmonary disease

    Directory of Open Access Journals (Sweden)

    Inal-Ince Deniz

    2010-06-01

    Full Text Available Abstract Background and aims Fatigue is associated with longitudinal ratings of health in patients with chronic obstructive pulmonary disease (COPD. Although the degree of airflow obstruction is often used to grade disease severity in patients with COPD, multidimensional grading systems have recently been developed. The aim of this study was to investigate the relationship between perceived and actual fatigue level and multidimensional disease severity in patients with COPD. Materials and methods Twenty-two patients with COPD (aged 52-74 years took part in the study. Multidimensional disease severity was measured using the SAFE and BODE indices. Perceived fatigue was assessed using the Fatigue Severity Scale (FSS and the Fatigue Impact Scale (FIS. Peripheral muscle endurance was evaluated using the number of sit-ups, squats, and modified push-ups that each patient could do. Results Thirteen patients (59% had severe fatigue, and their St George's Respiratory Questionnaire scores were significantly higher (p Conclusions Peripheral muscle endurance and fatigue perception in patients with COPD was related to multidimensional disease severity measured with both the SAFE and BODE indices. Improvements in perceived and actual fatigue levels may positively affect multidimensional disease severity and health status in COPD patients. Further research is needed to investigate the effects of fatigue perception and exercise training on patients with different stages of multidimensional COPD severity.

  12. An introduction to biological NMR spectroscopy

    International Nuclear Information System (INIS)

    Marion, Dominique

    2013-01-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). (authors)

  13. NMR imaging of the brain: initial impressions

    International Nuclear Information System (INIS)

    Spencer, D.H.; Bydder, G.M.

    1983-01-01

    An NMR imaging system designed and built by Thorn-EMI Ltd was installed at Hammersmith Hospital in March 1981. In the first year of operation 180 patients and 40 volunteers have had cranial examinations and initial impressions bases on this experience are presented. Patients with a wide variety of neurological diseases have been studied to provide a basis for diagnostic interpretation, to define distinctive features, and to evaluate different types of scanning sequences. NMR imaging appears to be of considerable value in neurological diagnosis and has a number of advantages over CT. The detailed evaluation of NMR imaging will require much more work but the initial results are very promising

  14. Oriented solid-state NMR spectrosocpy

    DEFF Research Database (Denmark)

    Bertelsen, Kresten

    This thesis is concerned with driving forward oriented solid-state NMR spectroscopy as a viable technique for studying peptides in membrane bilayers. I will show that structural heterogeneity is an intrinsic part of the peptide/lipid system and that NMR can be used to characterize static...... and dynamic structural features of the peptides and its local surroundings. In fact one need to take into account the dynamical features of the system in order to correctly predict the structure from oriented solid-state NMR spectra.      ...

  15. NMR reaction monitoring in flow synthesis

    Directory of Open Access Journals (Sweden)

    M. Victoria Gomez

    2017-02-01

    Full Text Available Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed.

  16. NMR reaction monitoring in flow synthesis.

    Science.gov (United States)

    Gomez, M Victoria; de la Hoz, Antonio

    2017-01-01

    Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed.

  17. Introduction to some basic aspects of NMR

    International Nuclear Information System (INIS)

    Goldman, M.

    1992-01-01

    The principal interactions are reviewed that are experienced by nuclear spins making magnetic resonance feasible and which disturb it in a way that gives access to the properties of bulk matter. The interactions leading to NMR include Zeeman interaction, dipole-dipole interactions, and exchange interactions. Spin-lattice relaxation relevant to NMR is revisited next. It is followed by an overview of spin temperature. Finally, the care of periodic Hamiltonian is discussed in detail as another contribution to NMR. (R.P.) 48 refs., 12 figs

  18. NMR study of LaPb2

    International Nuclear Information System (INIS)

    Ueda, K.; Kohara, T.; Yamada, Y.

    1995-01-01

    La and Pb NMR signals were observed in LaPb 2 with a superconducting transition temperature of about 7 K. The width of the Pb NMR spectrum with an asymmetric line shape was rather narrower than those of Er-, Gd- and Ho-Pb 2 . The spin-lattice relaxation time of Pb nuclei was twice longer than that of Pb metal. La NMR spectrum had satellites due to the electric quadrupole interaction. These results show that each local environment at La or Pb site in LaPb 2 compound is uniquely determined, compared with those in randomly substituted alloys. ((orig.))

  19. Graphical programming for pulse automated NMR experiments

    International Nuclear Information System (INIS)

    Belmonte, S.B.; Oliveira, I.S.; Guimaraes, A.P.

    1999-01-01

    We describe a software program designed to control a broadband pulse Nuclear Magnetic Resonance (NMR) spectrometer used in zero-field NMR studies of magnetic metals. The software is written in the graphical language LabVIEW. This type of programming allows modifications and the inclusion of new routines to be easily made by the non-specialist, without changing the basic structure of the program. The program corrects for differences in the gain of the two acquisition channels [U (phase) and V (quadrature)], and automatic baseline subtraction. We present examples of measurements of NMR spectra, spin-echo decay (T 2 ), and quadrupolar oscillations, performed in magnetic intermetallic compounds. (author)

  20. The characterisation of polymers using pulsed NMR

    International Nuclear Information System (INIS)

    Charlesby, A.

    1983-01-01

    Broad line pulsed NMR is applied to obtain information on radiation-induced polymer changes and other aspects of polymer science based on the interpretation of spin-spin relaxation curves. Calculations are made to determine the molecular weight, the crosslink density of simple, low molecular weight, flexible polymers. For higher molecular weight polymers, a conclusion can be drawn on the concentrations of entangled and crosslinked units by means of pulsed NMR. Some typical applications of the technique are illustrated by the examples of polyethylenes, rubbers, filled polymeric systems and aqueous polyethylene oxide solutions. The morphology of polymers can be followed by pulsed NMR. (V.N.)

  1. MAS NMR of HIV-1 protein assemblies

    Science.gov (United States)

    Suiter, Christopher L.; Quinn, Caitlin M.; Lu, Manman; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

    2015-04-01

    The negative global impact of the AIDS pandemic is well known. In this perspective article, the utility of magic angle spinning (MAS) NMR spectroscopy to answer pressing questions related to the structure and dynamics of HIV-1 protein assemblies is examined. In recent years, MAS NMR has undergone major technological developments enabling studies of large viral assemblies. We discuss some of these evolving methods and technologies and provide a perspective on the current state of MAS NMR as applied to the investigations into structure and dynamics of HIV-1 assemblies of CA capsid protein and of Gag maturation intermediates.

  2. Wild immunology assessed by multidimensional mass cytometry.

    Science.gov (United States)

    Japp, Alberto Sada; Hoffmann, Kerstin; Schlickeiser, Stephan; Glauben, Rainer; Nikolaou, Christos; Maecker, Holden T; Braun, Julian; Matzmohr, Nadine; Sawitzki, Birgit; Siegmund, Britta; Radbruch, Andreas; Volk, Hans-Dieter; Frentsch, Marco; Kunkel, Desiree; Thiel, Andreas

    2017-01-01

    A great part of our knowledge on mammalian immunology has been established in laboratory settings. The use of inbred mouse strains enabled controlled studies of immune cell and molecule functions in defined settings. These studies were usually performed in specific-pathogen free (SPF) environments providing standardized conditions. In contrast, mammalians including humans living in their natural habitat are continuously facing pathogen encounters throughout their life. The influences of environmental conditions on the signatures of the immune system and on experimental outcomes are yet not well defined. Thus, the transferability of results obtained in current experimental systems to the physiological human situation has always been a matter of debate. Studies elucidating the diversity of "wild immunology" imprintings in detail and comparing it with those of "clean" lab mice are sparse. Here, we applied multidimensional mass cytometry to dissect phenotypic and functional differences between distinct groups of laboratory and pet shop mice as a source for "wild mice". For this purpose, we developed a 31-antibody panel for murine leukocyte subsets identification and a 35-antibody panel assessing various cytokines. Established murine leukocyte populations were easily identified and diverse immune signatures indicative of numerous pathogen encounters were classified particularly in pet shop mice and to a lesser extent in quarantine and non-SPF mice as compared to SPF mice. In addition, unsupervised analysis identified distinct clusters that associated strongly with the degree of pathogenic priming, including increased frequencies of activated NK cells and antigen-experienced B- and T-cell subsets. Our study unravels the complexity of immune signatures altered under physiological pathogen challenges and highlights the importance of carefully adapting laboratory settings for immunological studies in mice, including drug and therapy testing. © 2016 International Society

  3. Multidimensional analysis: B-tagging at LEP

    International Nuclear Information System (INIS)

    de la Vaissiere, C.; Palma-Lopes, S.

    1989-01-01

    At the Z 0 , the cross-section for e + e - → b anti b is large (6.5 nb), as is the fraction of hadronic events leading to b anti b (22%). A jet topology allows to distinguish naturally the products of the b and anti b fragmentation and decays. The Z 0 looks therefore an attractive place to pursue B physics. Techniques previously used at PEP and PETRA to tag the b-flavor, have provided reasonable b-purities, at the cost of poor efficiencies. A first technique originally proposed to measure the b-lifetime was to use leptonic decays, but the corresponding branching ratios are at the 10% level. At Z 0 energies, P. Roudeau shows that a 91% purity and 6% efficiency can be obtained. The TASSO collaboration was the first to use a vertex detector for b-enrichment. They achieved a b-purity of about 68%, with a 16%-efficiency. The best way to increase these low yields is to improve the resolution of vertex detectors on impact parameters. DELPHI will be equipped with a silicon microstrip vertex detector which will provide an asymptotic accuracy of 20 μm on impact parameters in the plane transverse to the beam, to be compared with the 150 μm quoted by TASSO. However this 20 μm, combined with limited coverage, can not disentangle the multiple decays occurring in a b anti b event. In this intermediate situation multidimensional analysis may provide tagging of b anti b events with high purity and good efficiency. 11 refs., 2 figs., 2 tabs

  4. PERSPECTIVA MULTIDIMENSIONAL DO TRABALHO NA CONTEMPORANEIDADE

    Directory of Open Access Journals (Sweden)

    Lilian Carminatti

    2015-12-01

    Full Text Available O objetivo deste estudo é analisar a evolução do tema trabalho e novas formas de flexibilização das relações laborais que proporcionam identidade, significado e bem-estar. O trabalho, como uma atividade prazerosa, passa por uma mudança de postura das pessoas frente à atividade ocupacional, a partir do autoconhecimento, planejamento de carreira e de uma jornada de trabalho que vislumbre a melhora na qualidade de vida. A promoção do bem-estar presume a articulação entre as relações de trabalho atravessadas pelo sistema capitalista e a importância de equilibrar necessidades individuais e a competitividade organizacional. Como elementos balizadores surgem: a relação com os significados do trabalho, o planejamento de carreira e pós-carreira e a conexão entre valores pessoais e organizacionais. Adotou-se para a pesquisa uma estratégia metodológica qualitativa que se propõe a investigar a partir da exploração e descrição as dimensões do tema trabalho na sociedade contemporânea. Dessa forma, a promoção do bem-estar e o planejamento de carreira devem ser tratados como planejamento de vida durante todo o período funcional, a partir de uma visão multidimensional do colaborador inserida em um amplo contexto cultural e social que ultrapassa o ambiente organizacional.

  5. SAGE - MULTIDIMENSIONAL SELF-ADAPTIVE GRID CODE

    Science.gov (United States)

    Davies, C. B.

    1994-01-01

    SAGE, Self Adaptive Grid codE, is a flexible tool for adapting and restructuring both 2D and 3D grids. Solution-adaptive grid methods are useful tools for efficient and accurate flow predictions. In supersonic and hypersonic flows, strong gradient regions such as shocks, contact discontinuities, shear layers, etc., require careful distribution of grid points to minimize grid error and produce accurate flow-field predictions. SAGE helps the user obtain more accurate solutions by intelligently redistributing (i.e. adapting) the original grid points based on an initial or interim flow-field solution. The user then computes a new solution using the adapted grid as input to the flow solver. The adaptive-grid methodology poses the problem in an algebraic, unidirectional manner for multi-dimensional adaptations. The procedure is analogous to applying tension and torsion spring forces proportional to the local flow gradient at every grid point and finding the equilibrium position of the resulting system of grid points. The multi-dimensional problem of grid adaption is split into a series of one-dimensional problems along the computational coordinate lines. The reduced one dimensional problem then requires a tridiagonal solver to find the location of grid points along a coordinate line. Multi-directional adaption is achieved by the sequential application of the method in each coordinate direction. The tension forces direct the redistribution of points to the strong gradient region. To maintain smoothness and a measure of orthogonality of grid lines, torsional forces are introduced that relate information between the family of lines adjacent to one another. The smoothness and orthogonality constraints are direction-dependent, since they relate only the coordinate lines that are being adapted to the neighboring lines that have already been adapted. Therefore the solutions are non-unique and depend on the order and direction of adaption. Non-uniqueness of the adapted grid is

  6. Subrandom methods for multidimensional nonuniform sampling.

    Science.gov (United States)

    Worley, Bradley

    2016-08-01

    Methods of nonuniform sampling that utilize pseudorandom number sequences to select points from a weighted Nyquist grid are commonplace in biomolecular NMR studies, due to the beneficial incoherence introduced by pseudorandom sampling. However, these methods require the specification of a non-arbitrary seed number in order to initialize a pseudorandom number generator. Because the performance of pseudorandom sampling schedules can substantially vary based on seed number, this can complicate the task of routine data collection. Approaches such as jittered sampling and stochastic gap sampling are effective at reducing random seed dependence of nonuniform sampling schedules, but still require the specification of a seed number. This work formalizes the use of subrandom number sequences in nonuniform sampling as a means of seed-independent sampling, and compares the performance of three subrandom methods to their pseudorandom counterparts using commonly applied schedule performance metrics. Reconstruction results using experimental datasets are also provided to validate claims made using these performance metrics. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. 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.

  8. NMR mechanisms in gel dosimetry

    International Nuclear Information System (INIS)

    Schreiner, L J

    2009-01-01

    Nuclear magnetic resonance was critical to the development of gel dosimetry, as it established the potential for three dimensional dosimetry with chemical dosimeter systems through magnetic resonance imaging [1]. In the last two decades MRI has served as the gold standard for imaging, while NMR relaxometry has played an important role in the development and understanding of the behaviour of new gel dosimetry systems. Therefore, an appreciation of the relaxation mechanisms determining the NMR behaviour of irradiated gel dosimeters is important for a full comprehension of a considerable component of the literature on gel dosimetry. A number of excellent papers have presented this important theory, this brief review will highlight some of the salient points made previously [1-5]. The spin relaxation of gel dosimeters (which determines the dose dependence in most conventional MR imaging) is determined principally by the protons on water molecules in the system. These water protons exist in different environments, or groups (see Figure 1): on bulk water, on water hydrating the chemical species that are being modified under irradiation, and on water hydrating the gel matrix used to spatially stabilize the dosimeter (e.g., gelatin, agarose, etc). The spin relaxation depends on the inherent relaxation rate of each spin group, that is, on the relaxation rate which would be observed for the specific group if it were isolated. Also, the different water environments are not isolated from each other, and the observed relaxation rate also depends on the rate of exchange of magnetization between the groups, and on the fraction of protons in each group. In fact, the water exchanges quickly between the environments, so that relaxation is in what is usually termed the fast exchange regime. In the limit of fast exchange, the relaxation of the water protons is well characterized by a single exponential and hence by a single apparent relaxation rate. In irradiated gel dosimeters this

  9. Structural investigations of substituted indolizine derivatives by NMR studies

    International Nuclear Information System (INIS)

    Furdui, Bianca; Dinica, Rodica; Demeunynck, Martine; Druta, Ioan

    2008-01-01

    Owing to the increasing importance of indolizine heterocycles in the field of biology and pharmacology we have synthesized and investigated the obtained heterocycles by NMR techniques. In order to investigate the substituent effects on the spectroscopic properties, a series of indolizine derivatives were studied by 1 H-NMR, 13 C-NMR and 2D NMR (GCOSY, GHMBC and GHMQC spectra). (authors)

  10. NMR in the SPINE Structural Proteomics project.

    Science.gov (United States)

    Ab, E; Atkinson, A R; Banci, L; Bertini, I; Ciofi-Baffoni, S; Brunner, K; Diercks, T; Dötsch, V; Engelke, F; Folkers, G E; Griesinger, C; Gronwald, W; Günther, U; Habeck, M; de Jong, R N; Kalbitzer, H R; Kieffer, B; Leeflang, B R; Loss, S; Luchinat, C; Marquardsen, T; Moskau, D; Neidig, K P; Nilges, M; Piccioli, M; Pierattelli, R; Rieping, W; Schippmann, T; Schwalbe, H; Travé, G; Trenner, J; Wöhnert, J; Zweckstetter, M; Kaptein, R

    2006-10-01

    This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.

  11. NMR study of Albemoschus esculentus characterization

    International Nuclear Information System (INIS)

    Bathista, A.L.B.S; Silva, E.O.; Nogueira, Jose de S.; Tavares, M.I.B.

    2001-01-01

    The investigation of the main compounds presented in the Albemoschus esculentus has been carried out employing nuclear magnetic resonance spectroscopy (NMR), using solution and solid state NMR when it one was necessary. The evaluation of NMR data allowed us to characterize the main type of components presented in this kind of sample. It was necessary to use a total information from solid state NMR and also the solution response. From these information we could get that four main components were presented in this sample. One in the shell, that is cellulose, another one between the shell and seeds that is a polysaccharide and in the seed two components were found one is a starch and the second one is an oil, a triacylglycerol. These components are responsible by its physical chemistry properties. (author)

  12. Bayesian Peak Picking for NMR Spectra

    KAUST Repository

    Cheng, Yichen

    2014-02-01

    Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

  13. NMR and optical studies of piezoelectric polymers

    International Nuclear Information System (INIS)

    Schmidt, V.H.; Tuthill, G.F.

    1993-01-01

    Progress is reported in several areas dealing with piezoelectric (electroactive) polymers (mostly vinylidene fluoride, trifluoroethylene, copolymers, PVF 2 ) and liquid crystals. Optical studies, neutron scattering, NMR, thermal, theory and modeling were done

  14. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    2012-01-01

    High Resolution NMR: Theory and Chemical Applications discusses the principles and theory of nuclear magnetic resonance and how this concept is used in the chemical sciences. This book is written at an intermediate level, with mathematics used to augment verbal descriptions of the phenomena. This text pays attention to developing and interrelating four approaches - the steady state energy levels, the rotating vector picture, the density matrix, and the product operator formalism. The style of this book is based on the assumption that the reader has an acquaintance with the general principles of quantum mechanics, but no extensive background in quantum theory or proficiency in mathematics is required. This book begins with a description of the basic physics, together with a brief account of the historical development of the field. It looks at the study of NMR in liquids, including high resolution NMR in the solid state and the principles of NMR imaging and localized spectroscopy. This book is intended to assis...

  15. NMR studies of cerebral metabolism in vivo

    International Nuclear Information System (INIS)

    Prichard, J.W.

    1986-01-01

    The nature and extent of the potential synergism between PET and NMR methods is not yet well appreciated in the biomedical community. The long-range interest of medical neurobiology will be well served by efforts of PET and NMR scientists to follow each others' work so that opportunities for productive interchange can be efficiently exploited. Appreciation of the synergism by the rest of the biomedical community will follow naturally. PET is said by the people doing it to be still in its infancy, for they are more concerned with advancing their discipline than with admiring its already impressive achievements. On the scale of the same developmental metaphor, many NMR methods for studying the living human brain are still in utero. The best way to provide the reader a sense of the current status and future course of NMR research in medical neurobiology is by discussion of published in vivo studies. Such a discussion, adapted from another article is what follows

  16. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Development of Two-Dimensional NMR: Strucure Determination of Biomolecules in Solution. Anil Kumar. General Article Volume 20 Issue 11 November 2015 pp 995-1002 ...

  17. NMR spectroscopy of coal pyrolysis products

    Energy Technology Data Exchange (ETDEWEB)

    Polonov, V.M.; Kalabin, G.A.; Kushnarev, D.F.; Shevchenko, G.G.

    1985-12-01

    The authors consider the scope for using H 1 and C 13 NMR spectroscopy to describe the products from coal pyrolysis and hydrogenization. The accuracy of the structural information provided by the best NMR methods is also considered. The stuctural parameters derived from H 1 and C 13 NMR spectra are presented. Results demonstrate the high accuracy and sensitivity of the structural information provided by H 1 AND C 13 NMR spectra for coal products. There are substantial structural differences between the soluble products from medium-temperature coking of Cheremkhov coal and high-speed pyrolysis of Kan-Acha coal, and also differences in behavior during hydrogenation. These differences are related to the structure of the organic matter in the initial coal and to differences in the pyrolysis mechanisms.

  18. NMR study of hydride systems

    International Nuclear Information System (INIS)

    Peretz, M.

    1980-02-01

    The hydrides of thorium (ThH 2 , Th 4 H 15 and Th 4 D 15 ) and the intermetallic compound system (Zr(Vsub(1-x)Cosub(x)) 2 and its hydrides were investigated using the nuclear magnetic resonance (NMR) technique. From the results for the thorium hydride samples it was concluded that the density of states at the Fermi level n(Esub(f)) is higher in Th 4 H 15 than in ThH 2 ; there is an indirect reaction between the protons and the d electrons belonging to the Th atoms in Th 4 H 15 ; n(E) has a sharp structure near Esub(f). It was also found that the hydrogen diffusion mechanism changes with temperature. From the results for the intermetallic compound system conclusions were drawn concerning variations in the electronic structure, which explain the behavior of the system. In hydrogen diffusion studies in several samples it was found that Co atoms slow the diffusion rate. Quadrupole spectra obtained at low temperatures show that the H atoms preferably occupy tetrahedral sites formed by three V atoms and one Z atom. (H.K.)

  19. Frontiers of NMR in Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  20. NMR studies of multiphase flows II

    Energy Technology Data Exchange (ETDEWEB)

    Altobelli, S.A.; Caprihan, A.; Fukushima, E. [Lovelace Institutes, Albuquerque, NM (United States)] [and others

    1995-12-31

    NMR techniques for measurements of spatial distribution of material phase, velocity and velocity fluctuation are being developed and refined. Versions of these techniques which provide time average liquid fraction and fluid phase velocity have been applied to several concentrated suspension systems which will not be discussed extensively here. Technical developments required to further extend the use of NMR to the multi-phase flow arena and to provide measurements of previously unobtainable parameters are the focus of this report.

  1. observed by high pressure NMR and NQR

    Indian Academy of Sciences (India)

    Akogun, Hyogo 678-1297, Japan. ∗. Email: kohara@sci.himeji tech.ac.jp. Abstract. NMR and NQR studies on two interesting systems (URu2Si2, CeTIn5) were performed under high pressure. (1) URu2Si2: In the pressure range 3.0 to 8.3 kbar, we have observed new 29Si. NMR signals arising from the antiferromagnetic ...

  2. Multidimensional scaling for large genomic data sets

    Directory of Open Access Journals (Sweden)

    Lu Henry

    2008-04-01

    Full Text Available Abstract Background Multi-dimensional scaling (MDS is aimed to represent high dimensional data in a low dimensional space with preservation of the similarities between data points. This reduction in dimensionality is crucial for analyzing and revealing the genuine structure hidden in the data. For noisy data, dimension reduction can effectively reduce the effect of noise on the embedded structure. For large data set, dimension reduction can effectively reduce information retrieval complexity. Thus, MDS techniques are used in many applications of data mining and gene network research. However, although there have been a number of studies that applied MDS techniques to genomics research, the number of analyzed data points was restricted by the high computational complexity of MDS. In general, a non-metric MDS method is faster than a metric MDS, but it does not preserve the true relationships. The computational complexity of most metric MDS methods is over O(N2, so that it is difficult to process a data set of a large number of genes N, such as in the case of whole genome microarray data. Results We developed a new rapid metric MDS method with a low computational complexity, making metric MDS applicable for large data sets. Computer simulation showed that the new method of split-and-combine MDS (SC-MDS is fast, accurate and efficient. Our empirical studies using microarray data on the yeast cell cycle showed that the performance of K-means in the reduced dimensional space is similar to or slightly better than that of K-means in the original space, but about three times faster to obtain the clustering results. Our clustering results using SC-MDS are more stable than those in the original space. Hence, the proposed SC-MDS is useful for analyzing whole genome data. Conclusion Our new method reduces the computational complexity from O(N3 to O(N when the dimension of the feature space is far less than the number of genes N, and it successfully

  3. NMRbox: A Resource for Biomolecular NMR Computation.

    Science.gov (United States)

    Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

    2017-04-25

    Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

  4. A microscale protein NMR sample screening pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Rossi, Paolo; Swapna, G. V. T.; Huang, Yuanpeng J.; Aramini, James M. [State University of New Jersey, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers (United States); Anklin, Clemens [Bruker Biospin Corporation (United States); Conover, Kenith; Hamilton, Keith; Xiao, Rong; Acton, Thomas B.; Ertekin, Asli; Everett, John K.; Montelione, Gaetano T., E-mail: guy@cabm.rutgers.ed [State University of New Jersey, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers (United States)

    2010-01-15

    As part of efforts to develop improved methods for NMR protein sample preparation and structure determination, the Northeast Structural Genomics Consortium (NESG) has implemented an NMR screening pipeline for protein target selection, construct optimization, and buffer optimization, incorporating efficient microscale NMR screening of proteins using a micro-cryoprobe. The process is feasible because the newest generation probe requires only small amounts of protein, typically 30-200 {mu}g in 8-35 {mu}l volume. Extensive automation has been made possible by the combination of database tools, mechanization of key process steps, and the use of a micro-cryoprobe that gives excellent data while requiring little optimization and manual setup. In this perspective, we describe the overall process used by the NESG for screening NMR samples as part of a sample optimization process, assessing optimal construct design and solution conditions, as well as for determining protein rotational correlation times in order to assess protein oligomerization states. Database infrastructure has been developed to allow for flexible implementation of new screening protocols and harvesting of the resulting output. The NESG micro NMR screening pipeline has also been used for detergent screening of membrane proteins. Descriptions of the individual steps in the NESG NMR sample design, production, and screening pipeline are presented in the format of a standard operating procedure.

  5. O-17 NMR measurement of water

    International Nuclear Information System (INIS)

    Fukazawa, Nobuyuki

    1990-01-01

    Recently, attention has been paid to the various treatment of water and the utilization of water by magnetic treatment, electric field treatment and so on. It has been said that by these treatments, the change in the properties of water arises. The state of this treated water cannot be explained by the properties of water from conventional physical and chemical standpoints. In addition, the method of measurement of whether the change arose or not is not yet determined. It is necessary to establish the method of measurement for the basic state of water. In this study, O-17 NMR which observes the state of water directly at molecular or atomic level was investigated as the method of measuring water. The measurement of O-17 NMR was carried out with a JNR 90Q FT NMR of Fourier transformation type of JEOL Ltd. The experimental method and the results are reported. The result of measurement of the O-17 NMR spectrum for distilled ion exchange water is shown. It is know that it has very wide line width as compared with the NMR spectra of protons and C-13. The relative sensitivity of O-17 observation is about 1/100,000 of that of protons. As to the information on the state of water obtained by O-17 NMR, there are chemical shift and line width. As temperature rose, the line width showed decrease, which seemed to be related to the decrease of hydrogen combination. (K.I.)

  6. Activation and thermodynamic parameter study of the heteronuclear C=O···H-N hydrogen bonding of diphenylurethane isomeric structures by FT-IR spectroscopy using the regularized inversion of an eigenvalue problem.

    Science.gov (United States)

    Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro

    2012-08-02

    The doublet of the ν(C=O) carbonyl band in isomeric urethane systems has been extensively discussed in qualitative terms on the basis of FT-IR spectroscopy of the macromolecular structures. Recently, a reaction extent model was proposed as an inverse kinetic problem for the synthesis of diphenylurethane for which hydrogen-bonded and non-hydrogen-bonded C=O functionalities were identified. In this article, the heteronuclear C=O···H-N hydrogen bonding in the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol was investigated via FT-IR spectroscopy, using a methodology of regularization for the inverse reaction extent model through an eigenvalue problem. The kinetic and thermodynamic parameters of this system were derived directly from the spectroscopic data. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied. The study determined the enthalpy (ΔH = 15.25 kJ/mol), entropy (TΔS = 14.61 kJ/mol), and free energy (ΔG = 0.6 kJ/mol) of heteronuclear C=O···H-N hydrogen bonding by FT-IR spectroscopy through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S, and δΔ(‡)G) at equilibrium in the chemical reaction system. The parameters obtained in this study may contribute toward a better understanding of the properties of, and interactions in, supramolecular systems, such as the switching behavior of hydrogen bonding.

  7. Automated Peak Picking and Peak Integration in Macromolecular NMR Spectra Using AUTOPSY

    Science.gov (United States)

    Koradi, Reto; Billeter, Martin; Engeli, Max; Güntert, Peter; Wüthrich, Kurt

    1998-12-01

    A new approach for automated peak picking of multidimensional protein NMR spectra with strong overlap is introduced, which makes use of the program AUTOPSY (automatedpeak picking for NMRspectroscopy). The main elements of this program are a novel function for local noise level calculation, the use of symmetry considerations, and the use of lineshapes extracted from well-separated peaks for resolving groups of strongly overlapping peaks. The algorithm generates peak lists with precise chemical shift and integral intensities, and a reliability measure for the recognition of each peak. The results of automated peak picking of NOESY spectra with AUTOPSY were tested in combination with the combined automated NOESY cross peak assignment and structure calculation routine NOAH implemented in the program DYANA. The quality of the resulting structures was found to be comparable with those from corresponding data obtained with manual peak picking.

  8. Basics of spectroscopic instruments. Hardware of NMR spectrometer

    International Nuclear Information System (INIS)

    Sato, Hajime

    2009-01-01

    NMR is a powerful tool for structure analysis of small molecules, natural products, biological macromolecules, synthesized polymers, samples from material science and so on. Magnetic Resonance Imaging (MRI) is applicable to plants and animals Because most of NMR experiments can be done by an automation mode, one can forget hardware of NMR spectrometers. It would be good to understand features and performance of NMR spectrometers. Here I present hardware of a modern NMR spectrometer which is fully equipped with digital technology. (author)

  9. 33S NMR cryogenic probe for taurine detection

    Science.gov (United States)

    Hobo, Fumio; Takahashi, Masato; Maeda, Hideaki

    2009-03-01

    With the goal of a S33 nuclear magnetic resonance (NMR) probe applicable to in vivo NMR on taurine-biological samples, we have developed the S33 NMR cryogenic probe, which is applicable to taurine solutions. The NMR sensitivity gain relative to a conventional broadband probe is as large as 3.5. This work suggests that improvements in the preamplifier could allow NMR measurements on 100 μM taurine solutions, which is the level of sensitivity necessary for biological samples.

  10. Petrophysical properties of greensand as predicted from NMR measurements

    DEFF Research Database (Denmark)

    Hossain, Zakir; Grattoni, Carlos A.; Solymar, Mikael

    2011-01-01

    ABSTRACT: Nuclear magnetic resonance (NMR) is a useful tool in reservoir evaluation. The objective of this study is to predict petrophysical properties from NMR T2 distributions. A series of laboratory experiments including core analysis, capillary pressure measurements, NMR T2 measurements...... with macro-pores. Permeability may be predicted from NMR by using Kozeny's equation when surface relaxivity is known. Capillary pressure drainage curves may be predicted from NMR T2 distribution when pore size distribution within a sample is homogeneous....

  11. NMR experiments for resonance assignments of 13C, 15N doubly-labeled flexible polypeptides: Application to the human prion protein hPrP(23-230)

    International Nuclear Information System (INIS)

    Liu Aizhuo; Riek, Roland; Wider, Gerhard; Schroetter, Christine von; Zahn, Ralph; Wuethrich, Kurt

    2000-01-01

    A combination of three heteronuclear three-dimensional NMR experiments tailored for sequential resonance assignments in uniformly 15 N, 13 C-labeled flexible polypeptide chains is described. The 3D (H)N(CO-TOCSY)NH, 3D (H)CA(CO-TOCSY)NH and 3D (H)CBCA(CO-TOCSY)NH schemes make use of the favorable 15 N chemical shift dispersion in unfolded polypeptides, exploit the slow transverse 15 N relaxation rates of unfolded polypeptides in high resolution constant-time [ 1 H, 15 N]-correlation experiments, and use carbonyl carbon homonuclear isotropic mixing to transfer magnetization sequentially along the amino acid sequence. Practical applications are demonstrated with the 100-residue flexible tail of the recombinant human prion protein, making use of spectral resolution up to 0.6 Hz in the 15 N dimension, simultaneous correlation with the two adjacent amino acid residues to overcome problems associated with spectral overlap, and the potential of the presently described experiments to establish nearest-neighbor correlations across proline residues in the amino acid sequence

  12. Understanding API-polymer proximities in amorphous stabilized composite drug products using fluorine-carbon 2D HETCOR solid-state NMR.

    Science.gov (United States)

    Abraham, Anuji; Crull, George

    2014-10-06

    A simple and robust method for obtaining fluorine-carbon proximities was established using a (19)F-(13)C heteronuclear correlation (HETCOR) two-dimensional (2D) solid-state nuclear magnetic resonance (ssNMR) experiment under magic-angle spinning (MAS). The method was applied to study a crystalline active pharmaceutical ingredient (API), avagacestat, containing two types of fluorine atoms and its API-polymer composite drug product. These results provide insight into the molecular structure, aid with assigning the carbon resonances, and probe API-polymer proximities in amorphous spray dried dispersions (SDD). This method has an advantage over the commonly used (1)H-(13)C HETCOR because of the large chemical shift dispersion in the fluorine dimension. In the present study, fluorine-carbon distances up to 8 Å were probed, giving insight into the API structure, crystal packing, and assignments. Most importantly, the study demonstrates a method for probing an intimate molecular level contact between an amorphous API and a polymer in an SDD, giving insights into molecular association and understanding of the role of the polymer in API stability (such as recrystallization, degradation, etc.) in such novel composite drug products.

  13. Visual modeling in an analysis of multidimensional data

    Science.gov (United States)

    Zakharova, A. A.; Vekhter, E. V.; Shklyar, A. V.; Pak, A. J.

    2018-01-01

    The article proposes an approach to solve visualization problems and the subsequent analysis of multidimensional data. Requirements to the properties of visual models, which were created to solve analysis problems, are described. As a perspective direction for the development of visual analysis tools for multidimensional and voluminous data, there was suggested an active use of factors of subjective perception and dynamic visualization. Practical results of solving the problem of multidimensional data analysis are shown using the example of a visual model of empirical data on the current state of studying processes of obtaining silicon carbide by an electric arc method. There are several results of solving this problem. At first, an idea of possibilities of determining the strategy for the development of the domain, secondly, the reliability of the published data on this subject, and changes in the areas of attention of researchers over time.

  14. A new multidimensional model with text dimensions: definition and implementation

    Directory of Open Access Journals (Sweden)

    MariaJ. Martin-Bautista

    2013-02-01

    Full Text Available We present a new multidimensional model with textual dimensions based on a knowledge structure extracted from the texts, where any textual attribute in a database can be processed, and not only XML texts. This dimension allows to treat the textual data in the same way as the non-textual one in an automatic way, without user's intervention, so all the classical operations in the multidimensional model can been defined for this textual dimension. While most of the models dealing with texts that can be found in the literature are not implemented, in this proposal, the multidimensional model and the OLAP system have been implemented in a software tool, so it can be tested on real data. A case study with medical data is included in this work.

  15. Multidimensional poverty: an alternative measurement approach for the United States?

    Science.gov (United States)

    Waglé, Udaya R

    2008-06-01

    International poverty research has increasingly underscored the need to use multidimensional approaches to measure poverty. Largely embraced in Europe and elsewhere, this has not had much impact on the way poverty is measured in the United States. In this paper, I use a comprehensive multidimensional framework including economic well-being, capability, and social inclusion to examine poverty in the US. Data from the 2004 General Social Survey support the interconnectedness among these poverty dimensions, indicating that the multidimensional framework utilizing a comprehensive set of information provides a compelling value added to poverty measurement. The suggested demographic characteristics of the various categories of the poor are somewhat similar between this approach and other traditional approaches. But the more comprehensive and accurate measurement outcomes from this approach help policymakers target resources at the specific groups.

  16. Multidimensional Scaling Localization Algorithm in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Zhang Dongyang

    2014-02-01

    Full Text Available Due to the localization algorithm in large-scale wireless sensor network exists shortcomings both in positioning accuracy and time complexity compared to traditional localization algorithm, this paper presents a fast multidimensional scaling location algorithm. By positioning algorithm for fast multidimensional scaling, fast mapping initialization, fast mapping and coordinate transform can get schematic coordinates of node, coordinates Initialize of MDS algorithm, an accurate estimate of the node coordinates and using the PRORUSTES to analysis alignment of the coordinate and final position coordinates of nodes etc. There are four steps, and the thesis gives specific implementation steps of the algorithm. Finally, compared with stochastic algorithms and classical MDS algorithm experiment, the thesis takes application of specific examples. Experimental results show that: the proposed localization algorithm has fast multidimensional scaling positioning accuracy in ensuring certain circumstances, but also greatly improves the speed of operation.

  17. Quantum and Multidimensional Explanations in a Neurobiological Context of Mind.

    Science.gov (United States)

    Korf, Jakob

    2015-08-01

    This article examines the possible relevance of physical-mathematical multidimensional or quantum concepts aiming at understanding the (human) mind in a neurobiological context. Some typical features of the quantum and multidimensional concepts are briefly introduced, including entanglement, superposition, holonomic, and quantum field theories. Next, we consider neurobiological principles, such as the brain and its emerging (physical) mind, evolutionary and ontological origins, entropy, syntropy/neg-entropy, causation, and brain energy metabolism. In many biological processes, including biochemical conversions, protein folding, and sensory perception, the ubiquitous involvement of quantum mechanisms is well recognized. Quantum and multidimensional approaches might be expected to help describe and model both brain and mental processes, but an understanding of their direct involvement in mental activity, that is, without mediation by molecular processes, remains elusive. More work has to be done to bridge the gap between current neurobiological and physical-mathematical concepts with their associated quantum-mind theories. © The Author(s) 2014.

  18. Conservative Initial Mapping For Multidimensional Simulations of Stellar Explosions

    International Nuclear Information System (INIS)

    Chen, Ke-Jung; Heger, Alexander; Almgren, Ann

    2012-01-01

    Mapping one-dimensional stellar profiles onto multidimensional grids as initial conditions for hydrodynamics calculations can lead to numerical artifacts, one of the most severe of which is the violation of conservation laws for physical quantities such as energy and mass. Here we introduce a numerical scheme for mapping one-dimensional spherically-symmetric data onto multidimensional meshes so that these physical quantities are conserved. We validate our scheme by porting a realistic 1D Lagrangian stellar profile to the new multidimensional Eulerian hydro code CASTRO. Our results show that all important features in the profiles are reproduced on the new grid and that conservation laws are enforced at all resolutions after mapping.

  19. Multiple acquisition of magic angle spinning solid-state NMR experiments using one receiver: Application to microcrystalline and membrane protein preparations

    Science.gov (United States)

    Gopinath, T.; Veglia, Gianluigi

    2015-04-01

    Solid-state NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POE allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this perspective, we describe the first generation of POE, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic nuclear polarization (DNP), to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes.

  20. Continuous Flow 1H and 13C NMR Spectroscopy in Microfluidic Stripline NMR Chips

    NARCIS (Netherlands)

    Oosthoek-de Vries, Anna Jo; Bart, Jacob; Tiggelaar, Roald M.; Janssen, Johannes W.G.; van Bentum, Jan (P.J.M.); Gardeniers, Han J.G.E.; Kentgens, Arno P.M.

    2017-01-01

    Microfluidic stripline NMR technology not only allows for NMR experiments to be performed on small sample volumes in the submicroliter range, but also experiments can easily be performed in continuous flow because of the stripline's favorable geometry. In this study we demonstrate the possibility of

  1. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

    Science.gov (United States)

    van der Schot, Gijs; Bonvin, Alexandre M J J

    2015-08-01

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

  2. Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks

    Science.gov (United States)

    Simpson, Andre J.; Shirzadi, Azadeh; Burrow, Timothy E.; Dicks, Andrew P.; Lefebvre, Brent; Corrin, Tricia

    2009-01-01

    A laboratory experiment designed as part of an upper-level undergraduate analytical chemistry course is described. Students investigate two popular soft drinks (Red Bull Energy Drink and sugar-free Red Bull Energy Drink) by NMR spectroscopy. With assistance of modern NMR prediction software they identify and quantify major components in each…

  3. New methods for the correction of 31P NMR spectra in in vivo NMR spectroscopy

    International Nuclear Information System (INIS)

    Starcuk, Z.; Bartusek, K.; Starcuk, Z. jr.

    1994-01-01

    The new methods for the correction of 31 P NMR spectra in vivo NMR spectroscopy have been performed. A method for the baseline correction of the spectra which represents a combination of time-domain and frequency-domain has been discussed.The method is very fast and efficient for minimization of base line artifacts of biological tissues impact

  4. Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands.

    Science.gov (United States)

    Shemon, Anne N; Heil, Gary L; Granovsky, Alexey E; Clark, Mathew M; McElheny, Dan; Chimon, Alexander; Rosner, Marsha R; Koide, Shohei

    2010-05-05

    Raf kinase inhibitory protein (RKIP), also known as phoshaptidylethanolamine binding protein (PEBP), has been shown to inhibit Raf and thereby negatively regulate growth factor signaling by the Raf/MAP kinase pathway. RKIP has also been shown to suppress metastasis. We have previously demonstrated that RKIP/Raf interaction is regulated by two mechanisms: phosphorylation of RKIP at Ser-153, and occupation of RKIP's conserved ligand binding domain with a phospholipid (2-dihexanoyl-sn-glycero-3-phosphoethanolamine; DHPE). In addition to phospholipids, other ligands have been reported to bind this domain; however their binding properties remain uncharacterized. In this study, we used high-resolution heteronuclear NMR spectroscopy to screen a chemical library and assay a number of potential RKIP ligands for binding to the protein. Surprisingly, many compounds previously postulated as RKIP ligands showed no detectable binding in near-physiological solution conditions even at millimolar concentrations. In contrast, we found three novel ligands for RKIP that specifically bind to the RKIP pocket. Interestingly, unlike the phospholipid, DHPE, these newly identified ligands did not affect RKIP binding to Raf-1 or RKIP phosphorylation. One out of the three ligands displayed off target biological effects, impairing EGF-induced MAPK and metabolic activity. This work defines the binding properties of RKIP ligands under near physiological conditions, establishing RKIP's affinity for hydrophobic ligands and the importance of bulky aliphatic chains for inhibiting its function. The common structural elements of these compounds defines a minimal requirement for RKIP binding and thus they can be used as lead compounds for future design of RKIP ligands with therapeutic potential.

  5. Characterization of the Raf kinase inhibitory protein (RKIP binding pocket: NMR-based screening identifies small-molecule ligands.

    Directory of Open Access Journals (Sweden)

    Anne N Shemon

    2010-05-01

    Full Text Available Raf kinase inhibitory protein (RKIP, also known as phoshaptidylethanolamine binding protein (PEBP, has been shown to inhibit Raf and thereby negatively regulate growth factor signaling by the Raf/MAP kinase pathway. RKIP has also been shown to suppress metastasis. We have previously demonstrated that RKIP/Raf interaction is regulated by two mechanisms: phosphorylation of RKIP at Ser-153, and occupation of RKIP's conserved ligand binding domain with a phospholipid (2-dihexanoyl-sn-glycero-3-phosphoethanolamine; DHPE. In addition to phospholipids, other ligands have been reported to bind this domain; however their binding properties remain uncharacterized.In this study, we used high-resolution heteronuclear NMR spectroscopy to screen a chemical library and assay a number of potential RKIP ligands for binding to the protein. Surprisingly, many compounds previously postulated as RKIP ligands showed no detectable binding in near-physiological solution conditions even at millimolar concentrations. In contrast, we found three novel ligands for RKIP that specifically bind to the RKIP pocket. Interestingly, unlike the phospholipid, DHPE, these newly identified ligands did not affect RKIP binding to Raf-1 or RKIP phosphorylation. One out of the three ligands displayed off target biological effects, impairing EGF-induced MAPK and metabolic activity.This work defines the binding properties of RKIP ligands under near physiological conditions, establishing RKIP's affinity for hydrophobic ligands and the importance of bulky aliphatic chains for inhibiting its function. The common structural elements of these compounds defines a minimal requirement for RKIP binding and thus they can be used as lead compounds for future design of RKIP ligands with therapeutic potential.

  6. Controlling residual dipolar couplings in high-resolution NMR of proteins by strain induced alignment in a gel

    International Nuclear Information System (INIS)

    Ishii, Yoshitaka; Markus, Michelle A.; Tycko, Robert

    2001-01-01

    Water-soluble biological macromolecules can be weakly aligned by dissolution in a strained, hydrated gel such as cross-linked polyacrylamide, an effect termed 'strain-induced alignment in a gel' (SAG). SAG induces nonzero nuclear magnetic dipole-dipole couplings that can be measured in high-resolution NMR spectra and used as structural constraints. The dependence of experimental 15 N- 1 H dipolar couplings extracted from two-dimensional heteronuclear single quantum coherence (HSQC) spectra on several properties of compressed polyacrylamide, including the extent of compression, the polyacrylamide concentration, and the cross-link density, is reported for the B1 immunoglobulin binding domain of streptococcal protein G (protein G/B1, 57 residues). It is shown that the magnitude of macromolecular alignment can be widely varied by adjusting these properties, although the orientation and asymmetry of the alignment tensor are not affected significantly. The dependence of the 15 N relaxation times T 1 and T 2 of protein G/B1 on polyacrylamide concentration are also reported. In addition, the results of 15 N relaxation and HSQC experiments on the RNA binding domain of prokaryotic protein S4 from Bacillus stearothermophilus (S4 Δ41, residues 43-200) in a compressed polyacrylamide gel are presented. These results demonstrate the applicability of SAG to proteins of higher molecular weight and greater complexity. A modified in-phase/anti-phase (IPAP) HSQC technique is described that suppresses natural-abundance 15 N background signals from amide groups in polyacrylamide, resulting in cleaner HSQC spectra in SAG experiments. The mechanism of protein alignment in strained polyacrylamide gels is contrasted with that in liquid crystalline media

  7. SM4MQ: A Semantic Model for Multidimensional Queries

    DEFF Research Database (Denmark)

    Varga, Jovan; Dobrokhotova, Ekaterina; Romero, Oscar

    2017-01-01

    On-Line Analytical Processing (OLAP) is a data analysis approach to support decision-making. On top of that, Exploratory OLAP is a novel initiative for the convergence of OLAP and the Semantic Web (SW) that enables the use of OLAP techniques on SW data. Moreover, OLAP approaches exploit different......, sharing, and reuse on the SW. As OLAP is based on the underlying multidimensional (MD) data model we denote such queries as MD queries and define SM4MQ: A Semantic Model for Multidimensional Queries. Furthermore, we propose a method to automate the exploitation of queries by means of SPARQL. We apply...

  8. Multidimensional quantum entanglement with large-scale integrated optics

    DEFF Research Database (Denmark)

    Wang, Jianwei; Paesani, Stefano; Ding, Yunhong

    2018-01-01

    -dimensional entanglement. A programmable bipartite entangled system is realized with dimension up to 15 × 15 on a large-scale silicon-photonics quantum circuit. The device integrates more than 550 photonic components on a single chip, including 16 identical photon-pair sources. We verify the high precision, generality......The ability to control multidimensional quantum systems is key for the investigation of fundamental science and for the development of advanced quantum technologies. We demonstrate a multidimensional integrated quantum photonic platform able to generate, control and analyze high...

  9. Multi-Dimensional Customer Data Analysis in Online Auctions

    Institute of Scientific and Technical Information of China (English)

    LAO Guoling; XIONG Kuan; QIN Zheng

    2007-01-01

    In this paper, we designed a customer-centered data warehouse system with five subjects: listing, bidding, transaction,accounts, and customer contact based on the business process of online auction companies. For each subject, we analyzed its fact indexes and dimensions. Then take transaction subject as example,analyzed the data warehouse model in detail, and got the multi-dimensional analysis structure of transaction subject. At last, using data mining to do customer segmentation, we divided customers into four types: impulse customer, prudent customer, potential customer, and ordinary customer. By the result of multi-dimensional customer data analysis, online auction companies can do more target marketing and increase customer loyalty.

  10. HPLC-NMR revisited: Using time-slice HPLC-SPE-NMR with database assisted dereplication

    DEFF Research Database (Denmark)

    Johansen, Kenneth; Wubshet, Sileshi Gizachew; Nyberg, Nils

    2013-01-01

    Time based trapping of chromatographically separated compounds on to solid-phase extraction cartridges (SPE) and subsequent elution to NMR-tubes was done to emulate the function of HPLC–NMR for dereplication purposes. Sufficient mass sensitivity was obtained by the use of a state-of-the-art HPLC......–SPE–NMR-system with a cryogenically cooled probe head, designed for 1.7 mm NMR-tubes. The resulting 1H NMR spectra (600 MHz) were evaluated against a database of previously acquired and prepared spectra. The in-house developed matching algorithm, based on partitioning of the spectra and allowing for changes in the chemical shifts......, is described and the code included as Supplementary Information. Two mixtures of natural products was used to test the approach; one extract of Carthamus oxyacantha (wild safflower) containing an array of spiro compounds and one extract of the endophytic fungus Penicillum namyslowski containing griseofulvin...

  11. Real-time Kinetics of High-mobility Group Box 1 (HMGB1) Oxidation in Extracellular Fluids Studied by in Situ Protein NMR Spectroscopy*

    Science.gov (United States)

    Zandarashvili, Levani; Sahu, Debashish; Lee, Kwanbok; Lee, Yong Sun; Singh, Pomila; Rajarathnam, Krishna; Iwahara, Junji

    2013-01-01

    Some extracellular proteins are initially secreted in reduced forms via a non-canonical pathway bypassing the endoplasmic reticulum and become oxidized in the extracellular space. One such protein is HMGB1 (high-mobility group box 1). Extracellular HMGB1 has different redox states that play distinct roles in inflammation. Using a unique NMR-based approach, we have investigated the kinetics of HMGB1 oxidation and the half-lives of all-thiol and disulfide HMGB1 species in serum, saliva, and cell culture medium. In this approach, salt-free lyophilized 15N-labeled all-thiol HMGB1 was dissolved in actual extracellular fluids, and the oxidation and clearance kinetics were monitored in situ by recording a series of heteronuclear 1H-15N correlation spectra. We found that the half-life depends significantly on the extracellular environment. For example, the half-life of all-thiol HMGB1 ranged from ∼17 min (in human serum and saliva) to 3 h (in prostate cancer cell culture medium). Furthermore, the binding of ligands (glycyrrhizin and heparin) to HMGB1 significantly modulated the oxidation kinetics. Thus, the balance between the roles of all-thiol and disulfide HMGB1 proteins depends significantly on the extracellular environment and can also be artificially modulated by ligands. This is important because extracellular HMGB1 has been suggested as a therapeutic target for inflammatory diseases and cancer. Our work demonstrates that the in situ protein NMR approach is powerful for investigating the behavior of proteins in actual extracellular fluids containing an enormous number of different molecules. PMID:23447529

  12. NMR techniques in the study of cardiovascular structure and functions

    International Nuclear Information System (INIS)

    Osbakken, M.; Haselgrove, J.

    1987-01-01

    The chapter titles of this book are: Introduction to NMR Techniques;Theory of NMR Probe Design;Overview of Magnetic Resonance Imaging to Study the Cardiovascular System;Vascular Anatomy and Physiology Studied with NMR Techniques;Assessment of Myocardial Ischemia and Infarction by Nuclear Magnetic Resonance Imaging;The Use of MRI in Congenital Heart Disease;Cardiomyopathies and Myocarditis Studied with NMR Techniques;Determination of Myocardial Mechanical Function with Magnetic Resonance Imaging Techniques;Determination of Flow Using NMR Techniques;The Use of Contrast Agents in Cardiac MRI;Can Cardiovascular Disease Be Effectively Evaluated with NMR Spectroscopy? NMR Studies of ATP Synthesis Reactions in the Isolated Heart;Studies of Intermediary Metabolism in the Heart by 13C NMR Spectroscopy;23Na and 39K NMR Spectroscopic Studies of the Intact Beating Heart;and Evaluation of Skeletal Muscle Metabolism in Patients with Congestive Heart Failure Using Phosphorus Nuclear Magnetic Resonance

  13. High resolution NMR spectroscopy of synthetic polymers in bulk

    International Nuclear Information System (INIS)

    Komorski, R.A.

    1986-01-01

    The contents of this book are: Overview of high-resolution NMR of solid polymers; High-resolution NMR of glassy amorphous polymers; Carbon-13 solid-state NMR of semicrystalline polymers; Conformational analysis of polymers of solid-state NMR; High-resolution NMR studies of oriented polymers; High-resolution solid-state NMR of protons in polymers; and Deuterium NMR of solid polymers. This work brings together the various approaches for high-resolution NMR studies of bulk polymers into one volume. Heavy emphasis is, of course, given to 13C NMR studies both above and below Tg. Standard high-power pulse and wide-line techniques are not covered

  14. Nuclear magnetic resonance (NMR): principles and applications

    International Nuclear Information System (INIS)

    Quibilan, E.I.

    The basis for the phenomenon of nuclear magnetic resonance (NMR) is the ability of certain nuclei possessing both intrinsic angular momentum or ''spin'' I and magnetic moment to absorb electromagnetic energy in the radio frequency range. In principle, there are approximately 200 nuclei which may be investigated using the NMR technique. The NMR spectrum consists of intensity peaks along an axis calibrated in terms of the steady magnetic field or the frequency of the radiofrequency electromagnetic radiation. Analysis of the number, spacing, position and intensity of the lines in an NMR spectrum consists of intensity peaks along an axis calibrated in terms of the steady magnetic field or the frequency of the radiofrequency electromagnetic radiation. Analysis of the number, spacing, position and intensity of the lines in an NMR spectrum provides a variety of qualitative and quantitative analytical applications. The most obvious applications consist of the measurements of nuclear properties, such as spin number and nuclear magnetic moment. In liquids, the fine structure of resonance spectra provides a tool for chemical identification and molecular structure analysis. Other applications include the measurements of self-diffusion coefficients, magnetic fields and field homogeneity, inter-nuclear distances, and, in some cases, the water content of biological materials. (author)

  15. Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA

    Science.gov (United States)

    Mroue, Kamal H.; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H.; Morris, Michael D.; Ramamoorthy, Ayyalusamy

    2014-07-01

    Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.

  16. Balanced sensitivity functions for tuning multi-dimensional Bayesian network classifiers

    NARCIS (Netherlands)

    Bolt, J.H.; van der Gaag, L.C.

    Multi-dimensional Bayesian network classifiers are Bayesian networks of restricted topological structure, which are tailored to classifying data instances into multiple dimensions. Like more traditional classifiers, multi-dimensional classifiers are typically learned from data and may include

  17. Analysis of Local Dependence and Multidimensionality in Graphical Loglinear Rasch Models

    DEFF Research Database (Denmark)

    Kreiner, Svend; Christensen, Karl Bang

    2004-01-01

    Local independence; Multidimensionality; Differential item functioning; Uniform local dependence and DIF; Graphical Rasch models; Loglinear Rasch model......Local independence; Multidimensionality; Differential item functioning; Uniform local dependence and DIF; Graphical Rasch models; Loglinear Rasch model...

  18. DaqProVis, a toolkit for acquisition, interactive analysis, processing and visualization of multidimensional data

    Energy Technology Data Exchange (ETDEWEB)

    Morhac, M. [Institute of Physics, Slovak Academy of Sciences, Dubravska cesta 9, 845 11 Bratislava (Slovakia)]. E-mail: fyzimiro@savba.sk; Matousek, V. [Institute of Physics, Slovak Academy of Sciences, Dubravska cesta 9, 845 11 Bratislava (Slovakia); Turzo, I. [Institute of Physics, Slovak Academy of Sciences, Dubravska cesta 9, 845 11 Bratislava (Slovakia); Kliman, J. [Institute of Physics, Slovak Academy of Sciences, Dubravska cesta 9, 845 11 Bratislava (Slovakia)

    2006-04-01

    Multidimensional data acquisition, processing and visualization system to analyze experimental data in nuclear physics is described. It includes a large number of sophisticated algorithms of the multidimensional spectra processing, including background elimination, deconvolution, peak searching and fitting.

  19. Robust and transferable quantification of NMR spectral quality using IROC analysis

    Science.gov (United States)

    Zambrello, Matthew A.; Maciejewski, Mark W.; Schuyler, Adam D.; Weatherby, Gerard; Hoch, Jeffrey C.

    2017-12-01

    Non-Fourier methods are increasingly utilized in NMR spectroscopy because of their ability to handle nonuniformly-sampled data. However, non-Fourier methods present unique challenges due to their nonlinearity, which can produce nonrandom noise and render conventional metrics for spectral quality such as signal-to-noise ratio unreliable. The lack of robust and transferable metrics (i.e. applicable to methods exhibiting different nonlinearities) has hampered comparison of non-Fourier methods and nonuniform sampling schemes, preventing the identification of best practices. We describe a novel method, in situ receiver operating characteristic analysis (IROC), for characterizing spectral quality based on the Receiver Operating Characteristic curve. IROC utilizes synthetic signals added to empirical data as "ground truth", and provides several robust scalar-valued metrics for spectral quality. This approach avoids problems posed by nonlinear spectral estimates, and provides a versatile quantitative means of characterizing many aspects of spectral quality. We demonstrate applications to parameter optimization in Fourier and non-Fourier spectral estimation, critical comparison of different methods for spectrum analysis, and optimization of nonuniform sampling schemes. The approach will accelerate the discovery of optimal approaches to nonuniform sampling experiment design and non-Fourier spectrum analysis for multidimensional NMR.

  20. NMR Phase Noise in Bitter Magnets

    Science.gov (United States)

    Sigmund, E. E.; Calder, E. S.; Thomas, G. W.; Mitrović, V. F.; Bachman, H. N.; Halperin, W. P.; Kuhns, P. L.; Reyes, A. P.

    2001-02-01

    We have studied the temporal instability of a high field resistive Bitter magnet through nuclear magnetic resonance (NMR). This instability leads to transverse spin decoherence in repeated and accumulated NMR experiments as is normally performed during signal averaging. We demonstrate this effect via Hahn echo and Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation experiments in a 23-T resistive magnet. Quantitative analysis was found to be consistent with separate measurements of the magnetic field frequency fluctuation spectrum, as well as with independent NMR experiments performed in a magnetic field with a controlled instability. Finally, the CPMG sequence with short pulse delays is shown to be successful in recovering the intrinsic spin-spin relaxation even in the presence of magnetic field temporal instability.

  1. Remote tuning of NMR probe circuits.

    Science.gov (United States)

    Kodibagkar, V D; Conradi, M S

    2000-05-01

    There are many circumstances in which the probe tuning adjustments cannot be located near the rf NMR coil. These may occur in high-temperature NMR, low-temperature NMR, and in the use of magnets with small diameter access bores. We address here circuitry for connecting a fixed-tuned probe circuit by a transmission line to a remotely located tuning network. In particular, the bandwidth over which the probe may be remotely tuned while keeping the losses in the transmission line acceptably low is considered. The results show that for all resonant circuit geometries (series, parallel, series-parallel), overcoupling of the line to the tuned circuit is key to obtaining a large tuning bandwidth. At equivalent extents of overcoupling, all resonant circuit geometries have nearly equal remote tuning bandwidths. Particularly for the case of low-loss transmission line, the tuning bandwidth can be many times the tuned circuit's bandwidth, f(o)/Q. Copyright 2000 Academic Press.

  2. Deuterium NMR, induced and intrinsic cholesteric lyomesophases

    International Nuclear Information System (INIS)

    Alcantara, M.R.

    1982-01-01

    Induced and intrinsic cholesteric lyotropic mesophases were studied. Induced cholesteric lyomesophases based on potassium laurate (KL) system, with small amounts of cholesterol added, were studied by deuterium NMR and by polarizing microscopy. Order profiles obtained from deuterium NMR of KL perdenderated chains in both induced cholesteric and normal mesophases were compared. The intrinsic cholesteric lyotropic mesophases were based on the amphiphile potassium N-lauroyl serinate (KLNS) in the resolved levo form. The study of the type I intrinsic cholesteric mesophase was made by optical microscopy under polarized light and the type II intrinsic cholesteric lyomesophase was characterized by deuterium NMR. The new texture was explained by the use of the theory of disclinations developed for thermotropic liquid crystals, specially for cholesteric type. (M.J.C.) [pt

  3. Determination of solid fat content by NMR

    International Nuclear Information System (INIS)

    Kawada, Tsukasa; Kato, Chihiro; Suzuki, Kazuaki

    1984-01-01

    To establish a standard method for determing solid fat content, the NMR method was tested at six laboratories and the results were examined for collaboration. Two types of instruments, pulse NMR and wide-line NMR were used. Standard deviation in results at six laboratories was less than 1.5 for the step wise method, but more than 1.5 for the rapid method. The standard deviation in results at a single laboratory was much less than either of these cases. No significant difference could be observed in the values obtained using both instruments. Solid fat content values measured for a mixture of fully hydrogenated rapeseed and rapeseed oil agreed well with the percentage of solid by weight. (author)

  4. Muscular pathology: echographic and NMR imaging aspects

    International Nuclear Information System (INIS)

    Pascal-Suisse, P.; Beaurain, P.; Mougniot, C.

    1995-01-01

    A comparison of echographic techniques and NMR imaging has been done for the diagnosis of muscular trauma and tumor pathologies. In traumatic pathology, the echographic analysis allows to determine the complete assessment of recent muscular injuries. NMR imaging can be used in granuloma or fibrous callosity appreciation and for the analysis of deep injury (muscles and muscles-tendon junctions) and of muscular aponeurosis. Echography must be used together with color coding Doppler technique in the diagnosis of tumor pathology and for the study of slow fluxes. The recently available energy Doppler technique seems to be powerful in the study of vascularization of small expansive formations, but their extension to adjacent bone or tissue can only be appreciated using NMR imaging. (J.S.)

  5. Conservation laws for multidimensional systems and related linear algebra problems

    NARCIS (Netherlands)

    Igonine, Sergei

    2002-01-01

    We consider multidimensional systems of PDEs of generalized evolution form with t-derivatives of arbitrary order on the left-hand side and with the right-hand side dependent on lower order t-derivatives and arbitrary space derivatives. For such systems we find an explicit necessary condition for the

  6. Conservation laws for multidimensional systems and related linear algebra problems

    NARCIS (Netherlands)

    Igonin, S.

    2002-01-01

    We consider multidimensional systems of PDEs of generalized evolution form with $t$-derivatives of arbitrary order on the left-hand side and with the right-hand side dependent on lower order $t$-derivatives and arbitrary space derivatives. For such systems we find an explicit necessary condition for

  7. The Measurement of Multidimensional Gender Inequality: Continuing the Debate

    Science.gov (United States)

    Permanyer, Inaki

    2010-01-01

    The measurement of multidimensional gender inequality is an increasingly important topic that has very relevant policy applications and implications but which has not received much attention from the academic literature. In this paper I make a comprehensive and critical review of the indices proposed in recent years in order to systematise the…

  8. The Structure and Validity of the Multidimensional Social Support Questionnaire

    Science.gov (United States)

    Hardesty, Patrick H.; Richardson, George B.

    2012-01-01

    The factor structure and concurrent validity of the Multidimensional Social Support Questionnaire, a brief measure of perceived social support for use with adolescents, was examined. Findings suggest that four dimensions of perceived social support may yield more information than assessments of the unitary construct of support. (Contains 8 tables…

  9. Multidimensional Poverty in China: Findings Based on the CHNS

    Science.gov (United States)

    Yu, Jiantuo

    2013-01-01

    This paper estimates multidimensional poverty in China by applying the Alkire-Foster methodology to the China Health and Nutrition Survey 2000-2009 data. Five dimensions are included: income, living standard, education, health and social security. Results suggest that rapid economic growth has resulted not only in a reduction in income poverty but…

  10. Integral and Multidimensional Linear Distinguishers with Correlation Zero

    DEFF Research Database (Denmark)

    Bogdanov, Andrey; Leander, Gregor; Nyberg, Kaisa

    2012-01-01

    Zero-correlation cryptanalysis uses linear approximations holding with probability exactly 1/2. In this paper, we reveal fundamental links of zero-correlation distinguishers to integral distinguishers and multidimensional linear distinguishers. We show that an integral implies zero-correlation li...... weak key assumptions. © International Association for Cryptologic Research 2012....

  11. Theme section: Multi-dimensional modelling, analysis and visualization

    DEFF Research Database (Denmark)

    Guilbert, Éric; Coltekin, Arzu; Antón Castro, Francesc/François

    2016-01-01

    (Biljecki et al., 2015) as well as the temporal, but also the scale dimension (Van Oosterom and Stoter, 2010) or, as mentioned by(Lu et al., 2016), multi-spectral and multi-sensor data. Such a view provides an organisation of multidimensional data around these different axes and it is time to explore each...

  12. Income and beyond: Multidimensional Poverty in Six Latin American Countries

    Science.gov (United States)

    Battiston, Diego; Cruces, Guillermo; Lopez-Calva, Luis Felipe; Lugo, Maria Ana; Santos, Maria Emma

    2013-01-01

    This paper studies multidimensional poverty for Argentina, Brazil, Chile, El Salvador, Mexico and Uruguay for the period 1992-2006. The approach overcomes the limitations of the two traditional methods of poverty analysis in Latin America (income-based and unmet basic needs) by combining income with five other dimensions: school attendance for…

  13. Nonparametric Bayesian inference for multidimensional compound Poisson processes

    NARCIS (Netherlands)

    Gugushvili, S.; van der Meulen, F.; Spreij, P.

    2015-01-01

    Given a sample from a discretely observed multidimensional compound Poisson process, we study the problem of nonparametric estimation of its jump size density r0 and intensity λ0. We take a nonparametric Bayesian approach to the problem and determine posterior contraction rates in this context,

  14. Evidence for a Multidimensional Self-Efficacy for Exercise Scale

    Science.gov (United States)

    Rodgers, W. M.; Wilson, P. M.; Hall, C. R.; Fraser, S. N.; Murray, T. C.

    2008-01-01

    This series of three studies considers the multidimensionality of exercise self-efficacy by examining the psychometric characteristics of an instrument designed to assess three behavioral subdomains: task, scheduling, and coping. In Study 1, exploratory factor analysis revealed the expected factor structure in a sample of 395 students.…

  15. Multidimensional adaptive testing with a minimum error-variance criterion

    NARCIS (Netherlands)

    van der Linden, Willem J.

    1997-01-01

    The case of adaptive testing under a multidimensional logistic response model is addressed. An adaptive algorithm is proposed that minimizes the (asymptotic) variance of the maximum-likelihood (ML) estimator of a linear combination of abilities of interest. The item selection criterion is a simple

  16. Psychometric properties of the Multidimensional Anxiety Scale for ...

    African Journals Online (AJOL)

    Aim: To determine the psychometric properties of the Multidimensional Anxiety Scale for Children (MASC) in Nairobi public secondary school children, Kenya. Method: Concurrent self-administration of the MASC and Children's Depression Inventory (CDI) to students in Nairobi public secondary schools. Results: The MASC ...

  17. Cognitive Age: A New Multidimensional Approach to Measuring Age Identity.

    Science.gov (United States)

    Barak, Benny

    1987-01-01

    Conducted exploratory field study to examine how age-concepts are experienced and to assess relationship of age identities to each other. Proposes Cognitive Age as a new multidimensional age scale that merges the standard scale, Identity Age, and Personal Age. Study results attest to Cognitive Age scale's reliability and validity. (Author/NB)

  18. Decay rate in a multi-dimensional fission problem

    Energy Technology Data Exchange (ETDEWEB)

    Brink, D M; Canto, L F

    1986-06-01

    The multi-dimensional diffusion approach of Zhang Jing Shang and Weidenmueller (1983 Phys. Rev. C28, 2190) is used to study a simplified model for induced fission. In this model it is shown that the coupling of the fission coordinate to the intrinsic degrees of freedom is equivalent to an extra friction and a mass correction in the corresponding one-dimensional problem.

  19. A comparison of multidimensional scaling methods for perceptual mapping

    NARCIS (Netherlands)

    Bijmolt, T.H.A.; Wedel, M.

    Multidimensional scaling has been applied to a wide range of marketing problems, in particular to perceptual mapping based on dissimilarity judgments. The introduction of methods based on the maximum likelihood principle is one of the most important developments. In this article, the authors compare

  20. The Multidimensionality of Child Poverty: Evidence from Afghanistan

    Science.gov (United States)

    Trani, Jean-Francois; Biggeri, Mario; Mauro, Vincenzo

    2013-01-01

    This paper examines multidimensional poverty among children in Afghanistan using the Alkire-Foster method. Several previous studies have underlined the need to separate children from their adult nexus when studying poverty and treat them according to their own specificities. From the capability approach, child poverty is understood to be the lack…